@article{krissanaprasit_mihalko_meinhold_simpson_sollinger_pandit_dupont_kjems_brown_labean_2024, title={A Functional RNA-Origami as Direct Thrombin Inhibitor with Fast-acting and Specific Single-Molecule Reversal Agents in vivo model}, volume={32}, ISSN={1525-0016}, url={http://dx.doi.org/10.1016/j.ymthe.2024.05.002}, DOI={10.1016/j.ymthe.2024.05.002}, abstractNote={Injectable anticoagulants are widely used in medical procedures to prevent unwanted blood clotting. However, many lack safe, effective reversal agents. Here, we present new data on a previously described RNA origami-based, direct thrombin inhibitor (HEX01). We describe a new, fast-acting, specific, single-molecule reversal agent (antidote) and present in vivo data for the first time, including efficacy, reversibility, preliminary safety, and initial biodistribution studies. HEX01 contains multiple thrombin-binding aptamers appended on an RNA origami. It exhibits excellent anticoagulation activity in vitro and in vivo. The new single-molecule, DNA antidote (HEX02) reverses anticoagulation activity of HEX01 in human plasma within 30 s in vitro and functions effectively in a murine liver laceration model. Biodistribution studies of HEX01 in whole mice using ex vivo imaging show accumulation mainly in the liver over 24 h and with 10-fold lower concentrations in the kidneys. Additionally, we show that the HEX01/HEX02 system is non-cytotoxic to epithelial cell lines and non-hemolytic in vitro. Furthermore, we found no serum cytokine response to HEX01/HEX02 in a murine model. HEX01 and HEX02 represent a safe and effective coagulation control system with a fast-acting, specific reversal agent showing promise for potential drug development.}, number={7}, journal={Molecular Therapy}, publisher={Elsevier BV}, author={Krissanaprasit, Abhichart and Mihalko, Emily and Meinhold, Katherine and Simpson, Aryssa and Sollinger, Jennifer and Pandit, Sanika and Dupont, Daniel M. and Kjems, Jørgen and Brown, Ashley C. and LaBean, Thomas H.}, year={2024}, month={May}, pages={2286–2298} }
 @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={AbstractCells integrate many mechanical and chemical cues to drive cell signalling responses. Because of the complex nature and interdependency of alterations in extracellular matrix (ECM) composition, ligand density, mechanics, and cellular responses it is difficult to tease out individual and combinatorial contributions of these various factors in driving cell behavior in homeostasis and disease. Tuning of material viscous and elastic properties, and ligand densities, in combinatorial fashions would enhance our understanding of how cells process complex signals. For example, it is known that increased ECM mechanics and transforming growth factor beta (TGF‐β) receptor (TGF‐β‐R) spacing/clustering independently drive TGF‐β signalling and associated myofibroblastic differentiation. However, it remains unknown how these inputs orthogonally contribute to cellular outcomes. Here, we describe the development of a novel material platform that combines microgel thin films with controllable viscoelastic properties and DNA origami to probe how viscoelastic properties and nanoscale spacing of TGF‐β‐Rs contribute to TGF‐β signalling and myofibroblastic differentiation. We found that highly viscous materials with non‐fixed TGF‐β‐R spacing promoted increased TGF‐β signalling and myofibroblastic differentiation. This is likely due to the ability of cells to better cluster receptors on these surfaces. These results provide insight into the contribution of substrate properties and receptor localisation on downstream signalling. Future studies allow for exploration into other receptor‐mediated processes.}, 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{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={AbstractAnticoagulants are commonly utilized during surgeries and to treat thrombotic diseases like stroke and deep vein thrombosis. However, conventional anticoagulants have serious side‐effects, narrow therapeutic windows, and lack safe reversal agents (antidotes). Here, an alternative RNA origami displaying RNA aptamers as target‐specific anticoagulant is described. Improved design and construction techniques for self‐folding, single‐molecule RNA origami as a platform for displaying pre‐selected RNA aptamers with precise orientational and spatial control are reported. Nuclease resistance is added using 2′‐fluoro‐modified pyrimidines during in vitro transcription. When four aptamers are displayed on the RNA origami platform, the measured thrombin inhibition and anticoagulation activity is higher than observed for free aptamers, ssRNA‐linked RNA aptamers, and RNA origami displaying fewer aptamers. Importantly, thrombin inhibition is immediately switched off by addition of specific reversal agents. Results for single‐stranded DNA (ssDNA) and single‐stranded peptide nucleic acid (PNA) antidotes show restoration of 63% and 95% coagulation activity, respectively. To demonstrate potential for practical, long‐term storage for clinical use, RNA origami is freeze‐dried, and stored at room temperature. Freshly produced and freeze‐dried RNA show identical levels of activity in coagulation assays. Compared to current commercial intravenous anticoagulants, RNA origami‐based molecules show promise as safer alternatives with rapid activity switching for future therapeutic applications.}, 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={AbstractNucleic acid aptamers selected for thrombin binding have been previously shown to possess anticoagulant activity; however, problems with rapid renal clearance and short circulation half‐life have prevented translation to clinical usefulness. Here, a family of self‐folding, functional RNA origami molecules bearing multiple thrombin‐binding RNA aptamers and showing significantly improved anticoagulant activity is described. These constructs may overcome earlier problems preventing clinical use of nucleic acid anticoagulants. RNA origami structures are designed in silico and produced by in vitro transcription from DNA templates. Incorporation of 2'‐fluoro‐modified C‐ and U‐nucleotides is shown to increase nuclease resistance and stability during long‐term storage. Specific binding to human thrombin as well as high stability in the presence of RNase A and in human plasma, comparatively more stable than DNA is demonstrated. The RNA origami constructs show anticoagulant activity sevenfold greater than free aptamer and higher than previous DNA weave tiles decorated with DNA aptamers. Anticoagulation activity is maintained after at least 3 months of storage in buffer at 4 °C. Additionally, inhibition of thrombin is shown to be reversed by addition of single‐stranded DNA antidotes. This project paves the way for development of RNA origami for potential therapeutic applications especially as a safer surgical anticoagulant.}, 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{gudnason_madsen_krissanaprasit_gothelf_birkedal_2018, title={Controlled aggregation of DNA functionalized poly(phenylene-vinylene)}, volume={54}, ISSN={["1364-548X"]}, DOI={10.1039/c8cc00943k}, abstractNote={We show that aggregation of DNA-functionalized poly(phenylene-vinylene) can be controlled in solution through ion and DNA interactions.}, number={44}, journal={CHEMICAL COMMUNICATIONS}, author={Gudnason, Daniel and Madsen, Mikael and Krissanaprasit, Abhichart and Gothelf, Kurt V. and Birkedal, Victoria}, year={2018}, month={Jun}, pages={5534–5537} }
 @article{ouyang_de stefano_krissanaprasit_kodal_rosen_liu_helmig_fan_gothelf_2017, title={Docking of Antibodies into the Cavities of DNA Origami Structures}, volume={56}, ISSN={["1521-3773"]}, DOI={10.1002/anie.201706765}, abstractNote={AbstractImmobilized antibodies are extensively employed for medical diagnostics, such as in enzyme‐linked immunosorbent assays. Despite their widespread use, the ability to control the orientation of immobilized antibodies on surfaces is very limited. Herein, we report a method for the covalent and orientation‐selective immobilization of antibodies in designed cavities in 2D and 3D DNA origami structures. Two tris(NTA)‐modified strands are inserted into the cavity to form NTA–metal complexes with histidine clusters on the Fc domain. Subsequent covalent linkage to the antibody was achieved by coupling to lysine residues. Atomic force microscopy (AFM) and transmission electron microscopy (TEM) confirmed the efficient immobilization of the antibodies in the origami structures. This increased control over the orientation of antibodies in nanostructures and on surfaces has the potential to direct the interactions between antibodies and targets and to provide more regular surface assemblies of antibodies.}, number={46}, journal={ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, author={Ouyang, Xiangyuan and De Stefano, Mattia and Krissanaprasit, Abhichart and Kodal, Anne Louise Bank and Rosen, Christian Bech and Liu, Tianqiang and Helmig, Sarah and Fan, Chunhai and Gothelf, Kurt V.}, year={2017}, month={Nov}, pages={14423–14427} }
 @article{madsen_christensen_krissanaprasit_bakke_riber_nielsen_zelikin_gothelf_2017, title={Preparation, Single-Molecule Manipulation, and Energy Transfer Investigation of a Polyfluorene-graft-DNA polymer}, volume={23}, ISSN={["1521-3765"]}, DOI={10.1002/chem.201702780}, abstractNote={AbstractConjugated polymers have been intensively studied due to their unique optical and electronic properties combined with their physical flexibility and scalable bottom up synthesis. Although the bulk qualities of conjugated polymers have been extensively utilized in research and industry, the ability to handle and manipulate conjugated polymers at the nanoscale lacks significantly behind. Here, the toolbox for controlled manipulation of conjugated polymers was expanded through the synthesis of a polyfluorene‐DNA graft‐type polymer (poly(F‐DNA)). The polymer possesses the characteristics associated with the conjugated polyfluorene backbone, but the protruding single‐stranded DNA provides the material with an exceptional addressability. This study demonstrates controlled single‐molecule patterning of poly(F‐DNA), as well as energy transfer between two different polymer–DNA conjugates. Finally, highly efficient DNA‐directed quenching of polyfluorene fluorescence was shown.}, number={44}, journal={CHEMISTRY-A EUROPEAN JOURNAL}, author={Madsen, Mikael and Christensen, Rasmus S. and Krissanaprasit, Abhichart and Bakke, Mette R. and Riber, Camilla F. and Nielsen, Karina S. and Zelikin, Alexander N. and Gothelf, Kurt V.}, year={2017}, month={Aug}, pages={10511–10515} }