Standard Article

Base Flipping

  1. Xiaodong Cheng1,
  2. Richard J Roberts2

Published Online: 15 FEB 2010

DOI: 10.1002/9780470015902.a0002714.pub2



How to Cite

Cheng, X. and Roberts, R. J. 2010. Base Flipping. eLS. .

Author Information

  1. 1

    Emory University School of Medicine, Atlanta, Georgia, USA

  2. 2

    New England Biolabs, Ipswich, Massachusetts, USA

Publication History

  1. Published Online: 15 FEB 2010

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Base flipping involves the rotation of backbone bonds in double-stranded deoxyribonucleic acid (DNA) to expose an out-of-stack base, which can then be a substrate for an enzyme-catalysed chemical reaction or for a specific protein-binding interaction. The phenomenon is fully established structurally and experimentally for DNA methyltransferases, for several key DNA repair enzymes, and for a few nonenzymatic DNA-binding proteins involved in the DNA methylation and repair pathways, and is likely to prove general for enzymes or proteins that require access to unpaired, mismatched, damaged or modified bases. Recent results suggest that it may also be involved in the initial opening of a DNA helix during the initiation of transcription.

Key Concept:

  • Base flipping is a key mechanism used by many DNA and RNA modifying enzymes, including DNA repair enzymes, to gain access to one or more bases in a double helix.


  • DNA methyltransferases;
  • DNA repair enzymes;
  • DNA modifying enzymes;
  • methyl-CpG binding proteins;
  • DNA lesion recognizing proteins