text: DNA nucleotides are held together with hydrogen bonds, which are relatively weak and can be easily broken.  Base flipping occurs on a millisecond timescale by breaking the hydrogen bonds between bases and unstacking the base from its neighbors.  The base is rotated out of the double helix by 180 degrees., typically via the major groove, and into the active site of an enzyme.  This opening leads to small conformational changes in the DNA backbone which are quickly stabilized by the increased enzyme-DNA interactions.    Studies looking at the free-energy profiles of base flipping have shown that the free-energy barrier to flipping can be lowered by 17 kcal/mol for M.HhaI in the closed conformation.
  There are two mechanisms of DNA base flipping: active and passive.   In the active mechanism, an enzyme binds to the DNA and then actively rotates the base, while in the passive mechanism a damaged base rotates out spontaneously first, then is recognized and bound by the enzyme.  Research has demonstrated both mechanisms: uracil-DNA glycosylase follows the passive mechanism and Tn10 transposase follows the active mechanism.
  Furthermore, studies have shown that DNA base flipping is used by many different enzymes in a variety biological processes such as DNA methylation, various DNA repair mechanisms, RNA transcription and DNA replication.