Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design.

ABSTRACT: DNA nick can be used as a design motif in programming the shape and reconfigurable deformation of synthetic DNA nanostructures, but its mechanical properties have rarely been systematically characterized at the level of base sequences. Here, we investigated sequence-dependent mechanical properties of DNA nicks through molecular dynamics simulation for a comprehensive set of distinct DNA oligomers constructed using all possible base-pair steps with and without a nick. We found that torsional rigidity was reduced by 28-82% at the nick depending on its sequence and location although bending and stretching rigidities remained similar to those of regular base-pair steps. No significant effect of a nick on mechanically coupled deformation such as the twist-stretch coupling was observed. These re

SUBMITTER: Lee JY 

PROVIDER: S-EPMC6326809 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature