Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif.

ABSTRACT: Selective gene regulation is mediated by recognition of specific DNA sequences by transcription factors (TFs). The extremely challenging task of searching out specific cognate DNA binding sites among several million putative sites within the eukaryotic genome is achieved by complex molecular recognition mechanisms. Elements of this recognition code include the core binding sequence, the flanking sequence context, and the shape and conformational flexibility of the composite binding site. To unravel the extent to which DNA flexibility modulates TF binding, in this study, we employed experimentally guided molecular dynamics simulations of ternary complex of closely related Hox heterodimers Exd-Ubx and Exd-Scr with DNA. Results demonstrate that flexibility signatures embedded in the flanking

SUBMITTER: Ghoshdastidar D 

PROVIDER: S-EPMC9674967 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature