@article{nash_manning_gulyuk_kuznetsov_yingling_2022, title={Gold nanoparticle design for RNA compaction}, volume={17}, ISSN={["1559-4106"]}, url={https://doi.org/10.1116/6.0002043}, DOI={10.1116/6.0002043}, abstractNote={RNA-based therapeutics hold a great promise in treating a variety of diseases. However, double-stranded RNAs (dsRNAs) are inherently unstable, highly charged, and stiff macromolecules that require a delivery vehicle. Cationic ligand functionalized gold nanoparticles (AuNPs) are able to compact nucleic acids and assist in RNA delivery. Here, we use large-scale all-atom molecular dynamics simulations to show that correlations between ligand length, metal core size, and ligand excess free volume control the ability of nanoparticles to bend dsRNA far below its persistence length. The analysis of ammonium binding sites showed that longer ligands that bind deep within the major groove did not cause bending. By limiting ligand length and, thus, excess free volume, we have designed nanoparticles with controlled internal binding to RNA's major groove. NPs that are able to induce RNA bending cause a periodic variation in RNA's major groove width. Density functional theory studies on smaller models support large-scale simulations. Our results are expected to have significant implications in packaging of nucleic acids for their applications in nanotechnology and gene delivery.}, number={6}, journal={BIOINTERPHASES}, author={Nash, Jessica A. and Manning, Matthew D. and Gulyuk, Alexey V. and Kuznetsov, Aleksey E. and Yingling, Yaroslava G.}, year={2022}, month={Nov} }
 @misc{nash_kwansa_peerless_kim_yingling_2017, title={Advances in Molecular Modeling of Nanoparticle Nucleic Acid Interfaces}, volume={28}, ISSN={["1043-1802"]}, url={https://publons.com/wos-op/publon/28057442/}, DOI={10.1021/acs.bioconjchem.6b00534}, abstractNote={Nanoparticles (NPs) play increasingly important roles in nanotechnology and nanomedicine in which nanoparticle surface chemistry allows for control over interactions with other nanoparticles and biomolecules. In particular, for applications in drug and gene delivery, a fundamental understanding of the NP-nucleic acid interface allows for development of more efficient and effective nanoparticle carriers. Computational modeling can provide insights of processes occurring at the inorganic NP-nucleic interface in detail that is difficult to access by experimental methods. With recent advances such as the use of graphics processing units (GPUs) for simulations, computational modeling has the potential to give unprecedented insight into inorganic-biological interfaces via the examination of increasingly large and complex systems. In this Topical Review, we briefly review computational methods relevant to the interactions of inorganic NPs and nucleic acids and highlight recent insights obtained from various computational methods that were applied to studies of inorganic nanoparticle-nanoparticle and nanoparticle-nucleic acid interfaces.}, number={1}, journal={BIOCONJUGATE CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Nash, Jessica A. and Kwansa, Albert L. and Peerless, James S. and Kim, Ho Shin and Yingling, Yaroslava G.}, year={2017}, month={Jan}, pages={3–10} }
 @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{nash_tucker_therriault_yingling_2016, title={Binding of single stranded nucleic acids to cationic ligand functionalized gold nanoparticles}, volume={11}, ISSN={["1559-4106"]}, url={https://publons.com/publon/28057454/}, DOI={10.1116/1.4966653}, abstractNote={The interactions of nanoparticles (NPs) with single stranded nucleic acids (NAs) have important implications in gene delivery, and nanotechnological and biomedical applications. Here, the complexation of cationic ligand functionalized gold nanoparticles with single stranded deoxyribose nucleic acid (DNA) and ribonucleic acid (RNA) are examined using all atom molecular dynamics simulations. The results indicated that complexation depends mostly on charge of nanoparticle, and, to lesser extent, sequence and type of nucleic acid. For cationic nanoparticles, electrostatic interactions between charged ligands and the nucleic acid backbone dominate binding regardless of nanoparticle charge. Highly charged nanoparticles bind more tightly and cause compaction of the single-stranded NAs through disruption of intrastrand π–π stacking and hydrogen bonding. However, poly-purine strands (polyA-DNA, polyA-RNA) show less change in structure than poly-pyrimidine strands (polyT-DNA, polyU-RNA). Overall, the results show that control over ssNA structure may be achieved with cationic NPs with a charge of more than 30, but the extent of the structural changes depends on sequence.}, number={4}, journal={BIOINTERPHASES}, author={Nash, Jessica A. and Tucker, Tasha L. and Therriault, William and Yingling, Yaroslava G.}, year={2016}, month={Dec} }
 @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{nash_singh_li_yingling_2015, title={Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics}, volume={9}, ISSN={["1936-086X"]}, url={https://publons.com/publon/5454552/}, DOI={10.1021/acsnano.5b05684}, abstractNote={The development of nucleic acid (NA) based nanotechnology applications rely on the efficient packaging of DNA and RNA. However, the atomic details of NA-nanoparticle binding remains to be comprehensively characterized. Here, we examined how nanoparticle and solvent properties affect NA compaction. Our large-scale, all-atom simulations of ligand-functionalized gold nanoparticle (NP) binding to double stranded NAs as a function of NP charge and solution salt concentration reveal different responses of RNA and DNA to cationic NPs. We demonstrate that the ability of a nanoparticle to bend DNA is directly correlated with the NPs charge and ligand corona shape, where more than 50% charge neutralization and spherical shape of the NP ligand corona ensured the DNA compaction. However, NP with 100% charge neutralization is needed to bend DNA almost as efficiently as the histone octamer. For RNA in 0.1 M NaCl, even the most highly charged nanoparticles are not capable of causing bending due to charged ligand end groups binding internally to the major groove of RNA. We show that RNA compaction can only be achieved through a combination of highly charged nanoparticles with low salt concentration. Upon interactions with highly charged NPs, DNA bends through periodic variation in groove widths and depths, whereas RNA bends through expansion of the major groove.}, number={12}, journal={ACS NANO}, publisher={American Chemical Society (ACS)}, author={Nash, Jessica A. and Singh, Abhishek and Li, Nan K. and Yingling, Yaroslava G.}, year={2015}, month={Dec}, pages={12374–12382} }
 @article{li_kim_nash_lim_yingling_2014, title={Progress in molecular modelling of DNA materials}, volume={40}, ISSN={["1029-0435"]}, url={https://publons.com/publon/9429685/}, DOI={10.1080/08927022.2014.913792}, abstractNote={The unique molecular recognition properties of DNA molecule, which store genetic information in cells, are responsible for the rise of DNA nanotechnology. In this article, we review the recent advances in atomistic and coarse-grained force fields along with simulations of DNA-based materials, as applied to DNA–nanoparticle assemblies for controlled material morphology, DNA–surface interactions for biosensor development and DNA origami. Evidently, currently available atomistic and coarse-grained representations of DNA are now at the stage of successfully reproducing and explaining experimentally observed phenomena. However, there is a clear need for the development of atomistic force fields which are robust at long timescales and in the improvement of the coarse-grained models.}, number={10-11}, journal={MOLECULAR SIMULATION}, publisher={Informa UK Limited}, author={Li, Nan K. and Kim, Ho Shin and Nash, Jessica A. and Lim, Mina and Yingling, Yaroslava G.}, year={2014}, pages={777–783} }