Base Flipping


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).



Arita K, Ariyoshi M, Tochio H, Nakamura Y and Shirakawa M (2008) Recognition of hemi‐methylated DNA by the SRA protein UHRF1 by a base‐flipping mechanism. Nature 455: 818–821.

Avvakumov GV, Walker JR, Xue S et al. (2008) Structural basis for recognition of hemi‐methylated DNA by the SRA domain of human UHRF1. Nature 455: 822–825.

Barrett TE, Savva R, Panayotou G et al. (1998) Crystal structure of a G:T/U mismatch‐specific DNA glycosylase: mismatch recognition by complementary‐strand interactions. Cell 92: 117–129.

Campagne S, Marsh ME, Capitani G, Vorholt JA and Allain FH (2014) Structural basis for −10 promoter element melting by environmentally induced sigma factors. Nature Structural & Molecular Biology 21: 269–276.

Cheng X and Blumenthal RM (1996) Finding a basis for flipping bases. Structure 4: 639–645.

Daniels DS, Woo TT, Luu KX et al. (2004) DNA binding and nucleotide flipping by the human DNA repair protein AGT. Nature Structural & Molecular Biology 11: 714–720.

Dong A, Yoder JA, Zhang X et al. (2001) Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant‐resistant binding to DNA. Nucleic Acids Research 29: 439–448.

Duguid EM, Rice PA and He C (2005) The structure of the human AGT protein bound to DNA and its implications for damage detection. Journal of Molecular Biology 350: 657–666.

Dunkle JA, Vinal K, Desai PM et al. (2014) Molecular recognition and modification of the 30 S ribosome by the aminoglycoside‐resistance methyltransferase NpmA. Proceedings of the National Academy of Sciences of the USA 111: 6275–6280.

Fromme JC, Banerjee A, Huang SJ and Verdine GL (2004) Structural basis for removal of adenine mispaired with 8‐oxoguanine by MutY adenine DNA glycosylase. Nature 427: 652–656.

Goedecke K, Pignot M, Goody RS, Scheidig AJ and Weinhold E (2001) Structure of the N6‐adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog. Nature Structural Biology 8: 121–125.

Goll MG, Kirpekar F, Maggert KA et al. (2006) Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 311: 395–398.

Hashimoto H, Hong S, Bhagwat AS, Zhang X and Cheng X (2012a) Excision of 5‐hydroxymethyluracil and 5‐carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation. Nucleic Acids Research 40: 10203–10214.

Hashimoto H, Horton JR, Zhang X et al. (2008) The SRA domain of UHRF1 flips 5‐methylcytosine out of the DNA helix. Nature 455: 826–829.

Hashimoto H, Pais JE, Zhang X et al. (2014) Structure of a Naegleria Tet‐like dioxygenase in complex with 5‐methylcytosine DNA. Nature 506: 391–395.

Hashimoto H, Zhang X and Cheng X (2012b) Excision of thymine and 5‐hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation. Nucleic Acids Research 40: 8276–8284.

He YF, Li BZ, Li Z et al. (2011) Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333: 1303–1307.

Horton JR, Liebert K, Bekes M, Jeltsch A and Cheng X (2006) Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase. Journal of Molecular Biology 358: 559–570.

Horton JR, Liebert K, Hattman S, Jeltsch A and Cheng X (2005) Transition from nonspecific to specific DNA interactions along the substrate‐recognition pathway of dam methyltransferase. Cell 121: 349–361.

Horton JR, Ratner G, Banavali NK et al. (2004) Caught in the act: visualization of an intermediate in the DNA base‐flipping pathway induced by HhaI methyltransferase. Nucleic Acids Research 32: 3877–3886.

Hosfield DJ, Guan Y, Haas BJ, Cunningham RP and Tainer JA (1999) Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell 98: 397–408.

Hu L, Li Z, Cheng J et al. (2013) Crystal structure of TET2‐DNA complex: insight into TET‐mediated 5mC oxidation. Cell 155: 1545–1555.

Klimasauskas S, Kumar S, Roberts RJ and Cheng X (1994) HhaI methyltransferase flips its target base out of the DNA helix. Cell 76: 357–369.

Klimasauskas S, Szyperski T, Serva S and Wuthrich K (1998) Dynamic modes of the flipped‐out cytosine during HhaI methyltransferase‐DNA interactions in solution. EMBO Journal 17: 317–324.

Kuttan A and Bass BL (2012) Mechanistic insights into editing‐site specificity of ADARs. Proceedings of the National Academy of Sciences of the USA 109: E3295–E3304.

Lariviere L and Morera S (2004) Structural evidence of a passive base‐flipping mechanism for beta‐glucosyltransferase. Journal of Biological Chemistry 279: 34715–34720.

Lariviere L, Sommer N and Morera S (2005) Structural evidence of a passive base‐flipping mechanism for AGT, an unusual GT‐B glycosyltransferase. Journal of Molecular Biology 352: 139–150.

Lau AY, Scharer OD, Samson L, Verdine GL and Ellenberger T (1998) Crystal structure of a human alkylbase‐DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision. Cell 95: 249–258.

Lee TT, Agarwalla S and Stroud RM (2005) A unique RNA Fold in the RumA‐RNA‐cofactor ternary complex contributes to substrate selectivity and enzymatic function. Cell 120: 599–611.

Lukin M and de Los Santos C (2006) NMR structures of damaged DNA. Chemical Reviews 106: 607–686.

Maiti A and Drohat AC (2011) Thymine DNA glycosylase can rapidly excise 5‐formylcytosine and 5‐carboxylcytosine: potential implications for active demethylation of CpG sites. Journal of Biological Chemistry 286: 35334–35338.

Maiti A, Morgan MT, Pozharski E and Drohat AC (2008) Crystal structure of human thymine DNA glycosylase bound to DNA elucidates sequence-specific mismatch recognition. Proceedings of the National Academy of Sciences of the United States of America 105: 8890–8895.

Mees A, Klar T, Gnau P et al. (2004) Crystal structure of a photolyase bound to a CPD‐like DNA lesion after in situ repair. Science 306: 1789–1793.

Min JH and Pavletich NP (2007) Recognition of DNA damage by the Rad4 nucleotide excision repair protein. Nature 449: 570–575.

Miyazono K, Furuta Y, Watanabe‐Matsui M et al. (2014) A sequence‐specific DNA glycosylase mediates restriction‐modification in Pyrococcus abyssi. Nature Communications 5: 3178.

Morera S, Grin I, Vigouroux A et al. (2012) Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5‐hydroxymethyuracil‐containing DNA. Nucleic Acids Research 40: 9917–9926.

O'Gara M, Horton JR, Roberts RJ and Cheng X (1998) Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base. Nature Structural Biology 5: 872–877.

Panayotou G, Brown T, Barlow T, Pearl LH and Savva R (1998) Direct measurement of the substrate preference of uracil‐DNA glycosylase. Journal of Biological Chemistry 273: 45–50.

Parikh SS, Mol CD, Slupphaug G et al. (1998) Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil‐DNA glycosylase with DNA. EMBO Journal 17: 5214–5226.

Parker JB, Bianchet MA, Krosky DJ et al. (2007) Enzymatic capture of an extrahelical thymine in the search for uracil in DNA. Nature 449: 433–437.

Reinisch KM, Chen L, Verdine GL and Lipscomb WN (1995) The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell 82: 143–153.

Roberts RJ (1995) On base flipping. Cell 82: 9–12.

Rubinson EH, Gowda AS, Spratt TE, Gold B and Eichman BF (2010) An unprecedented nucleic acid capture mechanism for excision of DNA damage. Nature 468: 406–411.

Schroeder LA, Gries TJ, Saecker RM et al. (2009) Evidence for a tyrosine‐adenine stacking interaction and for a short‐lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA. Journal of Molecular Biology 385: 339–349.

Scrima A, Konickova R, Czyzewski BK et al. (2008) Structural basis of UV DNA‐damage recognition by the DDB1‐DDB2 complex. Cell 135: 1213–1223.

Slupphaug G, Mol CD, Kavli B et al. (1996) A nucleotide‐flipping mechanism from the structure of human uracil‐DNA glycosylase bound to DNA. Nature 384: 87–92.

Song J, Teplova M, Ishibe‐Murakami S and Patel DJ (2012) Structure‐based mechanistic insights into DNMT1‐mediated maintenance DNA methylation. Science 335: 709–712.

Stivers JT, Pankiewicz KW and Watanabe KA (1999) Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase. Biochemistry 38: 952–963.

Sukackaite R, Grazulis S, Tamulaitis G and Siksnys V (2012) The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine. Nucleic Acids Research 40: 7552–7562.

Tsutakawa SE, Classen S, Chapados BR et al. (2011) Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily. Cell 145: 198–211.

Tubbs JL, Latypov V, Kanugula S et al. (2009) Flipping of alkylated DNA damage bridges base and nucleotide excision repair. Nature 459: 808–813.

Vassylyev DG, Kashiwagi T, Mikami Y et al. (1995) Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition. Cell 83: 773–782.

Werner RM, Jiang YL, Gordley RG et al. (2000) Stressing‐out DNA? The contribution of serine‐phosphodiester interactions in catalysis by uracil DNA glycosylase. Biochemistry 39: 12585–12594.

Yakubovskaya E, Mejia E, Byrnes J, Hambardjieva E and Garcia‐Diaz M (2010) Helix unwinding and base flipping enable human MTERF1 to terminate mitochondrial transcription. Cell 141: 982–993.

Yang CG, Yi C, Duguid EM et al. (2008) Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature 452: 961–965.

Zhang L, Lu X, Lu J et al. (2012) Thymine DNA glycosylase specifically recognizes 5‐carboxylcytosine‐modified DNA. Nature Chemical Biology 8: 328–330.

Further Reading

Bowman BR, Lee S, Wang S and Verdine GL (2008) Structure of the E. coli DNA glycosylase AlkA bound to the ends of duplex DNA: a system for the structure determination of lesion‐containing DNA. Structure 16: 1166–1174.

Cheng X and Blumenthal RM (2008) Mammalian DNA methyltransferases: a structural perspective. Structure 16: 341–350.

Macbeth MR, Schubert HL, Vandemark AP et al. (2005) Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing. Science 309: 1534–1539.

Malone T, Blumenthal RM and Cheng X (1995) Structure‐guided analysis reveals nine sequence motifs conserved among DNA amino‐methyltransferases, and suggests a catalytic mechanism for these enzymes. Journal of Molecular Biology 253: 618–632.

Park HW, Kim ST, Sancar A and Deisenhofer J (1995) Crystal structure of DNA photolyase from Escherichia coli. Science 268: 1866–1872.

Roberts RJ and Cheng X (1998) Base flipping. Annual Review of Biochemistry 67: 181–198.

Schluckebier G, O'Gara M, Saenger W and Cheng X (1995) Universal catalytic domain structure of AdoMet‐dependent methyltransferases. Journal of Molecular Biology 247: 16–20.

Tubbs JL, Pegg AE and Tainer JA (2007) DNA binding, nucleotide flipping, and the helix‐turn‐helix motif in base repair by O6‐alkylguanine‐DNA alkyltransferase and its implications for cancer chemotherapy. DNA Repair 6: 1100–1115.

Yang CG, Garcia K and He C (2009) Damage detection and base flipping in direct DNA alkylation repair. ChemBioChem 10: 417–423.

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How to Cite close
Cheng, Xiaodong, and Roberts, Richard J(Aug 2014) Base Flipping. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0002714.pub3]