RNA structure and dynamics: a base pairing perspective

S Halder, D Bhattacharyya - Progress in Biophysics and Molecular Biology, 2013 - Elsevier
RNA is now known to possess various structural, regulatory and enzymatic functions for
survival of cellular organisms. Functional RNA structures are generally created by three …

Structure and dynamics properties of liquid ethylene glycol from molecular dynamics simulations

N Zhang, MR Li, FS Zhang - Chemical Physics Letters, 2019 - Elsevier
Molecular dynamics simulations are performed for mixtures of ethylene glycol (EG) and
water with EG mass fraction of C i= 0%, 20%, 40%, 60%, 80%, 100%. The extensively …

Influence of divalent magnesium ion on DNA: molecular dynamics simulation studies

S Mukherjee, D Bhattacharyya - Journal of Biomolecular Structure …, 2013 - Taylor & Francis
A large amount of experimental evidence is available on the effect of magnesium ions on the
structure and stability of DNA double helix. Less is known, however, on how these ions affect …

Analysis of stacking overlap in nucleic acid structures: algorithm and application

PK Pingali, S Halder, D Mukherjee, S Basu… - Journal of computer …, 2014 - Springer
RNA contains different secondary structural motifs like pseudo-helices, hairpin loops,
internal loops, etc. in addition to anti-parallel double helices and random coils. The …

Effect of temperature on DNA double helix: An insight from molecular dynamics simulation

S Kundu, S Mukherjee, D Bhattacharyya - Journal of biosciences, 2012 - Springer
The three-dimensional structure of DNA contains various sequence-dependent structural
information, which control many cellular processes in life, such as replication, transcription …

Structural stability of tandemly occurring noncanonical basepairs within double helical fragments: molecular dynamics studies of functional RNA

S Halder, D Bhattacharyya - The Journal of Physical Chemistry B, 2010 - ACS Publications
Noncanonical basepairs have gained importance over the past few years because of their
various functions in RNA biochemistry. These basepairs appear quite frequently in different …

Sequence specificity in DNA–drug intercalation: MD simulation and density functional theory approaches

L Maganti, D Bhattacharyya - Journal of computer-aided molecular design, 2020 - Springer
DNA is an essential target for the treatment of various pathologies, especially cancer. Hence
targeting DNA double helix for alteration of its function has been attempted by several ways …

Stacking interactions in RNA and DNA: Roll‐slide energy hyperspace for ten unique dinucleotide steps

S Mukherjee, S Kailasam, M Bansal… - …, 2015 - Wiley Online Library
Understanding dinucleotide sequence directed structures of nuleic acids and their variability
from experimental observation remained ineffective due to unavailability of statistically …

An analysis of the capturing and passing ability of a DNA origami nanocarrier with the aid of molecular dynamics simulation

M Mogheiseh, RH Ghasemi - Molecular Biotechnology, 2023 - Springer
The present article aims to investigate the ability of a DNA origami nanocarrier to
successfully capture a cargo using molecular dynamics (MD) simulation. In addition, the …

Structural variations of single and tandem mismatches in RNA duplexes: a joint MD simulation and crystal structure database analysis

S Halder, D Bhattacharyya - The Journal of Physical Chemistry B, 2012 - ACS Publications
Internal loops within RNA duplex regions are formed by single or tandem basepairing
mismatches with flanking canonical Watson–Crick basepairs on both sides. They are the …