Base flipping

Annu Rev Biochem. 1998;67:181-98. doi: 10.1146/annurev.biochem.67.1.181.


Base flipping is the phenomenon whereby a base in normal B-DNA is swung completely out of the helix into an extrahelical position. It was discovered in 1994 when the first co-crystal structure was reported for a cytosine-5 DNA methyltransferase binding to DNA. Since then it has been shown to occur in many systems where enzymes need access to a DNA base to perform chemistry on it. Many DNA glycosylases that remove abnormal bases from DNA use this mechanism. This review describes systems known to use base flipping as well as many systems where it is likely to occur but has not yet been rigorously demonstrated. The mechanism and evolution of base flipping are also discussed.

Publication types

  • Research Support, U.S. Gov't, P.H.S.
  • Review

MeSH terms

  • Base Pair Mismatch
  • DNA / metabolism*
  • DNA Glycosylases*
  • DNA Ligases / metabolism
  • DNA Modification Methylases / metabolism
  • DNA Repair
  • DNA-Directed DNA Polymerase / metabolism
  • Evolution, Molecular
  • N-Glycosyl Hydrolases / metabolism
  • Nucleic Acid Conformation*
  • Uracil-DNA Glycosidase


  • DNA
  • DNA Modification Methylases
  • DNA-Directed DNA Polymerase
  • DNA Glycosylases
  • N-Glycosyl Hydrolases
  • Uracil-DNA Glycosidase
  • DNA Ligases