Protein-DNA interactions are central for transcription, replication, and various DNA repair
mechanisms. 1-5 Some proteins exert their effects by simple binding to DNA or RNA without …

Recent years have seen considerable progress in simulations of nucleic acids.
Improvements in force fields, simulation techniques and protocols, and increasing computer …

This volume is a timely and comprehensive description of the many facets of DNA and RNA
modification-editing processes and to some extent repair mechanisms. Each chapter offers …

The conformational pathways and the free energy variations for base opening into the major
and minor grooves of a B‐DNA duplex are studied using umbrella sampling molecular …

Structural distortions of DNA are essential for its biological function due to the genetic
information of DNA not being physically accessible in the duplex state. Base flipping is one …

We combine free-energy calculations and molecular dynamics to elucidate a mechanism for
DNA base-pair binding and unbinding in atomic detail. Specifically, transition-path sampling …

The process by which DNA repair enzymes recognize and selectively excise damaged
bases in duplex DNA is fundamental to our mechanistic understanding of these critical …

The opening of basepairs plays a key role in DNA replication and transcription, and in the
action of DNA repair and modification enzymes. In this article, we have used proton …

Carrying out chemistry on the bases of DNA, necessary for biological processes such as
methylation or repair, requires flipping the base into an accessible position. In this work …

This article illustrates by examples the limited acceptance by biologists of predictions made
with molecular dynamics simulations of biomolecules. Its purpose is to increase the …