93
3 Formation of DNA Lesions, its Prevention and Repair
196. Stivers JT (2004) Site-specific DNA damage recognition by enzyme-induced base flipping.
Prog Nucleic Acid Res Mol Biol 77:37–65
197. Jena NR, Bansal M (2011) Mutagenicity associated with O6-methylguanine-DNA damage
and mechanism of nucleotide flipping by AGT during repair. Phys Biol 8:046007
198. Friedman JI, Stivers JT (2010) Detection of damaged DNA bases by DNA glycosylase
enzymes. Biochemistry 49:4957–4967
199. Lyons DM, O’Brien PJ (2009) Efficient recognition of an unpaired lesion by a DNA repair
glycosylase. J Am Chem Soc 131:17742–17745
200. Yang CG, Garcia K, He C (2009) Damage detection and base flipping in direct DNA alkylation repair. Chembiochem 10:417–423
201. Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) Crystal
structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB. Nature
439:879–884
202. David SS, O’Shea VL, Kundu S (2007) Base-excision repair of oxidative DNA damage.
Nature 447:941–950
203. Kunkel TA, Wilson SH (1996) DNA repair. Push and pull of base flipping. Nature 384:25–
26
204. Scharer OD, Campbell AJ (2009) Wedging out DNA damage. Nat Struct Mol Biol 16:102–
104
205. Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL (2009) Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme. Nature 462:762–
766
206. Wolfe AE, O’Brien PJ (2009) Kinetic mechanism for the flipping and excision of 1,N(6)ethenoadenine by human alkyladenine DNA glycosylase. Biochemistry 48:11357–11369
207. Rubinson EH, Eichman BF (2012) Nucleic acid recognition by tandem helical repeats. Curr
Opin Struct Biol 22:101–109
208. Scharer OD, Jiricny J (2001) Recent progress in the biology, chemistry and structural biology of DNA glycosylases. Bioessays 23:270–281
209. Stivers JT, Jiang YL (2003) A mechanistic perspective on the chemistry of DNA repair
glycosylases. Chem Rev 103:2729–2759
210. Huffman JL, Sundheim O, Tainer JA (2005) DNA base damage recognition and removal:
new twists and grooves. Mutat Res 577:55–76
211. Fromme JC, Banerjee A, Verdine GL (2004) DNA glycosylase recognition and catalysis.
Curr Opin Struct Biol 14:43–49
212. Friedman JI, Stivers JT (2010) Detection of damaged DNA bases by DNA glycosylase
enzymes. Biochemistry 49:4957–4967
213. Dalhus B, Laerdahl JK, Backe PH, Bjørås M (2009) DNA base repair–recognition and
initiation of catalysis. FEMS Microbiol Rev 33:1044–1078
214. Li GM (2010) Novel molecular insights into the mechanism of GO removal by MutM. Cell
Res 20:116–118
215. Hollis T, Lau A, Ellenberger T (2000) Structural studies of human alkyladenine glycosylase
and E. Coli 3-methyladenine glycosylase. Mut Res 460:201–210
216. Slupphaug G, Mol CD, Kavil B, Arvai AS, Krokan HE, Tainer JA (1996) A nucleotideflipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.
Nature 384:87–92
217. Daniels DS, Woo TT, Luu KX, Noll DM, Clarke ND, Pegg AE, Tainer JA (2004) DNA
binding and nucleotide flipping by the human DNA repair protein AGT. Nat Struct Mol
Biol 11:714–720
218. Huang N, Banavali NK, MacKerell AD Jr (2003) Protein-facilitated base flipping in DNA
by cytosine-5-methyltransferase. Proc Natl Acad Sci U S A 100:68–73
219. Shieh FK, Youngblood B, Reich NO (2006) The role of Arg165 towards base flipping, base
stabilization and catalysis in M.HhaI. J Mol Biol 362:516–527
3 Formation of DNA Lesions, its Prevention and Repair
196. Stivers JT (2004) Site-specific DNA damage recognition by enzyme-induced base flipping.
Prog Nucleic Acid Res Mol Biol 77:37–65
197. Jena NR, Bansal M (2011) Mutagenicity associated with O6-methylguanine-DNA damage
and mechanism of nucleotide flipping by AGT during repair. Phys Biol 8:046007
198. Friedman JI, Stivers JT (2010) Detection of damaged DNA bases by DNA glycosylase
enzymes. Biochemistry 49:4957–4967
199. Lyons DM, O’Brien PJ (2009) Efficient recognition of an unpaired lesion by a DNA repair
glycosylase. J Am Chem Soc 131:17742–17745
200. Yang CG, Garcia K, He C (2009) Damage detection and base flipping in direct DNA alkylation repair. Chembiochem 10:417–423
201. Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) Crystal
structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB. Nature
439:879–884
202. David SS, O’Shea VL, Kundu S (2007) Base-excision repair of oxidative DNA damage.
Nature 447:941–950
203. Kunkel TA, Wilson SH (1996) DNA repair. Push and pull of base flipping. Nature 384:25–
26
204. Scharer OD, Campbell AJ (2009) Wedging out DNA damage. Nat Struct Mol Biol 16:102–
104
205. Qi Y, Spong MC, Nam K, Banerjee A, Jiralerspong S, Karplus M, Verdine GL (2009) Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme. Nature 462:762–
766
206. Wolfe AE, O’Brien PJ (2009) Kinetic mechanism for the flipping and excision of 1,N(6)ethenoadenine by human alkyladenine DNA glycosylase. Biochemistry 48:11357–11369
207. Rubinson EH, Eichman BF (2012) Nucleic acid recognition by tandem helical repeats. Curr
Opin Struct Biol 22:101–109
208. Scharer OD, Jiricny J (2001) Recent progress in the biology, chemistry and structural biology of DNA glycosylases. Bioessays 23:270–281
209. Stivers JT, Jiang YL (2003) A mechanistic perspective on the chemistry of DNA repair
glycosylases. Chem Rev 103:2729–2759
210. Huffman JL, Sundheim O, Tainer JA (2005) DNA base damage recognition and removal:
new twists and grooves. Mutat Res 577:55–76
211. Fromme JC, Banerjee A, Verdine GL (2004) DNA glycosylase recognition and catalysis.
Curr Opin Struct Biol 14:43–49
212. Friedman JI, Stivers JT (2010) Detection of damaged DNA bases by DNA glycosylase
enzymes. Biochemistry 49:4957–4967
213. Dalhus B, Laerdahl JK, Backe PH, Bjørås M (2009) DNA base repair–recognition and
initiation of catalysis. FEMS Microbiol Rev 33:1044–1078
214. Li GM (2010) Novel molecular insights into the mechanism of GO removal by MutM. Cell
Res 20:116–118
215. Hollis T, Lau A, Ellenberger T (2000) Structural studies of human alkyladenine glycosylase
and E. Coli 3-methyladenine glycosylase. Mut Res 460:201–210
216. Slupphaug G, Mol CD, Kavil B, Arvai AS, Krokan HE, Tainer JA (1996) A nucleotideflipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.
Nature 384:87–92
217. Daniels DS, Woo TT, Luu KX, Noll DM, Clarke ND, Pegg AE, Tainer JA (2004) DNA
binding and nucleotide flipping by the human DNA repair protein AGT. Nat Struct Mol
Biol 11:714–720
218. Huang N, Banavali NK, MacKerell AD Jr (2003) Protein-facilitated base flipping in DNA
by cytosine-5-methyltransferase. Proc Natl Acad Sci U S A 100:68–73
219. Shieh FK, Youngblood B, Reich NO (2006) The role of Arg165 towards base flipping, base
stabilization and catalysis in M.HhaI. J Mol Biol 362:516–527