@article{simpson_krissanaprasit_chester_koehler_labean_brown_2024, title={Utilizing multiscale engineered biomaterials to examine <scp>TGF‐β</scp>‐mediated myofibroblastic differentiation}, volume={3}, ISSN={1067-1927 1524-475X}, url={http://dx.doi.org/10.1111/wrr.13168}, DOI={10.1111/wrr.13168}, abstractNote={Abstract}, journal={Wound Repair and Regeneration}, publisher={Wiley}, author={Simpson, Aryssa and Krissanaprasit, Abhichart and Chester, Daniel and Koehler, Cynthia and LaBean, Thomas H. and Brown, Ashley C.}, year={2024}, month={Mar} }
 @article{hosseini_rahmanian_pirzada_frick_krissanaprasit_khan_labean_2022, title={DNA aerogels and DNA-wrapped CNT aerogels for neuromorphic applications}, volume={16}, ISSN={["2590-0064"]}, url={https://doi.org/10.1016/j.mtbio.2022.100440}, DOI={10.1016/j.mtbio.2022.100440}, abstractNote={Nucleic acids are programmable materials that can self-assemble into defined or stochastic three-dimensional network architectures. Various attributes of self-assembled, cross-linked Deoxyribonucleic acid (DNA) hydrogels have recently been investigated, including their mechanical properties and potential biomedical functions. Herein, for the first time, we describe the successful construction of pure DNA aerogels and DNA-wrapped carbon nanotube (CNT) composite (DNA-CNT) aerogels via a single-step freeze-drying of the respective hydrogels. These aerogels reveal highly porous and randomly branched structures with low density. The electrical properties of pure DNA aerogel mimic that of a simple capacitor; in contrast, the DNA-CNT aerogel displays a fascinating resistive switching behavior in response to an applied bias voltage sweep reminiscent of a volatile memristor. We believe these novel aerogels can serve as a platform for developing complex biomimetic devices for a wide range of applications, including real-time computation, neuromorphic computing, biochemical sensing, and biodegradable functional implants. More importantly, insight obtained here on self-assembling DNA to create aerogels will pave the way to construct novel aerogel-based material platforms from DNA coated or wrapped functional entities.}, journal={MATERIALS TODAY BIO}, author={Hosseini, Mahshid and Rahmanian, Vahid and Pirzada, Tahira and Frick, Nikolay and Krissanaprasit, Abhichart and Khan, Saad A. and LaBean, Thomas H.}, year={2022}, month={Dec} }
 @article{frick_hosseini_guilbaud_gao_labean_2022, title={Modeling and characterization of stochastic resistive switching in single Ag2S nanowires}, volume={12}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-022-09893-4}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Frick, Nikolay and Hosseini, Mahshid and Guilbaud, Damien and Gao, Ming and LaBean, Thomas H.}, year={2022}, month={Apr} }
 @article{hosseini_frick_guilbaud_gao_labean_2022, title={Resistive switching of two-dimensional Ag2S nanowire networks for neuromorphic applications}, volume={40}, ISSN={["2166-2754"]}, DOI={10.1116/6.0001867}, abstractNote={Randomly assembled networks of nanowires (NWs) can display complex memristive behaviors and are promising candidates for use as memory and computing elements in neuromorphic applications due to device fault tolerance and ease of fabrication. This study investigated resistive switching (RS) in two-dimensional, self-assembled silver sulfide (Ag2S) NW networks first experimentally and then theoretically using a previously reported stochastic RS model. The simulated switching behavior in these networks showed good correlation with experimental results. We also demonstrated fault-tolerance of a small NW network that retained RS property despite being severely damaged. Finally, we investigated information entropy in NW networks and showed unusual dynamics during switching as a result of self-organization of the memristive elements. The results of this work provide insights toward physical implementation of randomly assembled RS NW networks for reservoir and neuromorphic computing research.}, number={4}, journal={JOURNAL OF VACUUM SCIENCE & TECHNOLOGY B}, author={Hosseini, Mahshid and Frick, Nikolay and Guilbaud, Damien and Gao, Ming and LaBean, Thomas H.}, year={2022}, month={Jul} }
 @article{gao_krissanaprasit_miles_hsiao_labean_2021, title={Mechanical and Electrical Properties of DNA Hydrogel-Based Composites Containing Self-Assembled Three-Dimensional Nanocircuits}, volume={11}, ISSN={["2076-3417"]}, url={https://doi.org/10.3390/app11052245}, DOI={10.3390/app11052245}, abstractNote={Molecular self-assembly of DNA has been developed as an effective construction strategy for building complex materials. Among them, DNA hydrogels are known for their simple fabrication process and their tunable properties. In this study, we have engineered, built, and characterized a variety of pure DNA hydrogels using DNA tile-based crosslinkers and different sizes of linear DNA spacers, as well as DNA hydrogel/nanomaterial composites using DNA/nanomaterial conjugates with carbon nanotubes and gold nanoparticles as crosslinkers. We demonstrate the ability of this system to self-assemble into three-dimensional percolating networks when carbon nanotubes and gold nanoparticles are incorporated into the DNA hydrogel. These hydrogel composites showed interesting non-linear electrical properties. We also demonstrate the tuning of rheological properties of hydrogel-based composites using different types of crosslinkers and spacers. The viscoelasticity of DNA hydrogels is shown to dramatically increase by the use of a combination of interlocking DNA tiles and DNA/carbon nanotube crosslinkers. Finally, we present measurements and discuss electrically conductive nanomaterials for applications in nanoelectronics.}, number={5}, journal={APPLIED SCIENCES-BASEL}, author={Gao, Ming and Krissanaprasit, Abhichart and Miles, Austin and Hsiao, Lilian C. and LaBean, Thomas H.}, year={2021}, month={Mar} }
 @article{krissanaprasit_key_froehlich_pontula_mihalko_dupont_andersen_kjems_brown_labean_2021, title={Multivalent Aptamer‐Functionalized Single‐Strand RNA Origami as Effective, Target‐Specific Anticoagulants with Corresponding Reversal Agents}, volume={10}, ISSN={2192-2640 2192-2659}, url={http://dx.doi.org/10.1002/adhm.202001826}, DOI={10.1002/adhm.202001826}, abstractNote={Abstract}, number={11}, journal={Advanced Healthcare Materials}, publisher={Wiley}, author={Krissanaprasit, Abhichart and Key, Carson M. and Froehlich, Kristen and Pontula, Sahil and Mihalko, Emily and Dupont, Daniel M. and Andersen, Ebbe S. and Kjems, Jørgen and Brown, Ashley C. and LaBean, Thomas H.}, year={2021}, month={Apr} }
 @misc{krissanaprasit_key_pontula_labean_2021, title={Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers}, volume={121}, ISSN={["1520-6890"]}, DOI={10.1021/acs.chemrev.0c01332}, abstractNote={Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.}, number={22}, journal={CHEMICAL REVIEWS}, author={Krissanaprasit, Abhichart and Key, Carson M. and Pontula, Sahil and LaBean, Thomas H.}, year={2021}, month={Nov}, pages={13797–13868} }
 @article{krissanaprasit_key_fergione_froehlich_pontula_hart_carriel_kjems_andersen_labean_2019, title={Genetically Encoded, Functional Single-Strand RNA Origami: Anticoagulant}, volume={31}, ISSN={["1521-4095"]}, DOI={10.1002/adma.201808262}, abstractNote={Abstract}, number={21}, journal={ADVANCED MATERIALS}, author={Krissanaprasit, Abhichart and Key, Carson and Fergione, Michael and Froehlich, Kristen and Pontula, Sahil and Hart, Matthew and Carriel, Pedro and Kjems, Jorgen and Andersen, Ebbe Sloth and LaBean, Thomas H.}, year={2019}, month={May} }
 @article{hernandez-garcia_estrich_werten_maarel_labean_wolf_stuart_vries_2017, title={2Precise Coating of a Wide Range of DNA Templates by a Protein Polymer with a DNA Binding Domain}, volume={11}, ISSN={["1936-086X"]}, DOI={10.1021/acsnano.6b05938}, abstractNote={Emerging DNA-based nanotechnologies would benefit from the ability to modulate the properties (e.g., solubility, melting temperature, chemical stability) of diverse DNA templates (single molecules or origami nanostructures) through controlled, self-assembling coatings. We here introduce a DNA coating agent, called C8-BSso7d, which binds to and coats with high specificity and affinity, individual DNA molecules as well as folded origami nanostructures. C8-BSso7d coats and protects without condensing, collapsing or destroying the spatial structure of the underlying DNA template. C8-BSso7d combines the specific nonelectrostatic DNA binding affinity of an archeal-derived DNA binding domain (Sso7d, 7 kDa) with a long hydrophilic random coil polypeptide (C8, 73 kDa), which provides colloidal stability (solubility) through formation of polymer brushes around the DNA templates. C8-BSso7d is produced recombinantly in yeast and has a precise (but engineerable) amino acid sequence of precise length. Using electrophoresis, AFM, and fluorescence microscopy we demonstrate protein coat formation with stiffening of one-dimensional templates (linear dsDNA, supercoiled dsDNA and circular ssDNA), as well as coat formation without any structural distortion or disruption of two-dimensional DNA origami template. Combining the programmability of DNA with the nonperturbing precise coating capability of the engineered protein C8-BSso7d holds promise for future applications such as the creation of DNA-protein hybrid networks, or the efficient transfection of individual DNA nanostructures into cells.}, number={1}, journal={ACS NANO}, author={Hernandez-Garcia, Armando and Estrich, Nicole A. and Werten, Marc W. T. and Maarel, Johan R. C. and LaBean, Thomas H. and Wolf, Frits A. and Stuart, Martien A. Cohen and Vries, Renko}, year={2017}, month={Jan}, pages={144–152} }
 @article{estrich_hernandez-garcia_vries_labean_2017, title={Engineered Diblock Polypeptides Improve DNA and Gold Solubility during Molecular Assembly}, volume={11}, ISSN={["1936-086X"]}, DOI={10.1021/acsnano.6b07291}, abstractNote={Programmed molecular recognition is being developed for the bionanofabrication of mixed organic/inorganic supramolecular assemblies for applications in electronics, photonics, and medicine. For example, DNA-based nanotechnology seeks to exploit the easily programmed complementary base-pairing of DNA to direct assembly of complex, designed nanostructures. Optimal solution conditions for bionanofabrication, mimicking those of biological systems, may involve high concentrations of biomacromolecules (proteins, nucleic acids, etc.) and significant concentrations of various ions (Mg2+, Na+, Cl-, etc.). Given a desire to assemble diverse inorganic components (metallic nanoparticles, quantum dots, carbon nanostructures, etc.), it will be increasingly difficult to find solution conditions simultaneously compatible with all components. Frequently, the use of chemical surfactants is undesirable, leaving a need for the development of alternative strategies. Herein, we discuss the use of artificial, diblock polypeptides in the role of solution compatibilizing agents for molecular assembly. We describe the use of two distinct diblock polypeptides with affinity for DNA in the stabilization of DNA origami and DNA-functionalized gold nanoparticles (spheres and rods) in solution, protection of DNA from enzymatic degradation, as well as two 3D tetrahedral DNA origamis. We present initial data showing that the diblock polypeptides promote the formation in the solution of desired organic/inorganic assemblies.}, number={1}, journal={ACS NANO}, author={Estrich, Nicole A. and Hernandez-Garcia, Armando and Vries, Renko and LaBean, Thomas H.}, year={2017}, month={Jan}, pages={831–842} }
 @article{majikes_nash_labean_2017, title={Search for effective chemical quenching to arrest molecular assembly and directly monitor DNA nanostructure formation}, volume={9}, ISSN={["2040-3372"]}, DOI={10.1039/c6nr08433h}, abstractNote={Structural DNA nanotechnology has demonstrated both versatility and potential as a molecular manufacturing tool; the formation and processing of DNA nanostructures has therefore been subject to much interest. Characterization of the formation process itself is vital to understanding the role of design in production yield. We present our search for a robust new technique, chemical quenching, to arrest molecular folding in DNA systems for subsequent characterization. Toward this end we will introduce two miniM13 origami designs based on a 2.4 kb scaffold, each with diametrically opposed scaffold routing strategies (maximized scaffold crossovers versus maximized staple crossovers) to examine the relevance of design in the folding process. By chemically rendering single strand DNA inert and unable to hybridize, we probe the folding pathway of several scaffolded DNA origami structures.}, number={4}, journal={NANOSCALE}, author={Majikes, J. M. and Nash, J. A. and LaBean, T. H.}, year={2017}, month={Jan}, pages={1637–1644} }
 @article{majikes_ferraz_labean_2017, title={pH-Driven Actuation of DNA Origami via Parallel I-Motif Sequences in Solution and on Surfaces}, volume={28}, ISSN={["1043-1802"]}, DOI={10.1021/acs.bioconjchem.7b00288}, abstractNote={As bottom up DNA nanofabrication creates increasingly complex and dynamic mechanisms, the implementation of actuators within the DNA nanotechnology toolkit has grown increasingly important. One such actuator, the I-motif, is fairly simple in that it consists solely of standard DNA sequences and does not require any modification chemistry or special purification beyond that typical for DNA oligomer synthesis. This study presents a new implementation of parallel I-motif actuators, emphasizing their future potential as drivers of complex internal motion between substructures. Here we characterize internal motion between DNA origami substructures via AFM and image analysis. Such parallel I-motif design and quantification of actuation provide a useful step toward more complex and effective molecular machines.}, number={7}, journal={BIOCONJUGATE CHEMISTRY}, author={Majikes, Jacob M. and Ferraz, Lucas C. C. and LaBean, Thomas H.}, year={2017}, month={Jul}, pages={1821–1825} }
 @article{majumder_garg_labean_reif_2016, title={Activatable tiles for compact robust programmable molecular assembly and other applications}, volume={15}, ISSN={1567-7818 1572-9796}, url={http://dx.doi.org/10.1007/S11047-015-9532-3}, DOI={10.1007/S11047-015-9532-3}, number={4}, journal={Natural Computing}, publisher={Springer Science and Business Media LLC}, author={Majumder, Urmi and Garg, Sudhanshu and LaBean, Thomas H. and Reif, John H.}, year={2016}, month={Dec}, pages={611–634} }
 @article{majikes_nash_labean_2016, title={Competitive annealing of multiple DNA origami: formation of chimeric origami}, volume={18}, ISSN={["1367-2630"]}, DOI={10.1088/1367-2630/18/11/115001}, abstractNote={Scaffolded DNA origami are a robust tool for building discrete nanoscale objects at high yield. This strategy ensures, in the design process, that the desired nanostructure is the minimum free energy state for the designed set of DNA sequences. Despite aiming for the minimum free energy structure, the folding process which leads to that conformation is difficult to characterize, although it has been the subject of much research. In order to shed light on the molecular folding pathways, this study intentionally frustrates the folding process of these systems by simultaneously annealing the staple pools for multiple target or parent origami structures, forcing competition. A surprising result of these competitive, simultaneous anneals is the formation of chimeric DNA origami which inherit structural regions from both parent origami. By comparing the regions inherited from the parent origami, relative stability of substructures were compared. This allowed examination of the folding process with typical characterization techniques and materials. Anneal curves were then used as a means to rapidly generate a phase diagram of anticipated behavior as a function of staple excess and parent staple ratio. This initial study shows that competitive anneals provide an exciting way to create diverse new nanostructures and may be used to examine the relative stability of various structural motifs.}, journal={NEW JOURNAL OF PHYSICS}, author={Majikes, Jacob M. and Nash, Jessica A. and LaBean, Thomas H.}, year={2016}, month={Nov} }
 @article{rangnekar_nash_goodfred_yingling_labean_2016, title={Design of Potent and Controllable Anticoagulants Using DNA Aptamers and Nanostructures}, volume={21}, ISSN={["1420-3049"]}, url={https://doi.org/10.3390/molecules21020202}, DOI={10.3390/molecules21020202}, abstractNote={The regulation of thrombin activity offers an opportunity to regulate blood clotting because of the central role played by this molecule in the coagulation cascade. Thrombin-binding DNA aptamers have been used to inhibit thrombin activity. In the past, to address the low efficacy reported for these aptamers during clinical trials, multiple aptamers have been linked using DNA nanostructures. Here, we modify that strategy by linking multiple copies of various thrombin-binding aptamers using DNA weave tiles. The resulting constructs have very high anticoagulant activity in functional assays owing to their improved cooperative binding affinity to thrombin due to optimized spacing, orientation, and the high local concentration of aptamers. We also report the results of molecular dynamics simulations to gain insight into the solution conformations of the tiles. Moreover, by using DNA strand displacement, we were able to turn the coagulation cascade off and on as desired, thereby enabling significantly better control over blood coagulation.}, number={2}, journal={MOLECULES}, publisher={MDPI AG}, author={Rangnekar, Abhijit and Nash, Jessica A. and Goodfred, Bethany and Yingling, Yaroslava G. and LaBean, Thomas H.}, year={2016}, month={Feb} }
 @article{brown_majikes_martinez_giron_fennell_samano_labean_2015, title={An easy-to-prepare mini-scaffold for DNA origami}, volume={7}, ISSN={["2040-3372"]}, DOI={10.1039/c5nr04921k}, abstractNote={A system is described for easy ssDNA production; folding of the 2404-base scaffold into several DNA origami shapes is demonstrated.}, number={40}, journal={NANOSCALE}, author={Brown, S. and Majikes, J. and Martinez, A. and Giron, T. M. and Fennell, H. and Samano, E. C. and LaBean, T. H.}, year={2015}, pages={16621–16624} }
 @article{pedersen_kong_achim_labean_2015, title={Comparative Incorporation of PNA into DNA Nanostructures}, volume={20}, ISSN={["1420-3049"]}, DOI={10.3390/molecules200917645}, abstractNote={DNA has shown great promise as a building material for self-assembling nanoscale structures. To further develop the potential of this technology, more methods are needed for functionalizing DNA-based nanostructures to increase their chemical diversity. Peptide nucleic acid (PNA) holds great promise for realizing this goal, as it conveniently allows for inclusion of both amino acids and peptides in nucleic acid-based structures. In this work, we explored incorporation of a positively charged PNA within DNA nanostructures. We investigated the efficiency of annealing a lysine-containing PNA probe with complementary, single-stranded DNA sequences within nanostructures, as well as the efficiency of duplex invasion and its dependence on salt concentration. Our results show that PNA allows for toehold-free strand displacement and that incorporation yield depends critically on binding site geometry. These results provide guidance for the design of PNA binding sites on nucleic acid nanostructures with an eye towards optimizing fabrication yield.}, number={9}, journal={MOLECULES}, author={Pedersen, Ronnie O. and Kong, Jing and Achim, Catalina and LaBean, Thomas H.}, year={2015}, month={Sep}, pages={17645–17658} }
 @article{gnapareddy_ahn_dugasani_kim_amin_mitta_vellampatti_kim_kulkarni_kim_et al._2015, title={Coverage percentage and raman measurement of cross-tile and scaffold cross-tile based DNA nanostructures}, volume={135}, ISSN={["1873-4367"]}, DOI={10.1016/j.colsurfb.2015.08.013}, abstractNote={We present two free-solution annealed DNA nanostructures consisting of either cross-tile CT1 or CT2. The proposed nanostructures exhibit two distinct structural morphologies, with one-dimensional (1D) nanotubes for CT1 and 2D nanolattices for CT2. When we perform mica-assisted growth annealing with CT1, a dramatic dimensional change occurs where the 1D nanotubes transform into 2D nanolattices due to the presence of the substrate. We assessed the coverage percentage of the 2D nanolattices grown on the mica substrate with CT1 and CT2 as a function of the concentration of the DNA monomer. Furthermore, we fabricated a scaffold cross-tile (SCT), which is a new design of a modified cross-tile that consists of four four-arm junctions with a square aspect ratio. For SCT, eight oligonucleotides are designed in such a way that adjacent strands with sticky ends can produce continuous arms in both the horizontal and vertical directions. The SCT was fabricated via free-solution annealing, and self-assembled SCT produces 2D nanolattices with periodic square cavities. All structures were observed via atomic force microscopy. Finally, we fabricated divalent nickel ion (Ni(2+))- and trivalent dysprosium ion (Dy(3+))-modified 2D nanolattices constructed with CT2 on a quartz substrate, and the ion coordinations were examined via Raman spectroscopy.}, journal={COLLOIDS AND SURFACES B-BIOINTERFACES}, author={Gnapareddy, Bramaramba and Ahn, Sang Jung and Dugasani, Sreekantha Reddy and Kim, Jang Ah and Amin, Rashid and Mitta, Sekhar Babu and Vellampatti, Srivithya and Kim, Byeonghoon and Kulkarni, Atul and Kim, Taesung and et al.}, year={2015}, month={Nov}, pages={677–681} }
 @article{garg_chandran_gopalkrishnan_labean_reif_2015, title={Directed Enzymatic Activation of 1-D DNA Tiles}, volume={9}, ISSN={["1936-086X"]}, DOI={10.1021/nn504556v}, abstractNote={The tile assembly model is a Turing universal model of self-assembly where a set of square shaped tiles with programmable sticky sides undergo coordinated self-assembly to form arbitrary shapes, thereby computing arbitrary functions. Activatable tiles are a theoretical extension to the Tile assembly model that enhances its robustness by protecting the sticky sides of tiles until a tile is partially incorporated into a growing assembly. In this article, we experimentally demonstrate a simplified version of the Activatable tile assembly model. In particular, we demonstrate the simultaneous assembly of protected DNA tiles where a set of inert tiles are activated via a DNA polymerase to undergo linear assembly. We then demonstrate stepwise activated assembly where a set of inert tiles are activated sequentially one after another as a result of attachment to a growing 1-D assembly. We hope that these results will pave the way for more sophisticated demonstrations of activated assemblies.}, number={2}, journal={ACS NANO}, author={Garg, Sudhanshu and Chandran, Harish and Gopalkrishnan, Nikhil and LaBean, Thomas H. and Reif, John}, year={2015}, month={Feb}, pages={1072–1079} }
 @article{campos_zhang_majikes_ferraz_labean_dong_ferapontova_2015, title={Electronically addressable nanomechanical switching of i-motif DNA origami assembled on basal plane HOPG}, volume={51}, DOI={10.1039/c5cc04678e}, abstractNote={Here, a pH-induced nanomechanical switching of i-motif structures incorporated into DNA origami bound onto cysteamine-modified basal plane HOPG was electronically addressed, demonstrating for the first time the electrochemical read-out of the nanomechanics of DNA origami.}, number={74}, journal={Chemical Communications}, author={Campos, R. and Zhang, S. and Majikes, J. M. and Ferraz, L. C. C. and LaBean, T. H. and Dong, M. D. and Ferapontova, E. E.}, year={2015}, pages={14111–14114} }
 @misc{rangnekar_labean_2014, title={Building DNA DNA Nanostructures for Molecular Computation, Templated Assembly, and Biological Applications}, volume={47}, ISSN={["1520-4898"]}, DOI={10.1021/ar500023b}, abstractNote={CONSPECTUS: DNA is a critical biomolecule well-known for its roles in biology and genetics. Moreover, its double-helical structure and the Watson-Crick pairing of its bases make DNA structurally predictable. This predictability enables design and synthesis of artificial DNA nanostructures by suitable programming of the base sequences of DNA strands. Since the advent of the field of DNA nanotechnology in 1982, a variety of DNA nanostructures have been designed and used for numerous applications. In this Account, we discuss the progress made by our lab which has contributed toward the overall advancement of the field. Tile-based DNA nanostructures are an integral part of structural DNA nanotechnology. These structures are formed using several short, chemically synthesized DNA strands by programming their base sequences so that they self-assemble into desired constructs. Design and assembly of several DNA tiles will be discussed in this Account. Tiles include, for example, TX tiles with three parallel, coplanar duplexes, 4 × 4 cross-tiles with four arms, and weave-tiles with weave-like architecture. Another category of tiles we will present involve multiple parallel duplexes that assemble to form closed tubular structures. All of these tile types have been used to form micrometer-scale one- and two-dimensional arrays and lattices. Origami-based structures constitute another category where a long single-stranded DNA scaffold is folded into desired shapes by association with multiple short staple strands. This Account will describe the efforts by our lab in devising new strategies to improve the maximum size of origami structures. The various DNA nanostructures detailed here have been used in a wide variety of different applications. This Account will discuss the use of DNA tiles for logical computation, encoding information as molecular barcodes, and functionalization for patterning of other nanoscale organic and inorganic materials. Consequently, we have used DNA nanostructures for templating metallic nanowires as well as for programmed assembly of proteins and nanoparticles with controlled spacings. Among other applications, we have used DNA nanotechnology in biosensors that detect target DNA sequences and to affect cell surface receptor clustering for communicating with a cell signaling pathway. We used DNA weave-tiles to control the spacing between thrombin-binding aptamers which resulted in very high antithrombin and anticoagulant activity of the construct. We believe that the tremendous progress in DNA nanotechnology over the past three decades will open even more research avenues in the near future for applications in a wide variety of disciplines including electronics, photonics, biomedical engineering, biosensing, therapeutics, and nucleic-acid-based drug delivery.}, number={6}, journal={ACCOUNTS OF CHEMICAL RESEARCH}, author={Rangnekar, Abhijit and LaBean, Thomas H.}, year={2014}, month={Jun}, pages={1778–1788} }
 @article{shi_lu_wang_pan_cui_xu_labean_2014, title={Programmable DNA tile self-assembly using a hierarchical sub-tile strategy}, volume={25}, ISSN={["1361-6528"]}, DOI={10.1088/0957-4484/25/7/075602}, abstractNote={DNA tile based self-assembly provides a bottom-up approach to construct desired nanostructures. DNA tiles have been directly constructed from ssDNA and readily self-assembled into 2D lattices and 3D superstructures. However, for more complex lattice designs including algorithmic assemblies requiring larger tile sets, a more modular approach could prove useful. This paper reports a new DNA ‘sub-tile’ strategy to easily create whole families of programmable tiles. Here, we demonstrate the stability and flexibility of our sub-tile structures by constructing 3-, 4- and 6-arm DNA tiles that are subsequently assembled into 2D lattices and 3D nanotubes according to a hierarchical design. Assembly of sub-tiles, tiles, and superstructures was analyzed using polyacrylamide gel electrophoresis and atomic force microscopy. DNA tile self-assembly methods provide a bottom-up approach to create desired nanostructures; the sub-tile strategy adds a useful new layer to this technique. Complex units can be made from simple parts. The sub-tile approach enables the rapid redesign and prototyping of complex DNA tile sets and tiles with asymmetric designs.}, number={7}, journal={NANOTECHNOLOGY}, author={Shi, Xiaolong and Lu, Wei and Wang, Zhiyu and Pan, Linqiang and Cui, Guangzhao and Xu, Jin and LaBean, Thomas H.}, year={2014}, month={Feb} }
 @article{hakker_marchi_harris_labean_agris_2014, title={Structural and thermodynamic analysis of modified nucleosides in self-assembled DNA cross-tiles}, volume={32}, ISSN={["1538-0254"]}, DOI={10.1080/07391102.2012.763184}, abstractNote={DNA Holliday junctions are important natural strand-exchange structures that form during homologous recombination. Immobile four-arm junctions, analogs to Holliday junctions, have been designed to self-assemble into cross-tile structures by maximizing Watson–Crick base pairing and fixed crossover points. The cross-tiles, self-assembled from base pair recognition between designed single-stranded DNAs, form higher order lattice structures through cohesion of self-associating sticky ends. These cross-tiles have 16 unpaired nucleosides in the central loop at the junction of the four duplex stems. The importance of the centralized unpaired nucleosides to the structure’s thermodynamic stability and self-assembly is unknown. Cross-tile DNA nanostructures were designed and constructed from nine single-stranded DNAs with four shell strands, four arms, and a central loop containing 16 unpaired bases. The 16 unpaired bases were either 2′-deoxyribothymidines, 2′-O-methylribouridines, or abasic 1′,2′-dideoxyribonucleosides. Thermodynamic profiles and structural base-stacking contributions were assessed using UV absorption spectroscopy during thermal denaturation and circular dichroism spectroscopy, respectively, and the resulting structures were observed by atomic force microscopy. There were surprisingly significant changes in the thermodynamic and structural properties of lattice formation as a result of altering only the 16 unpaired, centralized nucleosides. The 16 unpaired 2′-O-methyluridines were stabilizing and produced uniform tubular structures. In contrast, the abasic nucleosides were destabilizing producing a mixture of structures. These results strongly indicate the importance of a small number of centrally located unpaired nucleosides within the structures. Since minor modifications lead to palpable changes in lattice formation, DNA cross-tiles present an easily manipulated structure convenient for applications in biomedical and biosensing devices.}, number={2}, journal={JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS}, author={Hakker, Lauren and Marchi, Alexandria N. and Harris, Kimberly A. and LaBean, Thomas H. and Agris, Paul F.}, year={2014}, month={Feb}, pages={319–329} }
 @article{pilo-pais_watson_demers_labean_finkelstein_2014, title={Surface-Enhanced Raman Scattering Plasmonic Enhancement Using DNA Origami-Based Complex Metallic Nanostructures}, volume={14}, ISSN={["1530-6992"]}, DOI={10.1021/nl5003069}, abstractNote={DNA origami is a novel self-assembly technique allowing one to form various two-dimensional shapes and position matter with nanometer accuracy. We use DNA origami templates to engineer surface-enhanced Raman scattering substrates. Specifically, gold nanoparticles were selectively placed on the corners of rectangular origami and subsequently enlarged via solution-based metal deposition. The resulting assemblies exhibit "hot spots" of enhanced electromagnetic field between the nanoparticles. We observed a significant Raman signal enhancement from molecules covalently attached to the assemblies, as compared to control nanoparticle samples that lack interparticle hot spots. Furthermore, Raman molecules are used to map out the hot spots' distribution, as they are burned when experiencing a threshold electric field. Our method opens up the prospects of using DNA origami to rationally engineer and assemble plasmonic structures for molecular spectroscopy.}, number={4}, journal={NANO LETTERS}, author={Pilo-Pais, M. and Watson, A. and Demers, S. and LaBean, T. H. and Finkelstein, G.}, year={2014}, month={Apr}, pages={2099–2104} }
 @article{marchi_saaem_vogen_brown_labean_2014, title={Toward Larger DNA Origami}, volume={14}, ISSN={["1530-6992"]}, DOI={10.1021/nl502626s}, abstractNote={Structural DNA nanotechnology, and specifically scaffolded DNA origami, is rapidly developing as a versatile method for bottom-up fabrication of novel nanometer-scale materials and devices. However, lengths of conventional single-stranded scaffolds, for example, 7,249-nucleotide circular genomic DNA from the M13mp18 phage, limit the scales of these uniquely addressable structures. Additionally, increasing DNA origami size generates the cost burden of increased staple-strand synthesis. We addressed this 2-fold problem by developing the following methods: (1) production of the largest to-date biologically derived single-stranded scaffold using a λ/M13 hybrid virus to produce a 51 466-nucleotide DNA in a circular, single-stranded form and (2) inexpensive DNA synthesis via an inkjet-printing process on a chip embossed with functionalized micropillars made from cyclic olefin copolymer. We have experimentally demonstrated very efficient assembly of a 51-kilobasepair origami from the λ/M13 hybrid scaffold folded by chip-derived staple strands. In addition, we have demonstrated two-dimensional, asymmetric origami sheets with controlled global curvature such that they land on a substrate in predictable orientations that have been verified by atomic force microscopy.}, number={10}, journal={NANO LETTERS}, author={Marchi, Alexandria N. and Saaem, Ishtiaq and Vogen, Briana N. and Brown, Stanley and LaBean, Thomas H.}, year={2014}, month={Oct}, pages={5740–5747} }
 @article{chandran_rangnekar_shetty_schultes_reif_labean_2013, title={An autonomously self-assembling dendritic DNA nanostructure for target DNA detection}, volume={8}, ISSN={["1860-7314"]}, DOI={10.1002/biot.201100499}, abstractNote={Abstract}, number={2}, journal={BIOTECHNOLOGY JOURNAL}, author={Chandran, Harish and Rangnekar, Abhijit and Shetty, Geetha and Schultes, Erik A. and Reif, John H. and LaBean, Thomas H.}, year={2013}, month={Feb}, pages={221–227} }
 @article{marchi_saaem_tian_labean_2013, title={One-Pot Assembly of a Hetero-dimeric DNA Origami from Chip-Derived Staples and Double-Stranded Scaffold}, volume={7}, ISSN={["1936-0851"]}, DOI={10.1021/nn302322j}, abstractNote={Although structural DNA nanotechnology, and especially scaffolded DNA origami, hold great promise for bottom-up fabrication of novel nanoscale materials and devices, concerns about scalability have tempered widespread enthusiasm. Here we report a single-pot reaction where both strands of double-stranded M13-bacteriophage DNA are simultaneously folded into two distinct shapes that then heterodimerize with high yield. The fully addressable, two-dimensional heterodimer DNA origami, with twice the surface area of standard M13 origami, formed in high yield (81% of the well-formed monomers undergo dimerization). We also report the concurrent production of entire sets of staple strands by a unique, nicking strand-displacement amplification (nSDA) involving reusable surface-bound template strands that were synthesized in situ using a custom piezoelectric inkjet system. The combination of chip-based staple strand production, double-sized origami, and high-yield one-pot assembly markedly increases the useful scale of DNA origami.}, number={2}, journal={ACS NANO}, author={Marchi, Alexandria N. and Saaem, Ishtiaq and Tian, Jingdong and LaBean, Thomas H.}, year={2013}, month={Feb}, pages={903–910} }
 @misc{saaem_labean_2013, title={Overview of DNA origami for molecular self-assembly}, volume={5}, ISSN={["1939-0041"]}, DOI={10.1002/wnan.1204}, abstractNote={Abstract}, number={2}, journal={WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY}, author={Saaem, Ishtiaq and LaBean, Thomas H.}, year={2013}, pages={150–162} }
 @article{pedersen_loboa_labean_2013, title={Sensitization of Transforming Growth Factor-beta Signaling by Multiple Peptides Patterned on DNA Nanostructures}, volume={14}, ISSN={["1526-4602"]}, DOI={10.1021/bm4011722}, abstractNote={We report sensitization of a cellular signaling pathway by addition of functionalized DNA nanostructures. Signaling by transforming growth factor β (TGFβ) has been shown to be dependent on receptor clustering. By patterning a DNA nanostructure with closely spaced peptides that bind to TGFβ receptor, we observe increased sensitivity of NMuMG cells to TGFβ ligand. This is evidenced by translocation of secondary messenger proteins to the nucleus and stimulation of an inducible luciferase reporter at lower concentrations of TGFβ ligand. We believe this represents an important initial step toward realization of DNA as a self-assembling and biologically compatible material for use in tissue engineering and drug delivery.}, number={12}, journal={BIOMACROMOLECULES}, author={Pedersen, Ronnie O. and Loboa, Elizabeth G. and LaBean, Thomas H.}, year={2013}, month={Dec}, pages={4157–4160} }
 @article{qian_seo_kim_kim_lim_liu_kim_labean_park_kim_2012, title={DNA nanotube formation based on normal mode analysis}, volume={23}, ISSN={0957-4484 1361-6528}, url={http://dx.doi.org/10.1088/0957-4484/23/10/105704}, DOI={10.1088/0957-4484/23/10/105704}, abstractNote={Ever since its inception, a popular DNA motif called the cross tile has been recognized to self-assemble into addressable 2D templates consisting of periodic square cavities. Although this may be conceptually correct, in reality certain types of cross tiles can only form planar lattices if adjacent tiles are designed to bind in a corrugated manner, in the absence of which they roll up to form 3D nanotube structures. Here we present a theoretical study on why uncorrugated cross tiles self-assemble into counterintuitive 3D nanotube structures and not planar 2D lattices. Coarse-grained normal mode analysis of single and multiple cross tiles within the elastic network model was carried out to expound the vibration modes of the systems. While both single and multiple cross tile simulations produce results conducive to tube formations, the dominant modes of a unit of four cross tiles (one square cavity), termed a quadruplet, fully reflect the symmetries of the actual nanotubes found in experiments and firmly endorse circularization of an array of cross tiles.}, number={10}, journal={Nanotechnology}, publisher={IOP Publishing}, author={Qian, PengFei and Seo, Sangjae and Kim, Junghoon and Kim, Seungjae and Lim, Byeong Soo and Liu, Wing Kam and Kim, Bum Joon and LaBean, Thomas Henry and Park, Sung Ha and Kim, Moon Ki}, year={2012}, month={Feb}, pages={105704} }
 @article{lee_amin_kim_kim_lee_kim_labean_park_2012, title={Fabrication of zigzag and folded DNA nanostructures by an angle control scheme}, volume={8}, ISSN={1744-683X 1744-6848}, url={http://dx.doi.org/10.1039/c1sm06379k}, DOI={10.1039/c1sm06379k}, abstractNote={We fabricated zigzag and folded DNA nanostructures by an angle control scheme. In order to give a solid verification of its operation, an open tube structure was also designed and it shows drastic dimensional changes compared with 2 dimensional zigzag and folded structures. These self-assembled artificial DNA structures would provide nanoscale-resolution templates for the alignment of various functional materials.}, number={1}, journal={Soft Matter}, publisher={Royal Society of Chemistry (RSC)}, author={Lee, Junwye and Amin, Rashid and Kim, Byeonghoon and Kim, Soyeon and Lee, Chang-Won and Kim, Jong Min and LaBean, Thomas H. and Park, Sung Ha}, year={2012}, pages={44–47} }
 @article{rangnekar_zhang_li_bompiani_hansen_gothelf_sullenger_labean_2012, title={Increased anticoagulant activity of thrombin-binding DNA aptamers by nanoscale organization on DNA nanostructures}, volume={8}, ISSN={1549-9634}, url={http://dx.doi.org/10.1016/j.nano.2011.08.011}, DOI={10.1016/j.nano.2011.08.011}, abstractNote={Control over thrombin activity is much desired to regulate blood clotting in surgical and therapeutic situations. Thrombin-binding RNA and DNA aptamers have been used to inhibit thrombin activity and thus the coagulation cascade. Soluble DNA aptamers, as well as two different aptamers tethered by a flexible single-strand linker, have been shown to possess anticoagulant activity. Here, we link multiple aptamers at programmed positions on DNA nanostructures to optimize spacing and orientation of the aptamers and thereby to maximize anticoagulant activity in functional assays. By judicious engineering of the DNA nanostructures, we have created a novel, functional DNA nanostructure, which is a multi-aptamer inhibitor with activity eightfold higher than free aptamer. Reversal of the thrombin inhibition was also achieved by the use of single-stranded DNA antidotes, thus enabling significant control over blood coagulation.Thrombin inhibition via DNA aptamers has recently become a possibility. In this study, thrombin-binding DNA aptamers were further optimized by nanoscale organization on DNA nanostructures. The authors have created a novel, functional DNA nanostructure, which is a multi-aptamer inhibitor with activity eightfold higher than that of free aptamer. Reversal of thrombin inhibition was also achieved by single-stranded DNA antidotes, enabling significant control over the coagulation pathway.}, number={5}, journal={Nanomedicine: Nanotechnology, Biology and Medicine}, publisher={Elsevier BV}, author={Rangnekar, Abhijit and Zhang, Alex M. and Li, Susan Shiyuan and Bompiani, Kristin M. and Hansen, Majken N. and Gothelf, Kurt V. and Sullenger, Bruce A. and LaBean, Thomas H.}, year={2012}, month={Jul}, pages={673–681} }
 @article{pilo-pais_goldberg_samano_labean_finkelstein_2011, title={Connecting the Nanodots: Programmable Nanofabrication of Fused Metal Shapes on DNA Templates}, volume={11}, ISSN={1530-6984 1530-6992}, url={http://dx.doi.org/10.1021/nl202066c}, DOI={10.1021/nl202066c}, abstractNote={We present a novel method for producing complex metallic nanostructures of programmable design. DNA origami templates, modified to have DNA binding sites with a uniquely coded sequence, were adsorbed onto silicon dioxide substrates. Gold nanoparticles functionalized with the cDNA sequence were then attached. These seed nanoparticles were later enlarged, and even fused, by electroless deposition of silver. Using this method, we constructed a variety of metallic structures, including rings, pairs of bars, and H shapes.}, number={8}, journal={Nano Letters}, publisher={American Chemical Society (ACS)}, author={Pilo-Pais, M. and Goldberg, S. and Samano, E. and LaBean, T. H. and Finkelstein, G.}, year={2011}, month={Aug}, pages={3489–3492} }
 @article{majumder_rangnekar_gothelf_reif_labean_2011, title={Design and Construction of Double-Decker Tile as a Route to Three-Dimensional Periodic Assembly of DNA}, volume={133}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja1108886}, DOI={10.1021/ja1108886}, abstractNote={DNA is a useful material for nanoscale construction. Due to highly specific Watson-Crick base pairing, the DNA sequences can be designed to form small tiles or origami. Adjacent helices in such nanostructures are connected via Holliday junction-like crossovers. DNA tiles can have sticky ends which can then be programmed to form large one-dimensional and two-dimensional periodic lattices. Recently, a three-dimensional DNA lattice has also been constructed. Here we report the design and construction of a novel DNA cross tile, called the double-decker tile. Its arms are symmetric and have four double helices each. Using its sticky ends, large two-dimensional square lattices have been constructed which are on the order of tens of micrometers. Furthermore, it is proposed that the sticky ends of the double-decker tile can be programmed to form a three-dimensional periodic lattice with large cavities that could be used as a scaffold for precise positioning of molecules in space.}, number={11}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Majumder, Urmi and Rangnekar, Abhijit and Gothelf, Kurt V. and Reif, John H. and LaBean, Thomas H.}, year={2011}, month={Mar}, pages={3843–3845} }
 @article{rangnekar_gothelf_labean_2011, title={Design and synthesis of DNA four-helix bundles}, volume={22}, ISSN={0957-4484 1361-6528}, url={http://dx.doi.org/10.1088/0957-4484/22/23/235601}, DOI={10.1088/0957-4484/22/23/235601}, abstractNote={The field of DNA nanotechnology has evolved significantly in the past decade. Researchers have succeeded in synthesizing tile-based structures and using them to form periodic lattices in one, two and three dimensions. Origami-based structures have also been used to create nanoscale structures in two and three dimensions. Design and construction of DNA bundles with fixed circumference has added a new dimension to the field. Here we report the design and synthesis of a DNA four-helix bundle. It was found to be extremely rigid and stable. When several such bundles were assembled using appropriate sticky-ends, they formed micrometre-long filaments. However, when creation of two-dimensional sheet-like arrays of the four-helix bundles was attempted, nanoscale rings were observed instead. The exact reason behind the nanoring formation is yet to be ascertained, but it provides an exciting prospect for making programmable circular nanostructures using DNA.}, number={23}, journal={Nanotechnology}, publisher={IOP Publishing}, author={Rangnekar, Abhijit and Gothelf, Kurt V and LaBean, Thomas H}, year={2011}, month={Apr}, pages={235601} }
 @article{kim_kim_qian_shin_amin_ahn_labean_kim_park_2011, title={Intrinsic DNA curvature of double-crossover tiles}, volume={22}, ISSN={0957-4484 1361-6528}, url={http://dx.doi.org/10.1088/0957-4484/22/24/245706}, DOI={10.1088/0957-4484/22/24/245706}, abstractNote={A theoretical model which takes into account the structural distortion of double-crossover DNA tiles has been studied to investigate its effect on lattice formation sizes. It has been found that a single vector appropriately describes the curvature of the tiles, of which a higher magnitude hinders lattice growth. In conjunction with these calculations, normal mode analysis reveals that tiles with relative higher frequencies have an analogous effect. All the theoretical results are shown to be in good agreement with experimental data.}, number={24}, journal={Nanotechnology}, publisher={IOP Publishing}, author={Kim, Seungjae and Kim, Junghoon and Qian, Pengfei and Shin, Jihoon and Amin, Rashid and Ahn, Sang Jung and LaBean, Thomas H and Kim, Moon Ki and Park, Sung Ha}, year={2011}, month={May}, pages={245706} }
 @article{carter_labean_2011, title={Organization of Inorganic Nanomaterials via Programmable DNA Self-Assembly and Peptide Molecular Recognition}, volume={5}, ISSN={1936-0851 1936-086X}, url={http://dx.doi.org/10.1021/nn1033983}, DOI={10.1021/nn1033983}, abstractNote={An interesting alternative to top-down nanofabrication is to imitate biology, where nanoscale materials frequently integrate organic molecules for self-assembly and molecular recognition with ordered, inorganic minerals to achieve mechanical, sensory, or other advantageous functions. Using biological systems as inspiration, researchers have sought to mimic the nanoscale composite materials produced in nature. Here, we describe a combination of self-assembly, molecular recognition, and templating, relying on an oligonucleotide covalently conjugated to a high-affinity gold-binding peptide. After integration of the peptide-coupled DNA into a self-assembling superstructure, the templated peptides recognize and bind gold nanoparticles. In addition to providing new ways of building functional multinanoparticle systems, this work provides experimental proof that a single peptide molecule is sufficient for immobilization of a nanoparticle. This molecular construction strategy, combining DNA assembly and peptide recognition, can be thought of as programmable, granular, artificial biomineralization. We also describe the important observation that the addition of 1-2% Tween 20 surfactant to the solution during gold particle binding allows the gold nanoparticles to remain soluble within the magnesium-containing DNA assembly buffer under conditions that usually lead to the aggregation and precipitation of the nanoparticles.}, number={3}, journal={ACS Nano}, publisher={American Chemical Society (ACS)}, author={Carter, Joshua D. and LaBean, Thomas H.}, year={2011}, month={Feb}, pages={2200–2205} }
 @article{samano_pilo-pais_goldberg_vogen_finkelstein_labean_2011, title={Self-assembling DNA templates for programmed artificial biomineralization}, volume={7}, ISSN={1744-683X 1744-6848}, url={http://dx.doi.org/10.1039/c0sm01318h}, DOI={10.1039/c0sm01318h}, abstractNote={Complex materials with micron-scale dimensions and nanometre-scale feature resolution created via engineered DNA self-assembly represent an important new class of soft matter. These assemblies are increasingly being exploited as templates for the programmed assembly of functional inorganic materials that have not conventionally lent themselves to organization by molecular recognition processes. The current challenge is to apply these bioinspired DNA templates toward the fabrication of composite materials for use in electronics, photonics, and other fields of technology. This highlight focuses on methods we consider most useful for integration of DNA templated structures into functional composite nanomaterials, particularly, organization of preformed nanoparticles and metallization procedures.}, number={7}, journal={Soft Matter}, publisher={Royal Society of Chemistry (RSC)}, author={Samano, Enrique C. and Pilo-Pais, Mauricio and Goldberg, Sarah and Vogen, Briana N. and Finkelstein, Gleb and LaBean, Thomas H.}, year={2011}, pages={3240} }
 @article{saaem_ma_marchi_labean_tian_2010, title={In situ Synthesis of DNA Microarray on Functionalized Cyclic Olefin Copolymer Substrate}, volume={2}, ISSN={1944-8244 1944-8252}, url={http://dx.doi.org/10.1021/am900884b}, DOI={10.1021/am900884b}, abstractNote={Thermoplastic materials such as cyclic-olefin copolymers (COC) provide a versatile and cost-effective alternative to the traditional glass or silicon substrate for rapid prototyping and industrial scale fabrication of microdevices. To extend the utility of COC as an effective microarray substrate, we developed a new method that enabled for the first time in situ synthesis of DNA oligonucleotide microarrays on the COC substrate. To achieve high-quality DNA synthesis, a SiO(2) thin film array was prepatterned on the inert and hydrophobic COC surface using RF sputtering technique. The subsequent in situ DNA synthesis was confined to the surface of the prepatterned hydrophilic SiO(2) thin film features by precision delivery of the phosphoramidite chemistry using an inkjet DNA synthesizer. The in situ SiO(2)-COC DNA microarray demonstrated superior quality and stability in hybridization assays and thermal cycling reactions. Furthermore, we demonstrate that pools of high-quality mixed-oligos could be cleaved off the SiO(2)-COC microarrays and used directly for construction of DNA origami nanostructures. It is believed that this method will not only enable synthesis of high-quality and low-cost COC DNA microarrays but also provide a basis for further development of integrated microfluidics microarrays for a broad range of bioanalytical and biofabrication applications.}, number={2}, journal={ACS Applied Materials & Interfaces}, publisher={American Chemical Society (ACS)}, author={Saaem, Ishtiaq and Ma, Kuo-Sheng and Marchi, Alexandria N. and LaBean, Thomas H. and Tian, Jingdong}, year={2010}, month={Feb}, pages={491–497} }
 @article{hansen_zhang_rangnekar_bompiani_carter_gothelf_labean_2010, title={Weave Tile Architecture Construction Strategy for DNA Nanotechnology}, volume={132}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja104456p}, DOI={10.1021/ja104456p}, abstractNote={Architectural designs for DNA nanostructures typically fall within one of two broad categories: tile-based designs (assembled from chemically synthesized oligonucleotides) and origami designs (woven structures employing a biological scaffold strand and synthetic staple strands). Both previous designs typically contain many Holliday-type multi-arm junctions. Here we describe the design, implementation, and testing of a unique architectural strategy incorporating some aspects of each of the two previous design categories but without multi-arm junction motifs. Goals for the new design were to use only chemically synthesized DNA, to minimize the number of component strands, and to mimic the back-and-forth, woven strand routing of the origami architectures. The resulting architectural strategy employs "weave tiles" formed from only two oligonucleotides as basic building blocks, thus decreasing the burden of matching multiple strand stoichiometries compared to previous tile-based architectures and resulting in a structurally flexible tile. As an example application, we have shown that the four-helix weave tile can be used to increase the anticoagulant activity of thrombin-binding aptamers in vitro.}, number={41}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Hansen, Majken N. and Zhang, Alex M. and Rangnekar, Abhijit and Bompiani, Kristin M. and Carter, Joshua D. and Gothelf, Kurt V. and LaBean, Thomas H.}, year={2010}, month={Oct}, pages={14481–14486} }
 @article{labean_2009, title={Another dimension for DNA art}, volume={459}, ISSN={0028-0836 1476-4687}, url={http://dx.doi.org/10.1038/459331a}, DOI={10.1038/459331a}, abstractNote={Many of nature's intricate nanostructures self-assemble from subunits. Efforts to mimic these assembly processes enter a new phase with a method to design and build three-dimensional DNA nanostructures. An important goal in nanotechnology is the programmable self-assembly of complex, three-dimensional nanostructures. With DNA as the building block, synthesis techniques have developed to the stage where two-dimensional designer structures and certain three-dimensional structures can be produced. Douglas et al. describe a refinement of the scaffolded DNA origami technique capable of producing three-dimensional objects of more or less any desired form, to a scale of ten to a hundred nanometres, and with an impressive degree of control over the positions of the various DNA helices. The synthesis involves DNA helices arranged on pleated strands and assembled into honeycomb-like three-dimensional structures. The various strands link together via phosphate groups. The method produces complex objects that are slow to assemble. But it also provides a route towards assembling custom devices with nanometre-scale features, as demonstrated by the construction of objects with shapes resembling a square nut, slotted cross and wire-frame icosahedron.}, number={7245}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={LaBean, Thomas H.}, year={2009}, month={May}, pages={331–332} }
 @article{li_carter_labean_2009, title={Nanofabrication by DNA self-assembly}, volume={12}, ISSN={1369-7021}, url={http://dx.doi.org/10.1016/S1369-7021(09)70157-9}, DOI={10.1016/S1369-7021(09)70157-9}, abstractNote={Molecular self-assembly strategies involve the formation of nanometer scale objects and materials in the absence of significant external control. One increasingly popular self-assembly approach makes use of the unique properties of deoxyribonucleic acid (DNA) including its diminutive size and high capacity for information storage. For many applications, DNA stands alone as the top choice for the programmable construction of supramolecular materials due to its specific and well-understood base-pairing interactions. In this review, we will discuss recent advances in the fabrication of materials via DNA based self-assembly.}, number={5}, journal={Materials Today}, publisher={Elsevier BV}, author={Li, Hanying and Carter, Joshua D. and LaBean, Thomas H.}, year={2009}, month={May}, pages={24–32} }
 @article{sahu_labean_reif_2008, title={A DNA Nanotransport Device Powered by Polymerase ϕ29}, volume={8}, ISSN={1530-6984 1530-6992}, url={http://dx.doi.org/10.1021/nl802294d}, DOI={10.1021/nl802294d}, abstractNote={Polymerases are a family of enzymes responsible for copying or replication of nucleic acids (DNA or RNA) templates and hence sustenance of life processes. In this paper, we present a method to exploit a strand-displacing polymerase phi29 as a driving force for nanoscale transportation devices. The principal idea behind the device is strong strand displacement ability of phi29, which can displace any DNA strand from its template while extending a primer hybridized to the template. This capability of phi29 is used to power the movement of a target nanostructure on a DNA track. The major advantage of using a polymerase driven nanotransportation device as compared to other existing nanorobotical devices is its speed. phi29 polymerase can travel at the rate of 2000 nucleotides per minute at room temperature, which translates to approximately 680 nm min(-1) on a nanostructure. We also demonstrate transportation of a DNA cargo on a DNA track with the help of fluorescence resonance electron transfer data.}, number={11}, journal={Nano Letters}, publisher={American Chemical Society (ACS)}, author={Sahu, Sudheer and LaBean, Thomas H. and Reif, John H.}, year={2008}, month={Nov}, pages={3870–3878} }
 @inbook{majumder_labean_reif_2008, title={Activatable Tiles: Compact, Robust Programmable Assembly and Other Applications}, ISBN={9783540779612 9783540779629}, url={http://dx.doi.org/10.1007/978-3-540-77962-9_2}, DOI={10.1007/978-3-540-77962-9_2}, abstractNote={While algorithmic DNA self-assembly is, in theory, capable of forming complex patterns, its experimental demonstration has been limited by significant assembly errors. In this paper we describe a novel protection/deprotection strategy to strictly enforce the direction of tiling assembly growth to ensure the robustness of the assembly process. Tiles are initially inactive, meaning that each tile's output pads are protected and cannot bind with other tiles. After other tiles bind to the tile's input pads, the tile transitions to an active state and its output pads are exposed, allowing further growth. We prove that an activatable tile set is an instance of a compact, error-resilient and self-healing tile-set. We also describe a DNA design for activatable tiles and a deprotection mechanism using DNA polymerase enzymes and strand displacement. We conclude with a discussion on some applications of activatable tiles beyond computational tiling.}, booktitle={DNA Computing}, publisher={Springer Berlin Heidelberg}, author={Majumder, Urmi and LaBean, Thomas H. and Reif, John H.}, year={2008}, month={Feb}, pages={15–25} }
 @article{sebba_labean_lazarides_2008, title={Plasmon coupling in binary metal core–satellite assemblies}, volume={93}, ISSN={0946-2171 1432-0649}, url={http://dx.doi.org/10.1007/s00340-008-3212-2}, DOI={10.1007/s00340-008-3212-2}, number={1}, journal={Applied Physics B}, publisher={Springer Science and Business Media LLC}, author={Sebba, D. S. and LaBean, T. H. and Lazarides, A. A.}, year={2008}, month={Sep}, pages={69–78} }
 @article{sebba_mock_smith_labean_lazarides_2008, title={Reconfigurable Core−Satellite Nanoassemblies as Molecularly-Driven Plasmonic Switches}, volume={8}, ISSN={1530-6984 1530-6992}, url={http://dx.doi.org/10.1021/nl080029h}, DOI={10.1021/nl080029h}, abstractNote={Molecular control of plasmon coupling is investigated in sub-100 nm assemblies composed of 13 nm gold "satellite" particles tethered by reconfigurable DNA nanostructures to a 50 nm gold "core" particle. Reconfiguration of the DNA nanostructures from a compact to an extended state results in blue shifting of the assembly plasmon resonance, indicating reduced interparticle coupling and lengthening of the core-satellite tether. Scattering spectra of the core-satellite assemblies before and after reconfiguration are compared with spectra calculated using a structural model that incorporates the core/satellite ratio determined by TEM imaging and estimates of tether length based upon prior measurements of interparticle separation in DNA linked nanoparticle networks. A strong correspondence between measured and simulated difference spectra validates the structural models that link the observed plasmon modulation with DNA nanostructure reconfiguration.}, number={7}, journal={Nano Letters}, publisher={American Chemical Society (ACS)}, author={Sebba, David S. and Mock, Jack J. and Smith, David R. and LaBean, Thomas H. and Lazarides, Anne A.}, year={2008}, month={Jul}, pages={1803–1808} }
 @article{coskun_mebrahtu_huang_huang_sebba_biasco_makarovski_lazarides_labean_finkelstein_2008, title={Single-electron transistors made by chemical patterning of silicon dioxide substrates and selective deposition of gold nanoparticles}, volume={93}, ISSN={0003-6951 1077-3118}, url={http://dx.doi.org/10.1063/1.2981705}, DOI={10.1063/1.2981705}, abstractNote={We describe a method to pattern SiO2 surfaces with colloidal gold nanoparticles by e-beam lithography and selective nanoparticle deposition. The simple technique allows us to deposit nanoparticles in continuous straight lines, just one nanoparticle wide and many nanoparticles long. We contact the prepositioned nanoparticles with metal leads to form single electron transistors. The Coulomb blockade pattern surprisingly does not show the parasitic “offset charges” at low temperatures, indicating relatively little surface contamination.}, number={12}, journal={Applied Physics Letters}, publisher={AIP Publishing}, author={Coskun, Ulas C. and Mebrahtu, Henok and Huang, Paul B. and Huang, Jeremy and Sebba, David and Biasco, Adriana and Makarovski, Alex and Lazarides, Anne and LaBean, Thom H. and Finkelstein, Gleb}, year={2008}, month={Sep}, pages={123101} }
 @article{park_finkelstein_labean_2008, title={Stepwise Self-Assembly of DNA Tile Lattices Using dsDNA Bridges}, volume={130}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja078122f}, DOI={10.1021/ja078122f}, abstractNote={The simple helical motif of double-strand DNA (dsDNA) has typically been judged to be uninteresting for assembly in DNA-based nanotechnology applications. In this letter, we demonstrate construction of superstructures consisting of heterogeneous DNA motifs using dsDNA in conjunction with more complex, cross-tile building blocks. Incorporation of dsDNA bridges in stepwise assembly processes can be used for controlling length and directionality of superstructures and is analogous to the "reprogramming" of sticky-ends displayed on the DNA tiles. Two distinct self-assembled DNA lattices, fixed-size nanoarrays, and extended 2D crystals of nanotracks with nanobridges, are constructed and visualized by high-resolution, liquid-phase atomic force microscopy.}, number={1}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Park, Sung Ha and Finkelstein, Gleb and LaBean, Thomas H.}, year={2008}, month={Jan}, pages={40–41} }
 @inbook{reif_labean_2007, title={Autonomous Programmable Biomolecular Devices Using Self-assembled DNA Nanostructures}, ISBN={9783540734437 9783540734451}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/978-3-540-73445-1_21}, DOI={10.1007/978-3-540-73445-1_21}, abstractNote={The particular molecular-scale devices that are the topic of this article are known as DNA nanostructures. As will be explained, DNA nanostructures have some unique advantages among nanostructures: they are relatively easy to design, fairly predictable in their geometric structures, and have been experimentally implemented in a growing number of labs around the world. They are constructed primarily of synthetic DNA. A key principle in the study of DNA nanostructures is the use of self-assembly processes to actuate the molecular assembly. Since self-assembly operates naturally at the molecular scale, it does not suffer from the limitation in scale reduction that so restricts lithography or other more conventional top-down manufacturing techniques.}, booktitle={Logic, Language, Information and Computation}, publisher={Springer Berlin Heidelberg}, author={Reif, John H. and LaBean, Thomas H.}, year={2007}, pages={297–306} }
 @article{labean_li_2007, title={Constructing novel materials with DNA}, volume={2}, ISSN={1748-0132}, url={http://dx.doi.org/10.1016/S1748-0132(07)70056-7}, DOI={10.1016/S1748-0132(07)70056-7}, abstractNote={DNA, apart from being a natural biological information carrier, has also been recognized as a useful building material in the field of nanotechnology. Its miniature scale, geometric properties, and molecular recognition capacity make DNA an appealing candidate for the construction of novel nanomaterials. Here we summarize the latest developments and describe the challenges and emerging applications of this field.}, number={2}, journal={Nano Today}, publisher={Elsevier BV}, author={LaBean, Thom H. and Li, Hanying}, year={2007}, month={Apr}, pages={26–35} }
 @article{reza_josephs_yuan_van dyke_lin_feltz_chung_tian_heinz_tang_et al._2007, title={Engineering novel synthetic biological systems}, volume={1}, ISSN={1752-1394 1752-1408}, url={http://dx.doi.org/10.1049/iet-stb:20060004}, DOI={10.1049/iet-stb:20060004}, abstractNote={Engineering principles and new applications for the nascent field of synthetic biology are just beginning to be explored. Here, we report the engineering of four novel synthetic biological systems: (1) a Bacterial Dynamo, for generating electricity using modified magnetotactic bacteria on a microfabricated device; (2) Cancer StickyBots, for targeting and destroying tumour cells using engineered Escherichia coli cells; (3) Human Encryption, an information encoding, storage, and retrieval scheme for potential security and medical diagnostic applications; and (4) X-Verter, new strategies and tools for biological circuit design and BioBrick management. While each of these systems had distinct aims, they shared a common philosophy of rationally building useful and beneficial synthetic biological systems using fundamental engineering principles. They also demonstrated the potential usefulness of BioBricks and contributed to the Registry of Standard Biological Parts and synthetic biology community-at-large.}, number={1}, journal={IET Synthetic Biology}, publisher={Institution of Engineering and Technology (IET)}, author={Reza, F. and Josephs, E. and Yuan, F. and Van Dyke, B. and Lin, S. and Feltz, M. and Chung, H. and Tian, J. and Heinz, A. and Tang, N. and et al.}, year={2007}, month={Jun}, pages={48–52} }
 @article{labean_2006, title={DNA bulks up}, volume={5}, ISSN={1476-1122 1476-4660}, url={http://dx.doi.org/10.1038/nmat1745}, DOI={10.1038/nmat1745}, number={10}, journal={Nature Materials}, publisher={Springer Science and Business Media LLC}, author={LaBean, Thom}, year={2006}, month={Oct}, pages={767–768} }
 @inbook{majumder_sahu_labean_reif_2006, title={Design and Simulation of Self-repairing DNA Lattices}, ISBN={9783540490241 9783540684237}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/11925903_15}, DOI={10.1007/11925903_15}, abstractNote={Self-repair is essential to all living systems, providing the ability to remain functional in spite of gradual damage. In the context of self-assembly of self-repairing synthetic biomolecular systems, recently Winfree developed a method for transforming a set of DNA tiles into its self-healing counterpart at the cost of increasing the lattice area by a factor of 25. The overall focus of this paper, however, is to develop compact designs for self-repairing tiling assemblies with reasonable constraints on crystal growth. Specifically, we use a special class of DNA tiling designs called reversible tiling which when carefully designed can provide inherent self-repairing capabilities to patterned DNA lattices. We further note that we can transform any irreversible computational DNA tile set to its reversible counterpart and hence improve the self-repairability of the computational lattice. But doing the transform with an optimal number of tiles, is still an open question.}, booktitle={DNA Computing}, publisher={Springer Berlin Heidelberg}, author={Majumder, Urmi and Sahu, Sudheer and LaBean, Thomas H. and Reif, John H.}, year={2006}, pages={195–214} }
 @article{park_pistol_ahn_reif_lebeck_dwyer_labean_2006, title={Finite-Size, Fully Addressable DNA Tile Lattices Formed by Hierarchical Assembly Procedures}, volume={45}, ISSN={1433-7851 1521-3773}, url={http://dx.doi.org/10.1002/anie.200503797}, DOI={10.1002/anie.200503797}, abstractNote={The development of a versatile and readily programmable assembly system for the controlled placement of matter at the molecular scale remains a major goal for nanoscience, nanotechnology, and supramolecular chemistry. Herein, we present a significant step toward this goal by using selfassembling DNA nanostructures to construct fully addressable, finite-sized arrays displaying a variety of programmed patterns. We have assembled DNA tile arrays decorated with proteins in the shape of the letters “D”, “N”, and “A” that are less than 80 nm on a side. We demonstrate procedures that explore two extremes in hierarchical assembly strategies: 1) minimization of the number of unique molecular address labels (DNA sticky-end sequences) required for encoding tile associations, and 2) minimization of the depth (number of sequential steps) of the assembly process. Higher production yields of defect-free assemblies were achieved by procedures that minimize assembly depth (and maximize diversity of address labels). Some observations on scaling of these strategies to larger arrays are also presented.}, number={5}, journal={Angewandte Chemie International Edition}, publisher={Wiley}, author={Park, Sung Ha and Pistol, Constantin and Ahn, Sang Jung and Reif, John H. and Lebeck, Alvin R. and Dwyer, Chris and LaBean, Thomas H.}, year={2006}, month={Jan}, pages={735–739} }
 @article{park_pistol_ahn_reif_lebeck_dwyer_labean_2006, title={Finite-Size, Fully Addressable DNA Tile Lattices Formed by Hierarchical Assembly Procedures}, volume={45}, ISSN={1433-7851 1521-3773}, url={http://dx.doi.org/10.1002/anie.200690141}, DOI={10.1002/anie.200690141}, abstractNote={In Figure 1 B of this Communication, the tile labels in the annealing structure scheme appeared incorrectly. The correct numbering is shown below (Figure 1).1 DNA tile and NA structures and assembly schemes. A) Schematic drawings of the strand trace in cross tiles with strand names marked (arm, shell, and loop). B) MSS strategy and constructs. A converging-stream diagram of the four-step assembly process starting with eight tubes of two tiles each (i) and concluding with one tube containing all 16 tiles (iv). The blue and red diagram shows the placement of tiles (1 through 16) in the NA and the identity of loop strands (A-loops are blue and B-loops are red). The bottom six panels are AFM height images with dimensions as labeled and height scale from 0 to 3 nm. Panels i)–iv) correspond to the same labels as in the annealing scheme above; thus, i) 1×2 NA, ii) 2×2 NA, iii) 2×4 NA, and iv) 4×4 NA. The two bottom AFM images are zoom-out and zoom-in pictures of (iv), with error-free NAs in the zoom-out image circled in turquoise. C) MD strategy and constructs. A converging-stream diagram of the two-step assembly starts with 16 tubes with one tile each (i) and goes directly to one tube of 16 tiles (ii). The blue and red diagram shows the placement of A-loop and B-loop tiles in the final NA. The bottom four panels are AFM height images with i) showing single tiles and ii) showing complete 4×4 NAs. The two bottom panels are zoom-out images to show the increased production yield of defect-free assemblies from the two-step method.}, number={40}, journal={Angewandte Chemie International Edition}, publisher={Wiley}, author={Park, Sung Ha and Pistol, Constantin and Ahn, Sang Jung and Reif, John H. and Lebeck, Alvin R. and Dwyer, Chris and LaBean, Thomas H.}, year={2006}, month={Oct}, pages={6607–6607} }
 @article{park_prior_labean_finkelstein_2006, title={Optimized fabrication and electrical analysis of silver nanowires templated on DNA molecules}, volume={89}, ISSN={0003-6951 1077-3118}, url={http://dx.doi.org/10.1063/1.2234282}, DOI={10.1063/1.2234282}, abstractNote={We report on the electrical conductivity measurement of silver nanowires templated on native λ-bacteriophage and synthetic double-stranded DNA molecules. After an electroless chemical deposition, the metallized DNA wires have a diameter down to 15nm and are among the thinnest metallic nanowires available to date. Two-terminal I-V measurements demonstrating various conduction behaviors are presented. DNA templated functional nanowires may, in the near future, be targeted to connect at specific locations on larger-scale circuits and represent a potential breakthrough in the self-assembly of nanometer-scale structures for electronics layout.}, number={3}, journal={Applied Physics Letters}, publisher={AIP Publishing}, author={Park, Sung Ha and Prior, Matthew W. and LaBean, Thomas H. and Finkelstein, Gleb}, year={2006}, month={Jul}, pages={033901} }
 @article{li_labean_kenan_2006, title={Single-chain antibodies against DNA aptamers for use as adapter molecules on DNA tile arrays in nanoscale materials organization}, volume={4}, ISSN={1477-0520 1477-0539}, url={http://dx.doi.org/10.1039/b606391h}, DOI={10.1039/b606391h}, abstractNote={Complex DNA nanostructures have been developed as structural components for the construction of nanoscale objects. Recent advances have enabled self-assembly of organized DNA nanolattices and their use in patterning functional bio-macromolecules and other nanomaterials. Adapter molecules that bind specifically to both DNA lattices and nanomaterials would be useful components in a molecular construction kit for patterned nanodevices. Herein we describe the selection from phage display libraries of single-chain antibodies (scFv) for binding to a specific DNA aptamer and their development as adapter molecules for nanoscale construction. We demonstrate the decoration of various DNA tile structures with aptamers and show binding of the selected single-chain antibody as well as the self-assembly of mixed DNA-protein biomolecular lattices.}, number={18}, journal={Organic & Biomolecular Chemistry}, publisher={Royal Society of Chemistry (RSC)}, author={Li, Hanying and LaBean, Thomas H. and Kenan, Daniel J.}, year={2006}, pages={3420} }
 @article{gothelf_labean_2005, title={DNA-programmed assembly of nanostructures}, volume={3}, ISSN={1477-0520 1477-0539}, url={http://dx.doi.org/10.1039/b510551j}, DOI={10.1039/b510551j}, abstractNote={DNA is a unique material for nanotechnology since it is possible to use base sequences to encode instructions for assembly in a predetermined fashion at the nanometre scale. Synthetic oligonucleotides are readily obtained by automated synthesis and numerous techniques have been developed for conjugating DNA with other materials. The exact spatial positioning of materials is crucial for the future development of complex nanodevices and the emerging field of DNA-nanotechnology is now exploring DNA-programmed processes for the assembly of organic compounds, biomolecules, and inorganic materials.}, number={22}, journal={Organic & Biomolecular Chemistry}, publisher={Royal Society of Chemistry (RSC)}, author={Gothelf, Kurt V. and LaBean, Thomas H.}, year={2005}, pages={4023} }
 @inbook{reif_labean_sahu_yan_yin_2005, title={Design, Simulation, and Experimental Demonstration of Self-assembled DNA Nanostructures and Motors}, ISBN={9783540278849 9783540314820}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/11527800_14}, DOI={10.1007/11527800_14}, abstractNote={Self-assembly is the spontaneous self-ordering of substructures into superstructures, driven by the selective affinity of the substructures. Complementarity of DNA bases renders DNA an ideal material for programmable self-assembly of nanostructures. DNA self-assembly is the most advanced and versatile system that has been experimentally demonstrated for programmable construction of patterned systems on the molecular scale. The methodology of DNA self-assembly begins with the synthesis of single strand DNA molecules that self-assemble into macromolecular building blocks called DNA tiles. These tiles have single strand "sticky ends" that complement the sticky ends of other DNA tiles, facilitating further assembly into larger structures known as DNA tiling lattices. In principle, DNA tiling assemblies can form any computable two or three-dimensional pattern, however complex, with the appropriate choice of the tiles' component DNA. Two-dimensional DNA tiling lattices composed of hundreds of thousands of tiles have been demonstrated experimentally. These assemblies can be used as programmable scaffolding to position molecular electronics and robotics components with precision and specificity, facilitating fabrication of complex nanoscale devices. We overview the evolution of DNA self-assembly techniques from pure theory, through simulation and design, and then to experimental practice. In particular, we begin with an overview of theoretical models and algorithms for DNA lattice self-assembly. Then we describe our software for the simulation and design of DNA tiling assemblies and DNA nano-mechanical devices. As an example, we discuss models, algorithms, and computer simulations for the key problem of error control in DNA lattice self-assembly. We then briefly discuss our laboratory demonstrations of DNA lattices and motors, including those using the designs aided by our software. These experimental demonstrations of DNA self-assemblies include the assembly of patterned objects at the molecular scale, the execution of molecular computations, and the autonomous DNA walking and computing devices.}, booktitle={Lecture Notes in Computer Science}, publisher={Springer Berlin Heidelberg}, author={Reif, John H. and LaBean, Thomas H. and Sahu, Sudheer and Yan, Hao and Yin, Peng}, year={2005}, pages={173–187} }
 @article{park_yin_liu_reif_labean_yan_2005, title={Programmable DNA Self-Assemblies for Nanoscale Organization of Ligands and Proteins}, volume={5}, ISSN={1530-6984 1530-6992}, url={http://dx.doi.org/10.1021/nl050175c}, DOI={10.1021/nl050175c}, abstractNote={We demonstrate the precise control of periodic spacing between individual protein molecules by programming the self-assembly of DNA tile templates. In particular, we report the application of two self-assembled periodic DNA structures, two-dimensional nanogrids, and one-dimensional nanotrack, as template for programmable self-assembly of streptavidin protein arrays with controlled density.}, number={4}, journal={Nano Letters}, publisher={American Chemical Society (ACS)}, author={Park, Sung Ha and Yin, Peng and Liu, Yan and Reif, John H. and LaBean, Thomas H. and Yan, Hao}, year={2005}, month={Apr}, pages={729–733} }
 @article{park_barish_li_reif_finkelstein_yan_labean_2005, title={Three-Helix Bundle DNA Tiles Self-Assemble into 2D Lattice or 1D Templates for Silver Nanowires}, volume={5}, ISSN={1530-6984 1530-6992}, url={http://dx.doi.org/10.1021/nl050108i}, DOI={10.1021/nl050108i}, abstractNote={We present a DNA nanostructure, the three-helix bundle (3HB), which consists of three double helical DNA domains connected by six immobile crossover junctions such that the helix axes are not coplanar. The 3HB motif presents a triangular cross-section with one helix lying in the groove formed by the other two. By differential programming of sticky-ends, 3HB tiles can be arrayed in two distinct lattice conformations: one-dimensional filaments and two-dimensional lattices. Filaments and lattices have been visualized by high-resolution, tapping mode atomic force microscopy (AFM) under buffer. Their dimensions are shown to be in excellent agreement with designed structures. We also demonstrate an electroless chemical deposition for fabricating metallic nanowires templated on self-assembled filaments. The metallized nanowires have diameters down to 20 nm and display Ohmic current-voltage characteristic.}, number={4}, journal={Nano Letters}, publisher={American Chemical Society (ACS)}, author={Park, Sung Ha and Barish, Robert and Li, Hanying and Reif, John H. and Finkelstein, Gleb and Yan, Hao and LaBean, Thomas H.}, year={2005}, month={Apr}, pages={693–696} }
 @article{labean_2004, title={Bionanotechnology: Lessons from Nature.  By David S  Goodsell.  Hoboken (New Jersey): Wiley‐Liss. $79.95. xii + 337 p; ill.; index. ISBN: 0–471–41719–X. 2004.}, volume={79}, ISSN={0033-5770 1539-7718}, url={http://dx.doi.org/10.1086/428169}, DOI={10.1086/428169}, abstractNote={Previous articleNext article No AccessMolecular BiologyBionanotechnology: Lessons from Nature. By David S Goodsell. Hoboken (New Jersey): Wiley‐Liss. $79.95. xii + 337 p; ill.; index. ISBN: 0–471–41719–X. 2004.Thom LaBeanThom LaBeanComputer Science, Duke University, Durham, North Carolina Search for more articles by this author Computer Science, Duke University, Durham, North CarolinaPDFPDF PLUSFull Text Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmail SectionsMoreDetailsFiguresReferencesCited by The Quarterly Review of Biology Volume 79, Number 4December 2004 Published in association with Stony Brook University Article DOIhttps://doi.org/10.1086/428169 Views: 21Total views on this site PDF download Crossref reports no articles citing this article.}, number={4}, journal={The Quarterly Review of Biology}, publisher={University of Chicago Press}, author={LaBean, Thom}, year={2004}, month={Dec}, pages={415–415} }
 @article{liu_park_reif_labean_2004, title={DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires}, volume={101}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.0305860101}, DOI={10.1073/pnas.0305860101}, abstractNote={DNA-based nanotechnology is currently being developed as a general assembly method for nanopatterned materials that may find use in electronics, sensors, medicine, and many other fields. Here we present results on the construction and characterization of DNA nanotubes, a self-assembling superstructure composed of DNA tiles. Triple-crossover tiles modified with thiol-containing double-stranded DNA stems projected out of the tile plane were used as the basic building blocks. Triple-crossover nanotubes display a constant diameter of ≈25 nm and have been observed with lengths up to 20 μm. We present high-resolution images of the constructs, experimental evidence of their tube-like nature as well as data on metallization of the nanotubes to form nanowires, and electrical conductivity measurements through the nanowires. DNA nanotubes represent a potential breakthrough in the self-assembly of nanometer-scale circuits for electronics layout because they can be targeted to connect at specific locations on larger-scale structures and can subsequently be metallized to form nanometer-scale wires. The dimensions of these nanotubes are also perfectly suited for applications involving interconnection of molecular-scale devices with macroscale components fabricated by conventional photolithographic methods.}, number={3}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Liu, D. and Park, S. H. and Reif, J. H. and LaBean, T. H.}, year={2004}, month={Jan}, pages={717–722} }
 @article{li_park_reif_labean_yan_2004, title={DNA-Templated Self-Assembly of Protein and Nanoparticle Linear Arrays}, volume={126}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja0383367}, DOI={10.1021/ja0383367}, abstractNote={Self-assembling DNA tiling lattices represent a versatile system for nanoscale construction. Self-assembled DNA arrays provide an excellent template for spatially positioning other molecules with increased relative precision and programmability. Here we report an experiment using a linear array of DNA triple crossover tiles to controllably template the self-assembly of single-layer or double-layer linear arrays of streptavidin molecules and streptavidin-conjugated nanogold particles through biotin-streptavidin interaction. The organization of streptavidin and its conjugated gold nanoparticles into periodic arrays was visualized by atomic force microscopy and scanning electron microscopy.}, number={2}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Li, Hanying and Park, Sung Ha and Reif, John H. and LaBean, Thomas H. and Yan, Hao}, year={2004}, month={Jan}, pages={418–419} }
 @article{park_yan_reif_labean_finkelstein_2004, title={Electronic nanostructures templated on self-assembled DNA scaffolds}, volume={15}, ISSN={0957-4484 1361-6528}, url={http://dx.doi.org/10.1088/0957-4484/15/10/005}, DOI={10.1088/0957-4484/15/10/005}, abstractNote={We report on the self-assembly of one- and two-dimensional DNA scaffolds, which serve as templates for the targeted deposition of ordered nanoparticles and molecular arrays. The DNA nanostructures are easy to reprogram, and we demonstrate two distinct conformations: sheets and tubes. The DNA tubes and individual DNA molecules are metallized in solution to produce ultra-thin metal wires.}, number={10}, journal={Nanotechnology}, publisher={IOP Publishing}, author={Park, Sung Ha and Yan, Hao and Reif, John H and LaBean, Thomas H and Finkelstein, Gleb}, year={2004}, month={Jul}, pages={S525–S527} }
 @article{ahn_kaholek_lee_lamattina_labean_zauscher_2004, title={Surface-Initiated Polymerization on Nanopatterns Fabricated by Electron-Beam Lithography}, volume={16}, ISSN={0935-9648 1521-4095}, url={http://dx.doi.org/10.1002/adma.200401055}, DOI={10.1002/adma.200401055}, abstractNote={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}, number={23-24}, journal={Advanced Materials}, publisher={Wiley}, author={Ahn, S. J. and Kaholek, M. and Lee, W.-K. and LaMattina, B. and LaBean, T. H. and Zauscher, S.}, year={2004}, month={Dec}, pages={2141–2145} }
 @inbook{gehani_labean_reif_2003, title={DNA-based Cryptography}, ISBN={9783540207818 9783540246350}, ISSN={0302-9743 1611-3349}, url={http://dx.doi.org/10.1007/978-3-540-24635-0_12}, DOI={10.1007/978-3-540-24635-0_12}, abstractNote={Recent research has considered DNA as a medium for ultra-scale computation and for ultra-compact information storage. One potential key application is DNA-based, molecular cryptography systems. We present some procedures for DNA-based cryptography based on one-time-pads that are in principle unbreakable. Practical applications of cryptographic systems based on one-time-pads are limited in conventional electronic media by the size of the one-time-pad; however DNA provides a much more compact storage medium, and an extremely small amount of DNA suffices even for huge one-time-pads. We detail procedures for two DNA one-time-pad encryption schemes: (i) a substitution method using libraries of distinct pads, each of which defines a specific, randomly generated, pair-wise mapping; and (ii) an XOR scheme utilizing molecular computation and indexed, random key strings. These methods can be applied either for the encryption of natural DNA or for artificial DNA encoding binary data. In the latter case, we also present a novel use of chip-based DNA micro-array technology for 2D data input and output. Finally, we examine a class of DNA steganography systems, which secretly tag the input DNA and then hide it within collections of other DNA. We consider potential limitations of these steganographic techniques, proving that in theory the message hidden with such a method can be recovered by an adversary. We also discuss various modified DNA steganography methods which appear to have improved security.}, booktitle={Aspects of Molecular Computing}, publisher={Springer Berlin Heidelberg}, author={Gehani, Ashish and LaBean, Thomas and Reif, John}, year={2003}, pages={167–188} }