The predominant protein-centric perspective in protein–DNA-binding studies assumes that
the protein drives the interaction. Research focuses on protein structural motifs, electrostatic …

DNA molecules do the twist: The DNA double helix is a remarkably adaptable molecule that
can undergo major conformational rearrangements without being irreversibly damaged …

DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in
understanding the role of DNA structure in gene regulation, DNA damage recognition and …

We study the elasticity of DNA based on local principal axes of bending identified from over
0.9-μs all-atom molecular dynamics simulations of DNA oligos. The calculated order …

Thursday, February 25, 2021 221a sequences to superhelical apices. Base pair disruption
allows sharp bending at superhelical apices, which facilitates DNA writhing and, thus …

Experimental data on protein-DNA interactions highlight a surprising peculiarity of protein
binding to the minor groove: in contrast to major groove binding, which proceeds with heat …

We report a study of DNA deformations using a coarse-grained mechanical model and
quantitatively interpret the allosteric effects in protein–DNA binding affinity. A recent single …

DNA supercoiling results in compacted DNA structures that can bring distal sites into close
proximity. It also changes the local structure of the DNA, which can in turn influence the way …

We study the effective interaction between DNA-binding proteins that arises from elastic
stresses in the DNA when tension is applied. Using the wormlike chain model, we calculate …

Background Protein-DNA binding often involves dramatic conformational changes such as
protein folding and DNA bending. While thermodynamic aspects of this behavior are …