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PDBsum entry 178d
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DOI no:
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Biochemistry
33:10266-10270
(1994)
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PubMed id:
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Crystal structure of a DNA duplex containing 8-hydroxydeoxyguanine-adenine base pairs.
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K.E.McAuley-Hecht,
G.A.Leonard,
N.J.Gibson,
J.B.Thomson,
W.P.Watson,
W.N.Hunter,
T.Brown.
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ABSTRACT
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The crystal structure of the oligonucleotide d(CGCAAATTO8GGCG), containing the
chemically modified base 8-hydroxydeoxyguanine (O8G), has been determined at
2.5-A resolution and refined to a crystallographic R-factor of 16.8%. The B-type
DNA helix contains standard Watson-Crick base pairs except at the mismatch
sites, where O8G adopts a syn conformation and forms hydrogen bonds to adenine
in the anti conformation. The thermodynamic stability of the duplex was found by
UV melting techniques to be intermediate between the native oligonucleotide
d(CGCAAATTTGCG) and an oligonucleotide containing A.G mispairs d(CGCAAATTGGCG).
Comparison of the structure of the O8G(syn).A(anti) base pair with those of
Watson-Crick base pairs has given a reason why O8G.A base pairs are not well
repaired by DNA proofreading enzymes.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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G.A.Locatelli,
H.Pospiech,
N.Tanguy Le Gac,
B.van Loon,
U.Hubscher,
S.Parkkinen,
J.E.Syväoja,
and
G.Villani
(2010).
Effect of 8-oxoguanine and abasic site DNA lesions on in vitro elongation by human DNA polymerase in the presence of replication protein A and proliferating-cell nuclear antigen.
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Biochem J,
429,
573-582.
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J.Beckman,
M.Wang,
G.Blaha,
J.Wang,
and
W.H.Konigsberg
(2010).
Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to be inserted opposite 7,8-dihydro-8-oxoguanine .
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Biochemistry,
49,
4116-4125.
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PDB codes:
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V.K.Batra,
W.A.Beard,
E.W.Hou,
L.C.Pedersen,
R.Prasad,
and
S.H.Wilson
(2010).
Mutagenic conformation of 8-oxo-7,8-dihydro-2'-dGTP in the confines of a DNA polymerase active site.
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Nat Struct Mol Biol,
17,
889-890.
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PDB code:
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J.N.Patro,
M.Urban,
and
R.D.Kuchta
(2009).
Role of the 2-amino group of purines during dNTP polymerization by human DNA polymerase alpha.
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Biochemistry,
48,
180-189.
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J.N.Patro,
M.Urban,
and
R.D.Kuchta
(2009).
Interaction of human DNA polymerase alpha and DNA polymerase I from Bacillus stearothermophilus with hypoxanthine and 8-oxoguanine nucleotides.
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Biochemistry,
48,
8271-8278.
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O.Rechkoblit,
L.Malinina,
Y.Cheng,
N.E.Geacintov,
S.Broyde,
and
D.J.Patel
(2009).
Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases.
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Structure,
17,
725-736.
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PDB codes:
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R.L.Eoff,
R.Sanchez-Ponce,
and
F.P.Guengerich
(2009).
Conformational Changes during Nucleotide Selection by Sulfolobus solfataricus DNA Polymerase Dpo4.
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J Biol Chem,
284,
21090-21099.
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S.D.McCulloch,
R.J.Kokoska,
P.Garg,
P.M.Burgers,
and
T.A.Kunkel
(2009).
The efficiency and fidelity of 8-oxo-guanine bypass by DNA polymerases delta and eta.
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Nucleic Acids Res,
37,
2830-2840.
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A.Inase-Hashimoto,
S.Yoshikawa,
Y.Kawasaki,
T.S.Kodama,
and
S.Iwai
(2008).
Characterization of distamycin A binding to damaged DNA.
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Bioorg Med Chem,
16,
164-170.
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B.R.Bowman,
S.Lee,
S.Wang,
and
G.L.Verdine
(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.
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Structure,
16,
1166-1174.
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PDB codes:
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M.Dizdaroglu,
G.Kirkali,
and
P.Jaruga
(2008).
Formamidopyrimidines in DNA: mechanisms of formation, repair, and biological effects.
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Free Radic Biol Med,
45,
1610-1621.
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S.D.McCulloch,
and
T.A.Kunkel
(2008).
The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases.
|
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Cell Res,
18,
148-161.
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V.S.Sidorenko,
G.V.Mechetin,
G.A.Nevinsky,
and
D.O.Zharkov
(2008).
Ionic strength and magnesium affect the specificity of Escherichia coli and human 8-oxoguanine-DNA glycosylases.
|
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FEBS J,
275,
3747-3760.
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E.Rotman,
and
A.Kuzminov
(2007).
The mutT defect does not elevate chromosomal fragmentation in Escherichia coli because of the surprisingly low levels of MutM/MutY-recognized DNA modifications.
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J Bacteriol,
189,
6976-6988.
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M.de Vega,
and
M.Salas
(2007).
A highly conserved Tyrosine residue of family B DNA polymerases contributes to dictate translesion synthesis past 8-oxo-7,8-dihydro-2'-deoxyguanosine.
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Nucleic Acids Res,
35,
5096-5107.
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R.L.Eoff,
A.Irimia,
K.C.Angel,
M.Egli,
and
F.P.Guengerich
(2007).
Hydrogen bonding of 7,8-dihydro-8-oxodeoxyguanosine with a charged residue in the little finger domain determines miscoding events in Sulfolobus solfataricus DNA polymerase Dpo4.
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J Biol Chem,
282,
19831-19843.
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PDB codes:
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H.Zang,
A.Irimia,
J.Y.Choi,
K.C.Angel,
L.V.Loukachevitch,
M.Egli,
and
F.P.Guengerich
(2006).
Efficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA polymerase Dpo4.
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J Biol Chem,
281,
2358-2372.
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PDB codes:
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M.A.Kalam,
K.Haraguchi,
S.Chandani,
E.L.Loechler,
M.Moriya,
M.M.Greenberg,
and
A.K.Basu
(2006).
Genetic effects of oxidative DNA damages: comparative mutagenesis of the imidazole ring-opened formamidopyrimidines (Fapy lesions) and 8-oxo-purines in simian kidney cells.
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Nucleic Acids Res,
34,
2305-2315.
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M.L.Hamm,
and
K.Billig
(2006).
Synthesis, oligonucleotide incorporation and base pair stability of 7-methyl-8-oxo-2'-deoxyguanosine.
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Org Biomol Chem,
4,
4068-4070.
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R.E.Johnson,
L.Haracska,
L.Prakash,
and
S.Prakash
(2006).
Role of hoogsteen edge hydrogen bonding at template purines in nucleotide incorporation by human DNA polymerase iota.
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Mol Cell Biol,
26,
6435-6441.
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Y.Wang,
and
Y.Wang
(2006).
Synthesis and thermodynamic studies of oligodeoxyribonucleotides containing tandem lesions of thymidine glycol and 8-oxo-2'-deoxyguanosine.
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Chem Res Toxicol,
19,
837-843.
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K.D.Carlson,
and
M.T.Washington
(2005).
Mechanism of efficient and accurate nucleotide incorporation opposite 7,8-dihydro-8-oxoguanine by Saccharomyces cerevisiae DNA polymerase eta.
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Mol Cell Biol,
25,
2169-2176.
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N.Oka,
and
M.M.Greenberg
(2005).
The effect of the 2-amino group of 7,8-dihydro-8-oxo-2'-deoxyguanosine on translesion synthesis and duplex stability.
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Nucleic Acids Res,
33,
1637-1643.
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E.Freisinger,
A.P.Grollman,
H.Miller,
and
C.Kisker
(2004).
Lesion (in)tolerance reveals insights into DNA replication fidelity.
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EMBO J,
23,
1494-1505.
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PDB codes:
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F.Coste,
M.Ober,
T.Carell,
S.Boiteux,
C.Zelwer,
and
B.Castaing
(2004).
Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase.
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J Biol Chem,
279,
44074-44083.
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PDB codes:
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J.C.Fromme,
A.Banerjee,
S.J.Huang,
and
G.L.Verdine
(2004).
Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase.
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Nature,
427,
652-656.
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PDB codes:
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L.G.Brieba,
B.F.Eichman,
R.J.Kokoska,
S.Doublié,
T.A.Kunkel,
and
T.Ellenberger
(2004).
Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase.
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EMBO J,
23,
3452-3461.
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PDB codes:
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T.M.Hitchcock,
H.Gao,
and
W.Cao
(2004).
Cleavage of deoxyoxanosine-containing oligodeoxyribonucleotides by bacterial endonuclease V.
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Nucleic Acids Res,
32,
4071-4080.
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I.Kuraoka,
M.Endou,
Y.Yamaguchi,
T.Wada,
H.Handa,
and
K.Tanaka
(2003).
Effects of endogenous DNA base lesions on transcription elongation by mammalian RNA polymerase II. Implications for transcription-coupled DNA repair and transcriptional mutagenesis.
|
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J Biol Chem,
278,
7294-7299.
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J.C.Fromme,
and
G.L.Verdine
(2003).
DNA lesion recognition by the bacterial repair enzyme MutM.
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J Biol Chem,
278,
51543-51548.
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PDB codes:
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J.M.Krahn,
W.A.Beard,
H.Miller,
A.P.Grollman,
and
S.H.Wilson
(2003).
Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential.
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Structure,
11,
121-127.
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PDB codes:
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M.T.Washington,
S.A.Helquist,
E.T.Kool,
L.Prakash,
and
S.Prakash
(2003).
Requirement of Watson-Crick hydrogen bonding for DNA synthesis by yeast DNA polymerase eta.
|
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Mol Cell Biol,
23,
5107-5112.
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A.S.Bernards,
J.K.Miller,
K.K.Bao,
and
I.Wong
(2002).
Flipping duplex DNA inside out: a double base-flipping reaction mechanism by Escherichia coli MutY adenine glycosylase.
|
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J Biol Chem,
277,
20960-20964.
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K.Asagoshi,
H.Terato,
Y.Ohyama,
and
H.Ide
(2002).
Effects of a guanine-derived formamidopyrimidine lesion on DNA replication: translesion DNA synthesis, nucleotide insertion, and extension kinetics.
|
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J Biol Chem,
277,
14589-14597.
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L.T.Burgdorf,
and
T.Carell
(2002).
Synthesis, stability, and conformation of the formamidopyrimidine G DNA lesion.
|
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Chemistry,
8,
293-301.
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S.S.Wallace
(2002).
Biological consequences of free radical-damaged DNA bases.
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Free Radic Biol Med,
33,
1.
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T.E.Messick,
N.H.Chmiel,
M.P.Golinelli,
M.R.Langer,
L.Joshua-Tor,
and
S.S.David
(2002).
Noncysteinyl coordination to the [4Fe-4S]2+ cluster of the DNA repair adenine glycosylase MutY introduced via site-directed mutagenesis. Structural characterization of an unusual histidinyl-coordinated cluster.
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Biochemistry,
41,
3931-3942.
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PDB code:
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M.T.Washington,
L.Prakash,
and
S.Prakash
(2001).
Yeast DNA polymerase eta utilizes an induced-fit mechanism of nucleotide incorporation.
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Cell,
107,
917-927.
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M.T.Washington,
R.E.Johnson,
L.Prakash,
and
S.Prakash
(2001).
Accuracy of lesion bypass by yeast and human DNA polymerase eta.
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Proc Natl Acad Sci U S A,
98,
8355-8360.
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N.H.Chmiel,
M.P.Golinelli,
A.W.Francis,
and
S.S.David
(2001).
Efficient recognition of substrates and substrate analogs by the adenine glycosylase MutY requires the C-terminal domain.
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Nucleic Acids Res,
29,
553-564.
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R.E.Johnson,
L.Haracska,
S.Prakash,
and
L.Prakash
(2001).
Role of DNA polymerase zeta in the bypass of a (6-4) TT photoproduct.
|
| |
Mol Cell Biol,
21,
3558-3563.
|
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D.C.Malins,
N.L.Polissar,
G.K.Ostrander,
and
M.A.Vinson
(2000).
Single 8-oxo-guanine and 8-oxo-adenine lesions induce marked changes in the backbone structure of a 25-base DNA strand.
|
| |
Proc Natl Acad Sci U S A,
97,
12442-12445.
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D.O.Zharkov,
R.Gilboa,
I.Yagil,
J.H.Kycia,
S.E.Gerchman,
G.Shoham,
and
A.P.Grollman
(2000).
Role for lysine 142 in the excision of adenine from A:G mispairs by MutY DNA glycosylase of Escherichia coli.
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Biochemistry,
39,
14768-14778.
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H.Kamiya,
and
H.Kasai
(2000).
2-hydroxyadenine in DNA is a very poor substrate of the Escherichia coli MutY protein.
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J Radiat Res (Tokyo),
41,
349-354.
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H.Miller,
R.Prasad,
S.H.Wilson,
F.Johnson,
and
A.P.Grollman
(2000).
8-oxodGTP incorporation by DNA polymerase beta is modified by active-site residue Asn279.
|
| |
Biochemistry,
39,
1029-1033.
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K.Shinmura,
S.Yamaguchi,
T.Saitoh,
M.Takeuchi-Sasaki,
S.R.Kim,
T.Nohmi,
and
J.Yokota
(2000).
Adenine excisional repair function of MYH protein on the adenine:8-hydroxyguanine base pair in double-stranded DNA.
|
| |
Nucleic Acids Res,
28,
4912-4918.
|
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L.Haracska,
S.Prakash,
and
L.Prakash
(2000).
Replication past O(6)-methylguanine by yeast and human DNA polymerase eta.
|
| |
Mol Cell Biol,
20,
8001-8007.
|
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M.L.Coté,
S.J.Yohannan,
and
M.M.Georgiadis
(2000).
Use of an N-terminal fragment from moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing G-A mispairs.
|
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Acta Crystallogr D Biol Crystallogr,
56,
1120-1131.
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PDB code:
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C.D.Mol,
S.S.Parikh,
C.D.Putnam,
T.P.Lo,
and
J.A.Tainer
(1999).
DNA repair mechanisms for the recognition and removal of damaged DNA bases.
|
| |
Annu Rev Biophys Biomol Struct,
28,
101-128.
|
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C.L.Chepanoske,
S.L.Porello,
T.Fujiwara,
H.Sugiyama,
and
S.S.David
(1999).
Substrate recognition by Escherichia coli MutY using substrate analogs.
|
| |
Nucleic Acids Res,
27,
3197-3204.
|
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|
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L.L.Furge,
and
F.P.Guengerich
(1999).
Explanation of pre-steady-state kinetics and decreased burst amplitude of HIV-1 reverse transcriptase at sites of modified DNA bases with an additional, nonproductive enzyme-DNA-nucleotide complex.
|
| |
Biochemistry,
38,
4818-4825.
|
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P.Pourquier,
L.M.Ueng,
J.Fertala,
D.Wang,
H.J.Park,
J.M.Essigmann,
M.A.Bjornsti,
and
Y.Pommier
(1999).
Induction of reversible complexes between eukaryotic DNA topoisomerase I and DNA-containing oxidative base damages. 7, 8-dihydro-8-oxoguanine and 5-hydroxycytosine.
|
| |
J Biol Chem,
274,
8516-8523.
|
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X.Shui,
L.McFail-Isom,
G.G.Hu,
and
L.D.Williams
(1998).
The B-DNA dodecamer at high resolution reveals a spine of water on sodium.
|
| |
Biochemistry,
37,
8341-8355.
|
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PDB code:
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Y.Guan,
R.C.Manuel,
A.S.Arvai,
S.S.Parikh,
C.D.Mol,
J.H.Miller,
S.Lloyd,
and
J.A.Tainer
(1998).
MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily.
|
| |
Nat Struct Biol,
5,
1058-1064.
|
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PDB codes:
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G.P.Mullen,
and
S.H.Wilson
(1997).
DNA polymerase beta in abasic site repair: a structurally conserved helix-hairpin-helix motif in lesion detection by base excision repair enzymes.
|
| |
Biochemistry,
36,
4713-4717.
|
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|
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L.L.Furge,
and
F.P.Guengerich
(1997).
Analysis of nucleotide insertion and extension at 8-oxo-7,8-dihydroguanine by replicative T7 polymerase exo- and human immunodeficiency virus-1 reverse transcriptase using steady-state and pre-steady-state kinetics.
|
| |
Biochemistry,
36,
6475-6487.
|
|
|
|
|
|
|
R.C.Manuel,
and
R.S.Lloyd
(1997).
Cloning, overexpression, and biochemical characterization of the catalytic domain of MutY.
|
| |
Biochemistry,
36,
11140-11152.
|
|
|
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|
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R.G.Fowler,
and
R.M.Schaaper
(1997).
The role of the mutT gene of Escherichia coli in maintaining replication fidelity.
|
| |
FEMS Microbiol Rev,
21,
43-54.
|
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|
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I.A.Bespalov,
A.A.Purmal,
M.P.Glackin,
S.S.Wallace,
and
R.J.Melamede
(1996).
Recombinant Phabs reactive with 7,8-dihydro-8-oxoguanine, a major oxidative DNA lesion.
|
| |
Biochemistry,
35,
2067-2078.
|
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|
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L.G.Lowe,
and
F.P.Guengerich
(1996).
Steady-state and pre-steady-state kinetic analysis of dNTP insertion opposite 8-oxo-7,8-dihydroguanine by Escherichia coli polymerases I exo- and II exo-.
|
| |
Biochemistry,
35,
9840-9849.
|
|
|
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|
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N.V.Bulychev,
C.V.Varaprasad,
G.Dormán,
J.H.Miller,
M.Eisenberg,
A.P.Grollman,
and
F.Johnson
(1996).
Substrate specificity of Escherichia coli MutY protein.
|
| |
Biochemistry,
35,
13147-13156.
|
|
|
|
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|
|
R.C.Manuel,
E.W.Czerwinski,
and
R.S.Lloyd
(1996).
Identification of the structural and functional domains of MutY, an Escherichia coli DNA mismatch repair enzyme.
|
| |
J Biol Chem,
271,
16218-16226.
|
|
|
|
|
|
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A.P.Breen,
and
J.A.Murphy
(1995).
Reactions of oxyl radicals with DNA.
|
| |
Free Radic Biol Med,
18,
1033-1077.
|
|
|
|
|
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|
D.S.Pilch,
G.E.Plum,
and
K.J.Breslauer
(1995).
The thermodynamics of DNA structures that contain lesions or guanine tetrads.
|
| |
Curr Opin Struct Biol,
5,
334-342.
|
|
|
|
|
|
|
L.A.Lipscomb,
M.E.Peek,
M.L.Morningstar,
S.M.Verghis,
E.M.Miller,
A.Rich,
J.M.Essigmann,
and
L.D.Williams
(1995).
X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine.
|
| |
Proc Natl Acad Sci U S A,
92,
719-723.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.C.Wahl,
and
M.Sundaralingam
(1995).
New crystal structures of nucleic acids and their complexes.
|
| |
Curr Opin Struct Biol,
5,
282-295.
|
|
|
|
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|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
|
Links
