Bending and flexibility of methylated and unmethylated EcoRI DNA

  • Nathan D
  • Crothers D
  • 44

    Readers

    Mendeley users who have this article in their library.
  • 52

    Citations

    Citations of this article.

Abstract

We used cyclization kinetics experiments and Monte Carlo simulations to determine a structural model for a DNA decamer containing the EcoRI restriction site. Our findings agree well with recent crystal and NMR structures of the EcoRI dodecamer, where an overall bend of seven degrees is distributed symmetrically over the molecule. Monte Carlo simulations indicate that the sequence has a higher flexibility, assumed to be isotropic, compared to that of a "generic" DNA sequence. This model was used as a starting point for the investigation of the effect of cytosine methylation on DNA bending and flexibility. While methylation did not affect bend magnitude or direction, it resulted in a reduction in bending flexibility and under-winding of the methylated nucleotides. We demonstrate that our approach can augment the understanding of DNA structure and dynamics by adding information about the global structure and flexibility of the sequence. We also show that cyclization kinetics can be used to study the properties of modified nucleotides. © 2002 Elsevier Science Ltd.

Author-supplied keywords

  • Cyclization kinetics
  • DNA bending and flexibility
  • DNA methylation
  • EcoRI restriction site
  • Monte Carlo simulations

Get free article suggestions today

Mendeley saves you time finding and organizing research

Sign up here
Already have an account ?Sign in

Find this document

Authors

  • Dafna Nathan

  • Donald M. Crothers

Cite this document

Choose a citation style from the tabs below

Save time finding and organizing research with Mendeley

Sign up for free