About 3D-NuS

    3D-NuS (3-Dimensional Nucleic Acid Structures) is a web server for modeling and visualization of 3-dimensional structures of right handed i) intra/intermolecular DNA/RNA duplexes with noncanonical base pairs along with their chimeric forms & ii) RNA-DNA hybrid duplexes, iii) left handed Z-DNA/Z-RNA duplexes, iv) triplexes and vi) intra/intermolecular G-quadruplexes in an automated way. It also generates an ensemble of conformations corresponding to the modeled structure.

    3D-NuS builds DNA and RNA duplexes containing all possible combinations of mismatches along with canonical base pairs in an automated way. 3D-NuS gives the facility for constructing various forms of triplexes and quadruplexes for different type of RNA/DNA strand combinations along with different strand orientations. At present, 3D-NuS can generate energy minimized models of 80 different types of triplexes, 58 types of intra/intermolecular quadruplexes, Z DNA/RNA and DNA/RNA chimera models along with a variety of mismatch containing DNA or RNA duplexes and RNA-DNA hybrid duplex for any user defined sequence and length. These are further detailed in the documentation and the corresponding molecular modeling page.

Application

    The models built by 3D-NuS will be useful to explore dynamics of aforementioned molecules in docking and simulation studies. Docking of these generated structures with proteins and other small molecules will facilitate the understanding of their sequence dependent structural roles in biological phenomenon such as replication, transcription, mismatch repair, recombination, aging, RNA interference, gene editing etc. 3D-NuS modeled structures can also be used to understrand the structural characteristics of nucleic acids under normal & diseased conditions (trinucleotide repeat expansion disorders, cancer etc.), to aid in DNA nanotechnology and to address the oligonucleotide based therapeutics like antigene and antisense strategies.