3D-NuS: A Web Server for Automated Modeling and Visualization of non-canonical 3-D imensional Nu cleic Acid S tructures

Ponoop Prasad Patro, L and Kumar, A and Kolimi, N and Rathinavelan, Thenmalarchelvi (2017) 3D-NuS: A Web Server for Automated Modeling and Visualization of non-canonical 3-D imensional Nu cleic Acid S tructures. Journal of Molecular Biology, 429 (16). pp. 2438-2448. ISSN 0022-2836

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Abstract

The inherent conformational flexibility of nucleic acids facilitate the formation of a range of conformations such as duplex, triplex, quadruplex etc. that play crucial roles in biological processes. Elucidation about the influence of non-canonical base pair mismatches on DNA/RNA structures at different sequence contexts to understand mismatch repair and misregulation of alternative splicing mechanisms as well as the sequence dependent effect of RNA-DNA hybrid in relevance to antisense strategy demand their three-dimensional structural information. Further, structural insights about nucleic acid triplexes, which are generally not tractable to structure determination by X-ray crystallography or NMR techniques, are essential to establish their biological function(s). A web server, namely 3D-NuS (http://iith.ac.in/3dnus/), has been developed to generate energy minimized models of 80 different types of triplexes, 64 types of G-quadruplexes, left handed Z-DNA/RNA duplexes, RNA-DNA hybrid duplex along with inter- and intra-molecular DNA or RNA duplexes comprising a variety of mismatches and their chimeric forms for any user defined sequence and length. It also generates an ensemble of conformations corresponding to the modeled structure. These structures may serve as good starting models for docking proteins & small molecules with nucleic acids, NMR structure determination, cryo-electron microscope modeling, DNA/RNA nanotechnology applications and molecular dynamics simulation studies.

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