3dDNA: A Computational Method of Building DNA 3D Structures

Considerable progress has been made in the prediction methods of 3D structures of RNAs. In contrast, no such methods are available for DNAs. The determination of 3D structures of the latter is also increasingly needed for understanding their functions and designing new DNA molecules. Since the number of experimental structures of DNA is limited at present, here, we propose a computational and template-based method, 3dDNA, which combines DNA and RNA template libraries to predict DNA 3D structures. It was benchmarked on three test sets with different numbers of chains, and the results show that 3dDNA can predict DNA 3D structures with a mean RMSD of about 2.36 angstrom for those with one or two chains and fewer than 4 angstrom with three or more chains.

Automated summary

Considerable progress has been made in predicting 3D structures of RNAs, but no such methods are available for DNAs. This study introduces a computational and template-based method, 3dDNA, which combines DNA and RNA template libraries to predict DNA 3D structures. Benchmark tests show that 3dDNA can accurately predict DNA structures with a mean RMSD of 2.36 angstroms or less.