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Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization.

ABSTRACT: The classical view of DNA posits that DNA must be stiff below the persistence length [<150 base pairs (bp)], but recent studies addressing this have yielded contradictory results. We developed a fluorescence-based, protein-free assay for studying the cyclization of single DNA molecules in real time. The assay samples the equilibrium population of a sharply bent, transient species that is entirely suppressed in single-molecule mechanical measurements and is biologically more relevant than the annealed species sampled in the traditional ligase-based assay. The looping rate has a weak length dependence between 67 and 106 bp that cannot be described by the worm-like chain model. Many biologically important protein-DNA interactions that involve looping and bending of DNA below 100 bp likely use this intrinsic bendability of DNA.

SUBMITTER: Vafabakhsh R

PROVIDER: S-EPMC3565842 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature

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Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization.

Vafabakhsh Reza R Ha Taekjip T

Science (New York, N.Y.) 20120801 6098

The classical view of DNA posits that DNA must be stiff below the persistence length [<150 base pairs (bp)], but recent studies addressing this have yielded contradictory results. We developed a fluorescence-based, protein-free assay for studying the cyclization of single DNA molecules in real time. The assay samples the equilibrium population of a sharply bent, transient species that is entirely suppressed in single-molecule mechanical measurements and is biologically more relevant than the ann ...[more]

PMID: 22936778

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