The abasic site as a challenge to DNA polymerase

Cuniasse, Ph; Fazakerley, G. Victor; Guschlbauer, Wilhelm; Kaplan, Bruce; Sowers, Lawrence C.

doi:10.1016/s0022-2836(05)80192-5

Cited by 168 publications

(151 citation statements)

References 22 publications

Supporting

Mentioning

137

Contrasting

Order By: Relevance

“…This is in accordance with the A rule, where an A residue is incorporated opposite an abasic lesion with a 10-fold higher efficiency than a G residue (18). A physical basis for the A rule has been provided by NMR studies showing that A residues opposite abasic sites stack better in the intrahelical configuration than do other bases and cause no helical distortion (22)(23)(24). The G residue opposite the 3Ј T of the Dewar product distorts more severely the overall helical configuration and shows poorer stacking interactions than does an A residue.…”

Section: Discussionsupporting

confidence: 72%

See 1 more Smart Citation

The Dewar photoproduct of thymidylyl(3′→5′)- thymidine (Dewar product) exhibits mutagenic behavior in accordance with the “A rule”

Lee

Bae

Choi

2000

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

In contrast to the highly mutagenic pyrimidine(6 -4)pyrimidone photoproduct, its Dewar valence isomer (Dewar product) has low mutagenic potential and produces a broad range of mutations [LeClerc, J. E., Borden, A. & Lawrence, C. W. (1991) Proc. Natl. Acad. Sci. USA 88, 9685-9689]. To determine the origin of the mutagenic property of the Dewar product, we used experimental NMR restraints and molecular dynamics to determine the solution structure of a Dewar-lesion DNA decamer duplex. This DNA decamer duplex (DW͞GA duplex) contains a mismatched base pair between the 3 T residue of the Dewar lesion (T6) and an opposed G residue (G15). The 3 T (T6) of the Dewar lesion formed stable hydrogen bonds with the opposing G15 residue. However, the helical bending and unwinding angles of the DW͞GA duplex were much larger than those of a second duplex that contains the Dewar lesion and opposing A15 and A16 residues (DW͞AA duplex). The DW͞GA duplex showed poorer stacking interactions at the two bases of the Dewar product and at the adjacent A7⅐T14 base pair than did the DW͞AA duplex. These structural features imply that no thermal stability or conformational benefit is obtained by incorporating a G instead of an A opposite the 3 T of the Dewar lesion. These properties may thus facilitate the preferential incorporation of an A in accordance with the A rule during translesion replication and lead to the low frequency of 3 T3 C mutations observed at this site.I rradiation of DNA with UV light produces a variety of photoproducts that block DNA replication (1-6). When an SOS response is induced by UV irradiation, these photoproducts are bypassed with modest efficiency by DNA polymerase and give rise to mutations (5, 6). This process has been termed translesion replication (TR) or bypass synthesis, and mutations are caused by the tendency of DNA polymerase to insert an incorrect nucleotide opposite the lesion during TR (7,8).Although both the pyrimidine (6-4)pyrimidone photoproduct [(6-4) adduct], which is one of the major classes of UV-induced DNA photoproducts (9, 10), and its Dewar valence isomer (Dewar product) (Fig. 1A) cause mutations during TR, their mutagenic properties differ. The (6-4) adduct is highly mutagenic and yields a specific mutation (6,11,12). In SOS-induced Escherichia coli cells, the marked preference for the insertion of a guanine residue opposite the 3Ј T of (6-4) adducts during TR leads to a predominant 3Ј T3C transition with 85% replicating error frequency (6). In contrast, the Dewar product is less mutagenic and induces a broader range of mutations than does the (6-4) adduct (6, 12). In SOS-induced E. coli cells, adenine was found to be incorporated into the site opposite the 3Ј T of the Dewar product with a frequency of 72%, whereas G was incorporated only 21% of the time (6). Thus, the 3Ј T3C transition, which is the major class of mutations induced by the Dewar product, is produced with 13% replicating error frequency during TR (6).Enzyme repair rates of 49-residue oligonucleotides that contain site-spec...

show abstract

Section: Discussionsupporting

confidence: 72%

“…This preferential incorporation of an A residue opposite an abasic lesion is referred to as the ''A rule'' (19)(20)(21). NMR studies suggest that the A residue opposite an abasic site stacks better in an intrahelical configuration than do other bases and thus causes no helical distortion (22)(23)(24).…”

mentioning

confidence: 99%

The Dewar photoproduct of thymidylyl(3′→5′)- thymidine (Dewar product) exhibits mutagenic behavior in accordance with the “A rule”

Lee

Bae

Choi

2000

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…Structural and thermodynamic analysis of abasic sites in duplex DNA indicates that they disturb local stacking interactions with the adjacent base pairs, but not the global DNA conformation (42,43). Structures of a Y-family DNA polymerase, Sulfolobus solfataricus DNA polymerase IV, complexed with DNA containing abasic sites indicate that the conformation of the abasic site was dependent on the surrounding DNA sequence (44).…”

Section: Discussionmentioning

confidence: 99%

Influence of DNA Structure on DNA Polymerase β Active Site Function

Beard

Shock

Wilson

2004

Journal of Biological Chemistry

104

View full text Add to dashboard Cite

In the ternary substrate complex of DNA polymerase (pol) ␤, the nascent base pair (templating and incoming nucleotides) is sandwiched between the duplex DNA terminus and polymerase. To probe molecular interactions in the dNTP-binding pocket, we analyzed the kinetic behavior of wild-type pol ␤ on modified DNA substrates that alter the structure of the DNA terminus and represent mutagenic intermediates. The DNA substrates were modified to 1) alter the sequence of the duplex terminus (matched and mismatched), 2) introduce abasic sites near the nascent base pair, and 3) insert extra bases in the primer or template strands to mimic frameshift intermediates. The results indicate that the nucleotide insertion efficiency (k cat /K m , dGTP-dC) is highly dependent on the sequence identity of the matched (i.e. WatsonCrick base pair) DNA terminus (template/primer, G/C ϳ A/T > T/A ϳ C/G). Mismatches at the primer terminus strongly diminish correct nucleotide insertion efficiency but do not affect DNA binding affinity. Transition intermediates are generally extended more easily than transversions. Most mismatched primer termini decrease the rate of insertion and binding affinity of the incoming nucleotide. In contrast, the loss of catalytic efficiency with homopurine mismatches at the duplex DNA terminus is entirely due to the inability to insert the incoming nucleotide, since K d(dGTP) is not affected. Abasic sites and extra nucleotides in and around the duplex terminus decrease catalytic efficiency and are more detrimental to the nascent base pair binding pocket when situated in the primer strand than the equivalent position in the template strand.DNA polymerases select (bind and incorporate) a nucleoside triphosphate (dNTP) from a pool of structurally similar molecules to preserve Watson-Crick base pairing rules. DNA polymerase (pol) 1 ␤ is a model polymerase to study mechanisms utilized to assure efficient and faithful DNA synthesis. Its small size, lack of essential accessory proteins, and absence of a proofreading exonuclease have facilitated its biochemical, kinetic, and structural characterization. More importantly, it shares many general structural and mechanistic features exhibited by other DNA polymerases (1).DNA polymerase ␤ contributes two important enzymatic activities during single-nucleotide base excision DNA repair. A deoxyribose phosphate lyase activity is associated with the amino-terminal 8-kDa lyase domain. This activity excises a deoxyribose phosphate intermediate during repair of abasic sites and generates a 5Ј-phosphate in a single-nucleotide gap.The nucleotidyl transferase activity of pol ␤ is associated with the 31-kDa polymerase domain that fills the single-nucleotide gap. In addition, the polymerase activity of pol ␤ is necessary for several alternate repair pathways that require longer gapfilling DNA synthesis (e.g. long patch base excision repair) (2, 3). A general feature observed in the structures of all DNA polymerases that include a template overhang (i.e. singlestranded DNA) is that the tra...

show abstract

“…However, in contrast to the specific insertion of a C opposite this lesion by Rev1, Pol primarily incorporates an A, and to a lesser extent, a G opposite this lesion site (13). The specificity of Rev1 for C insertion opposite an abasic site is enigmatic, because when a pyrimidine is positioned opposite the abasic site, both the pyrimidine and the abasic sugar are extrahelical and the helix collapses (24). By contrast, when an A is positioned opposite the AP site, the DNA retains the B-form, and both the unpaired A and the abasic residues remain intrahelical (24 -26).…”

Section: -Oxomentioning

confidence: 99%

Yeast Rev1 Protein Is a G Template-specific DNA Polymerase

Haracska

Prakash

2002

Journal of Biological Chemistry

151

141

View full text Add to dashboard Cite

Rev1 protein of Saccharomyces cerevisiae functions with DNA polymerase in mutagenic trans-lesion synthesis. Because of the reported preferential incorporation of a C residue opposite an abasic site, Rev1 has been referred to as a deoxycytidyltransferase. Here, we use steady-state kinetics to examine nucleotide incorporation by Rev1 opposite undamaged and damaged template residues. We show that Rev1 specifically inserts a C residue opposite template G, and it is ϳ25-, 40-, and 400-fold less efficient at inserting a C residue opposite an abasic site, an O 6 -methylguanine, and an 8-oxoguanine lesion, respectively. Rev1 misincorporates G, A, and T residues opposite template G with a frequency of ϳ10 ؊3 to 10 ؊4 . Consistent with this finding, Rev1 replicates DNA containing a string of Gs in a template-specific manner, but it has a low processivity incorporating 1.6 nucleotides per DNA binding event on the average. From these observations, we infer that Rev1 is a G template-specific DNA polymerase.

show abstract

The abasic site as a challenge to DNA polymerase

Cited by 168 publications

References 22 publications

The Dewar photoproduct of thymidylyl(3′→5′)- thymidine (Dewar product) exhibits mutagenic behavior in accordance with the “A rule”

The Dewar photoproduct of thymidylyl(3′→5′)- thymidine (Dewar product) exhibits mutagenic behavior in accordance with the “A rule”

Influence of DNA Structure on DNA Polymerase β Active Site Function

Yeast Rev1 Protein Is a G Template-specific DNA Polymerase

Contact Info

Product

Resources

About