1932
0
  1. Home
  2. A-Z Publications
  3. Annual Review of Biochemistry
  4. Volume 67, 1998
  5. Article

Annual Review of Biochemistry

Volume 67, 1998

BASE FLIPPING

Abstract

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.

Keyword(s): DNA methyltransferases, DNA repair enzymes, DNA-modifying enzymes, evolution
Loading

Article metrics loading...

/content/journals/10.1146/annurev.biochem.67.1.181
1998-07-01
2024-04-27
Loading full text...

Full text loading...

/deliver/fulltext/biochem/67/1/annurev.biochem.67.1.181.html?itemId=/content/journals/10.1146/annurev.biochem.67.1.181&mimeType=html&fmt=ahah

Literature Cited

  1. Pabo CO, Sauer RT. 1992. Annu. Rev. Biochem. 61:1053–95
  2. Kim YC, Geiger JH, Hahn S, Sigler PB. 1993. Nature 365:512–20
  3. Kim JL, Nikolov DB, Burley SK. 1993. Nature 365:520–27
  4. Travers A. 1997. Curr. Biol. 7:252–54
  5. Kim YC, Grable JC, Love R, Greene PJ, Rosenberg JM. 1990. Science 249:1307–9
  6. Winkler FK, Banner DW, Oefner C, Tsernoglou D, Brown RS. et al. 1993. EMBO J. 12:1781–95
  7. Cheng XD, Kumar S, Posfai J, Pflugrath JW, Roberts RJ. 1993. Cell 74:299–307
  8. Cheng X, Kumar S, Klimasauskas S, Roberts RJ. 1993. Cold Spring Harbor Symp. Quant. Biol. 58:331–38
  9. Klimasauskas S, Kumar S, Roberts RJ, Cheng XD. 1994. Cell 76:357–69
  10. Kumar S, Cheng XD, Klimasauskas S, Mi S, Posfai J. et al. 1994. Nucleic Acids Res. 22:1–10
  11. Reinisch KM, Chen L, Verdine GL, Lipscomb WN. 1995. Cell 82:143–53
  12. Vassylyev DG, Kashiwagi T, Mikami Y, Ariyoshi M, Iwai S. et al. 1995. Structure 4:1381–85
  13. Roberts RJ. 1995. Cell 82:9–12
  14. Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA. 1996. Nature 384:87–92
  15. Roberts RJ, Myers PA, Morrison A, Murray K. 1976. J. Mol. Biol. 103:199–208
  16. Mann MB, Smith HO. 1979. In Proc. Conf. Transmethylation, ed. E Usdin, RT Borchardt, CR Creveling 483–92 New York: Elsevier
  17. O'Gara M, Klimasauskas S, Roberts RJ, Cheng XD. 1996. J. Mol. Biol. 261:634–45
  18. O'Gara M, Roberts RJ, Cheng XD. 1996. J. Mol. Biol. 263:597–606
  19. Kumar S, Horton JR, Jones GD, Walker RT, Roberts RJ, Cheng XD. 1997. Nucleic Acids Res. 25:2773–83
  20. Cheng XD. 1995. Curr. Opin. Struct. Biol. 5:4–10
  21. Cheng XD. 1995. Annu. Rev. Biophys. Biomol. Struct. 24:293–318
  22. Klimasauskas S, Roberts RJ. 1995. Nucleic Acids Res. 23:1388–95
  23. Beisler JA. 1978. J. Med. Chem. 21:204–8
  24. Creusot F, Acs G, Christman JK. 1982. J. Biol. Chem. 257:2041–48
  25. Wu JC, Santi DV. 1987. J. Biol. Chem. 262:4778–86
  26. Yang AS, Shen J-C, Zingg J-M, Mi S, Jones PA. 1995. Nucleic Acids Res. 23:1380–87
  27. Cheng XD, Blumenthal RM. 1996. Structure 4:639–45
  28. Lange C, Wild C, Trautner TA. 1996. EMBO J. 15:1443–50
  29. Mol CD, Arvai AS, Sanderson RJ, Slupphaug G, Kavli B. et al. 1995. Cell 82:701–8
  30. Mol CD, Arvai AS, Slupphaug G, Kavli B, Alseth I. et al. 1995. Cell 80:869–78
  31. Savva R, McAuley-Hecht K, Brown T, Pearl L. 1995. Nature 373:487–93
  32. Savva R, Pearl LH. 1995. Nat. Struct. Biol. 373:752–57
  33. Dodson ML, Michaels ML, Lloyd RS. 1994. J. Biol. Chem. 266:17631–39
  34. McCullough AK, Scharer O, Verdine GL, Lloyd RS. 1996. 27132147–52
  35. Vassylyev DG, Morikawa K. 1996. Structure 4:1381–85
  36. Vassylyev DG, Morikawa K. 1997. Curr. Opin. Struct. Biol. 7:103–9
  37. Verdine GL, Bruner SD. 1997. Chem. Biol. 4:329–34
  38. Cunningham RP. 1997. Mutat. Res. 383:189–96
  39. Labahn J, Granzin J, Schluckebier G, Robinson DP, Jack WE. et al. 1994. Proc. Natl. Acad. Sci. USA 91:10957–61
  40. Gong W, O'Gara M, Blumenthal RM, Cheng XD. 1997. Nucleic Acids Res. 25:2702–15
  41. Park H-W, Kim S-T, Sancar A, Deisenhofer J. 1995. Science 268:1866–72
  42. Thayer MM, Ahern H, Xing DX, Cunningham RP, Tainer JA. 1995. EMBO J. 14:4108–20
  43. Yamagata Y, Kato M, Odawara K, Tokuno Y, Nakashima Y. et al. 1996. Cell 86:311–19
  44. Labahn J, Scharer OD, Long A, Ezaz-Nikpay K, Verdine GL, Ellenberger TE. 1996. Cell 86:321–29
  45. Mol CD, Kuo C-F, Thayer MM, Cunningham RP, Tainer JA. 1995. Nature 374:381–86
  46. Vrielink A, Ruger W, Driessen HPC, Freemont PS. 1994. EMBO J. 13:3413–22
  47. Moore MH, Gulbis JM, Dodson EJ, Demple B, Moody PCE. 1994. EMBO J. 13:1495–501
  48. Schluckebier G, Labahn J, Granzin J, Schildkraut I, Saenger W. 1995. Gene 157:131–34
  49. Schluckebier G, O'Gara M, Saenger W, Cheng XD. 1995. J. Mol. Biol. 247:16–20
  50. Malone T, Blumenthal RM, Cheng XD. 1995. J. Mol. Biol. 253:618–32
  51. Allan BW, Reich NO. 1996. Biochemistry 35:14757–62
  52. Cal S, Connolly BA. 1997. J. Biol. Chem. 272:490–96
  53. Sancar A. 1994. Biochemistry 33:2–9
  54. Kuo CF, McRee DE, Fisher CL, O'Hadley SF, Cunningham RP, Tainer JA. 1992. Science 258:434–40
  55. Nikolov DB, Hu SH, Lin J, Gasch A, Hoffmann A. et al. 1992. Nature 360:40–46
  56. Oefner C, Suck D. 1986. J. Mol. Biol. 192:605–32
  57. Gallinari P, Jiricny J. 1996. Nature 383:735–38
  58. Subramanya HS, Doherty AJ, Ashford SR, Wigley DB. 1996. Cell 85:607–15
  59. Guest CR, Hochstrasser RA, Sowers LC, Millar DP. 1991. Biochemistry 30:3271–79
  60. Smith SS. 1994. Prog. Nucleic Acid Res. Mol. Biol. 49:65–111
  61. Lipscomb LA, Zhou FX, Presnell SR, Woo RJ, Peek ME. et al. 1996. Biochemistry 35:2818–23
  62. Hough RF, Bass BL. 1997. RNA 3:356–70
/content/journals/10.1146/annurev.biochem.67.1.181
Loading
BASE FLIPPING
Annual Review of Biochemistry 67, 181 (1998); https://doi.org/10.1146/annurev.biochem.67.1.181
/content/journals/10.1146/annurev.biochem.67.1.181
/content/journals/10.1146/annurev.biochem.67.1.181
Loading

Data & Media loading...

  • Article Type: Introduction

Most Cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error