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

Science. 2012 Aug 31;337(6098):1097-101. doi: 10.1126/science.1224139.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Avidin / chemistry
  • Base Sequence
  • Biotin / chemistry
  • Cyclization
  • DNA, Circular / chemistry*
  • Fluorescence
  • Fluorescence Resonance Energy Transfer / methods*
  • Nucleic Acid Conformation*
  • Polyethylene Glycols / chemistry


  • DNA, Circular
  • neutravidin
  • Avidin
  • Polyethylene Glycols
  • Biotin