Molecular insight into how the position of an abasic site and its sequence environment influence DNA duplex stability and dynamics.

ABSTRACT: Local perturbations to DNA base-pairing stability from lesions and chemical modifications can alter the stability and dynamics of an entire oligonucleotide. End effects may cause the position of a disruption within a short duplex to influence duplex stability and structural dynamics, yet this aspect of nucleic acid modifications is often overlooked. We investigate how the position of an abasic site (AP site) impacts the stability and dynamics of short DNA duplexes. Using a combination of steady-state and time-resolved spectroscopy and molecular dynamics simulations, we unravel an interplay between AP-site position and nucleobase sequence that controls energetic and dynamic disruption to the duplex. The duplex is disrupted into two segments by an entropic barrier for base pairing on each si

SUBMITTER: Ashwood B 

PROVIDER: S-EPMC10401965 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature