Base-pair mismatch can destabilize small DNA loops through cooperative kinking

Base pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule Fluorescence Resonance Energy Transfer (FRET), we measured the lifetimes of tightly bent DNA loops with and without base pair mismatch. Su...

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Bibliographic Details
Published in:arXiv.org 2019-01
Main Authors: Jeong, Jiyoun, Kim, Harold D
Format: Article
Language:English
Subjects:
Bending stresses
Deoxyribonucleic acid
DNA
Energy measurement
Energy transfer
Fluorescence
Kinking
Stability
Online Access:Get full text
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Summary:Base pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule Fluorescence Resonance Energy Transfer (FRET), we measured the lifetimes of tightly bent DNA loops with and without base pair mismatch. Surprisingly, for loops captured by stackable sticky ends, the mismatch decreased the loop lifetime despite reducing the overall bending stress, and the decrease was largest when the mismatch was placed at the DNA midpoint. These findings show that base pair mismatch transfers bending stress to the opposite side of the loop through an allosteric mechanism known as cooperative kinking. Based on this mechanism, we present a three-state model that explains the apparent dichotomy between thermodynamic and kinetic stability of DNA loops.
ISSN:2331-8422
DOI:10.48550/arxiv.1901.00263