NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures

Abstract

Software packages NUPARM and NUCGEN, are described, which can be used to understand sequence directed structural variations in nucleic acids, by analysis and generation of non-uniform structures. A set of local inter basepair parameters (viz. tilt, roll, twist, shift, slide and rise) have been defined, which use geometry and coordinates of two successive basepairs only and can be used to generate polymeric structures with varying geometries for each of the 16 possible dinucleotide steps. Intra basepair parameters, propeller, buckle, opening and the C6...C8 distance can also be varied, if required, while the sugar phosphate backbone atoms are fixed in some standard conformation in each of the nucleotides. NUPARM can be used to analyse both DNA and RNA structures, with single as well as double stranded helices. The NUCGEN software generates double helical models with the backbone fixed in B-form DNA, but with appropriate modifications in the input data, it can also generate A-form DNA and RNA duplex structures.

Structure of the Complex of [Ru(tpm)(dppz)py]2+ with a B‐DNA Oligonucleotide—A Single‐Substituent Binding Switch for a Metallo‐Intercalator

“…[48] Structure files for [RuA C H T U N G T R E N N U N G (tpm)-A C H T U N G T R E N N U N G (dppz)(py)]Cl 2 were created using xplo2d, [49] starting from the crystal structure of the 3-amino pyridine. Energy minimization and restrained molecular dynamics were carried out using XPLOR.…”

MD simulations of ligand-bound and ligand-free aptamer: Molecular level insights into the binding and switching mechanism of the add A-riboswitch

“…We also calculated the RMSF of the C19 atoms, in the trajectories of both the states, with reference to their respective initial positions at the beginning of the production run. The backbone torsion angles (d, x, z) of all the nucleotides were calculated using NUPARM (Bansal et al 1995). Base pairs were identified and analyzed using BPFIND (Das et al 2006) and 3DNA (Lu and Olson 2003).…”

Protein Interfacial Pocket Engineering via Coupled Computational Filtering and Biological Focusing Criterion

“…Then, in one approach, GATATC DNA substrate coordinates were extracted from R.EcoRV-D, and in the other B-form DNA substrate coordinates was generated de novo using NUCGEN. 5 Each GATATC substrate was then inserted into R.PvuII-D and affine space aligned along the CAGCTG DNA substrate using the shared second A and fifth T bases as spatial and directional coordinates of reference. Upon aligning, CAGCTG DNA substrate was deleted resulting in the R.PvuII Putative Engineered IP mutant-D, i.e., the mutant complexed with GATATC DNA substrate.…”