3DNA is a versatile, integrated software system for the analysis, rebuilding, and visualization of three-dimensional nucleic acid structures. This grant aims to: (i) Maintain refine and fully document 3DNA. 3DNA will be continually adapted and refined to meet the ever-changing needs of its ever-growing user community;3DNA-related questions will be answered quickly and concretely through the public online 3DNA forum;existing 3DNA program components will be documented and ilustrated with step-by-step worked-out examples;the three 3DNA-based services (BPS, w3DNA and 3DNALandscapes) will be maintained and improved;classification of RNA base pairs will be provided;hardware portability will be improved so that 3DNA can be compiled and run on all common operating systems. (ii) Improve and extend 3DNA's interoperability with other software packages. A bridge will be built between 3DNA and Curves+, so that users can easily switch between or take advantage of both types of nucleic acid structural analyses. 3DNA will also be integrated with the Nucleic Acid Building (NAB) project so that models of """"""""unusual"""""""" DNA and RNA structures can be conveniently generated. The object model in PyMOL will be explored to allow for more flexibility in combining 3DNA- specific features. (iii) Extend 3DNA to the analysis of DNA-protein complexes. A local amino-acid reference frame in the side chain will be defined, and the standard base reference frame will be used. The existing 3DNA algorithms will be applied to the analysis of DNA-protein interactions in a consistent, rigorous, and geometrically meaningful way. With the consolidation of existing ad hoc approximate solutions, a new standard for the analysis of DNA-protein complexes will hopefully be established. If these objectives are all met, 3DNA's continued and improved usefulness to the scientific community will be ensured. The software will become even more widely used, thereby enabling new scientific discoveries that will help the biomedical research community decipher how diseases occur and find therapeutics to cure them.
Understanding the three-dimensional structures of nucleic acids (DNA/RNA), and their complexes with proteins and small ligands, is crucial for deciphering their diverse biological functions, and allows for the rational design of therapeutics. 3DNA serves as a standard method for nucleic-acid structural analysis, and is used as a component of various bioinformatics resources, including the Protein Data Bank and the Nucleic Acid Database.
|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; Lu, Xiang-Jun; Olson, Wilma K (2013) Analyzing and building nucleic acid structures with 3DNA. J Vis Exp :e4401|
|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|
|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|