High-throughput approach for detection of DNA bending and flexibility based on cyclization

Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3161-6. doi: 10.1073/pnas.0530189100. Epub 2003 Mar 10.

Abstract

We have developed a high-throughput approach to the labor-intensive problems of DNA cyclization, which we use to characterize DNA curvature and mechanical properties. The method includes a combinatorial approach to make the DNA constructs needed and automated real-time measurement of the kinetics using fluorescence. We validated the approach and investigated the flexibility of two kinds of nicked DNA and AT dinucleotide repeats. We found that, although the nicks hardly alter the bending flexibility, they significantly increase the torsional flexibility, and that the AT repeat has 28% (+/-12%) lower bending rigidity than a generic DNA sequence.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.
  • Validation Study

MeSH terms

  • Base Sequence
  • DNA / chemical synthesis
  • DNA / chemistry*
  • DNA Ligases
  • Dinucleotide Repeats
  • Drug Design
  • Fluorescent Dyes
  • Molecular Structure
  • Nucleic Acid Conformation
  • Rhodamines
  • Spectrometry, Fluorescence

Substances

  • 5-carboxytetramethylrhodamine succinimidyl ester
  • Fluorescent Dyes
  • Rhodamines
  • DNA
  • DNA Ligases