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 …

One of the most important achievements in our understanding of the biochemistry of DNA is
our awareness that the double helix has considerable conformational flexibility. The concept …

The improving quality of empirical force field parameters along with other methodological
improvements and ever increasing computational resources have lead to more reliable …

The ribosome decodes the genetic information that resides in nucleic acids. A key
component of the decoding mechanism is a conformational switch in the decoding center of …

Molecular dynamics simulations were performed to investigate GC and AT base opening
events in DNA. Calculated equilibrium constants between the base open (or flipped) and …

DNA can adopt different conformations depending on the base sequence, solvent,
electrolyte composition and concentration, pH, temperature, and interaction with proteins …

Chapter 2 USING AMBER TO SIMULATE DNA AND RNA Page 1 45 Chapter 2 USING
AMBER TO SIMULATE DNA AND RNA Thomas E. Cheatham, III1 and David A. Case2 …

Empirical force field calculations of nucleic acids have become a standard method for
studying the relationship of structure and dynamics to the activity of these biologically …

The question of whether DNA conducts electric charges is intriguing to physicists and
biologists alike. The suggestion that electron transfer/transport in DNA might be biologically …

We describe a coarse-grained model for Z-DNA that mimics the DNA shape with a relatively
small number of repulsive interaction sites. In addition, negative charges are placed at the …