Accurate transcription of genetic information is crucial, involving precise recognition of the
binding motifs by DNA-binding proteins. While some proteins rely on short-range …

Base stacking is crucial in nucleic acid stabilization, from DNA duplex hybridization to single-
stranded DNA (ssDNA) protein binding. While stacking energies are tiny in ssDNA, they are …

Accurate transcription of genetic information is crucial, involving precise recognition of the
binding motifs by DNA-binding proteins. While some proteins rely on short-range …

Coarse-grained models have emerged as valuable tools to simulate long DNA molecules
while maintaining computational efficiency. These models aim at preserving interactions …

We employed all-atom molecular dynamics simulations to explore the mechanical response
of bending, twisting, and overwinding for double-stranded DNA (dsDNA). We analyzed the …

Allosteric effects, where interactions at one part of a complex affect interactions at another
part, offer a high degree of control in multi-species processes. These interactions play a …

Coarse-grained models have played an important role in the study of the behavior of DNA at
length scales beyond a few hundred base pairs. Traditionally, these models have relied on …