Base Flipping

Abstract

Base flipping involves 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 for DNA methyltransferases, for several key DNA repair enzymes, and for a few non‐enzymatic 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 or even undamaged and unmodified bases for specific functions. Although, detailed mechanistic information is emerging, it remains to be proven for each individual system whether base flipping is an active process in which the protein rotates the base out of the helix, or a passive one in which the protein binds to a transiently flipped base.

Key Concepts:

  • Base flipping is a key mechanism used by DNA and RNA modifying enzymes including DNA repair enzymes.

  • DNA and RNA methyltransferases use AdoMet as the methyl donor to methylate flipped nucleotides (cytosine or adenine).

  • The family of Fe(II)‐ and α‐ketoglutarate‐dependent dioxygenases includes members of the Tet family and AlkB‐like DNA/RNA repair enzymes.

  • To date, six structural superfamilies of DNA repair glycosylases and newly identified (non‐repair) sequence‐specific DNA glycosylases all use base‐flipping mechanism to access the target base.

  • Eukaryotic SRA domains share structural similarity to that of bacterial modification‐specific endonucleases (MspJI and AbaSI) in recognition of modified bases.

  • Base flipping provides a simple mechanism by which a DNA helix can be opened during the initiation of polymerisation by DNA or RNA polymerases and their associated factors.

Keywords: DNA methyltransferases; DNA repair enzymes; DNA modifying enzymes; hemi‐methyl‐CpG binding proteins; DNA lesion recognising proteins; DNA modification‐specific endonucleases; sequence‐specific DNA glycosylases; RNA modifying enzymes

Figure 1.

M.HhaI complexed to its substrate DNA (Protein Data Bank code 1mht).

Figure 2.

AAG complexed to DNA containing a pyrrolidine abasic nucleotide (Protein Data Bank code 1bnk).

Figure 3.

T4 endonuclease V complexed to DNA containing a thymine cyclobutane dimer (Protein Data Bank code 1vas).

Figure 4.

Pyrococcus abyssi PabI glycosylase complexes with its specific DNA (GTAC) and flips the guanine (yellow) and adenine (cyan).

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Further Reading

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Cheng, Xiaodong, and Roberts, Richard J(Aug 2014) Base Flipping. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0002714.pub3]