Insight into the three-dimensional architectures of nucleic acids is essential for understanding their diverse roles in biology and nanotechnology. 3DNA is a suite of programs for the analysis, rebuilding, and visualization of three-dimensional nucleic acid structures. The software has been widely used for biomedical research, and the design of pharmaceuticals and nanomaterials, thanks to its robust performance, easy integrability, and reliable support. The recent funding of this project has led to the creation of DSSR, an integrated software tool for dissecting the spatial structure of RNA, and SNAP, a program to characterize the structures of nucleic acid-protein complexes. These two developments have vastly extended the functionality of 3DNA for RNA structural analysis and for investigations of DNA-protein and RNA-protein assemblies. This renewal proposal aims to consolidate, refine, and expand 3DNA to the next level. Specially, we aim to: (i) Maintain 3DNA version 2, create and document version 3. We will continuously maintain v2.x: fixing any identified bugs, answering user questions, but adding no new features. 3DNA v3, including DSSR and SNAP, will employ a completely new codebase built upon our extensive experience in supporting 3DNA, growing knowledge of RNA and DNA structures, and refined skills of scientific programming. (ii) Build an integrated web-interface to 3DNA version 3. The ANSI C-based command-line programs in version 3 enable the creation of a consistent and sustainable interface to all of them. All nucleic acid structures in the Protein Data Bank (PDB) will be annotated with pertinent programs in version 3, and the results are made readily available. (iii) Characterize RNA junction loops with pseudoknots, and more. We will systematically characterize all pseudoknot-associated junction loops in the PDB to see how they link to tertiary folding and biological functions. We will also explore other possible applications enabled by 3DNA version 3, such as identifying DNA/RNA-protein recognition patterns (SNAP). As exemplified by its ~1050 citations in over 190 peer-reviewed journals and the 20 uniformly strong supporting letters from expert users and developers with diverse backgrounds, 3DNA is of significant value to scientific research on the structures of nucleic acids. Our track record in maintaining and refining 3DNA over 15 years leaves no doubt as to our dedication and capability to carry out the proposed project. The tremendous progress that we have made during the current funding period illustrates unambiguously what a dedicated mind with unique expertise can contribute to the community.
Insight into the three-dimensional architectures of nucleic acids is essential for understanding their diverse roles in biology and nanotechnology. 3DNA is a sophisticated software system for the analysis, rebuilding, and visualization of three-dimensional DNA and RNA structures. The software has been widely used for biomedical research in academic institutions and for the design of pharmaceuticals and nanomaterials in the industrial sector.
| Xu, Fei; Zheng, Hongning; Clauvelin, Nicolas et al. (2017) Parallels between DNA and collagen - comparing elastic models of the double and triple helix. Sci Rep 7:12802 |
| Hanson, Robert M; Lu, Xiang-Jun (2017) DSSR-enhanced visualization of nucleic acid structures in Jmol. Nucleic Acids Res 45:W528-W533 |
| Waters, James T; Kim, Harold D; Gumbart, James C et al. (2016) DNA Scrunching in the Packaging of Viral Genomes. J Phys Chem B 120:6200-7 |
| Waters, James T; Lu, Xiang-Jun; Galindo-Murillo, Rodrigo et al. (2016) Transitions of Double-Stranded DNA Between the A- and B-Forms. J Phys Chem B 120:8449-56 |
| Lu, Xiang-Jun; Bussemaker, Harmen J; Olson, Wilma K (2015) DSSR: an integrated software tool for dissecting the spatial structure of RNA. Nucleic Acids Res 43:e142 |
| Colasanti, Andrew V; Grosner, Michael A; Perez, Pamela J et al. (2013) Weak operator binding enhances simulated Lac repressor-mediated DNA looping. Biopolymers 99:1070-81 |
| Colasanti, Andrew V; Lu, Xiang-Jun; Olson, Wilma K (2013) Analyzing and building nucleic acid structures with 3DNA. J Vis Exp :e4401 |
| Mladek, Arnost; Sponer, Judit E; Kulhanek, Petr et al. (2012) Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. J Chem Theory Comput 8:335-347 |
