Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/apyrimidinic endonucleases.

Takeshita, Masaru; Chang, Chien-Neng; Johnson, Francis; Will, Stephen; Grollman, A.P.

doi:10.1016/s0021-9258(18)61093-2

Cited by 393 publications

(142 citation statements)

References 28 publications

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“…Overall, the structures of the abasic sites, excluding the unprotonated N moiety, are very similar. It is worth noting that these findings support the biochemical evidence (22) indicating that F serves as an effective analog of a natural AP site.…”

Section: Structures Of Abasic Sites As Determined By Quantum Chemistrysupporting

confidence: 84%

“…Several substrate modifications have been employed to identify DNA elements that are important for recognition and/or incision (22)(23)(24)(25). The human enzyme requires at least 4 bp 5′ and at least 3 bp 3′ of an AP site for incision and makes contacts within both the minor and major groove and with both strands of DNA around the lesion (24,25).…”

Section: Introductionmentioning

confidence: 99%

“…To test models I-III, we examined the effect of a positively charged pyrrolidine (N) abasic site ring structure [an inhibitor of several DNA glycosylases (32)], a non-polar 4-methylindole (4meInd) residue directly opposite the prototypical abasic site analog tetrahydrofuran (F), and an additional centrally located ('bulged') base on the incision and binding activity of Ape, ExoIII and EndoIV; incision of F was used as a reference point (22)(23)(24)(25). To test models I and IV, we measured the cleavage and binding activity of the mutant Ape protein F266A.…”

Section: Introductionmentioning

confidence: 99%

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Elements in abasic site recognition by the major human and Escherichia coli apurinic/apyrimidinic endonucleases

Erzberger

Barsky

Schärer

et al. 1998

Nucleic Acids Research

135

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Sites of base loss in DNA arise spontaneously, are induced by damaging agents or are generated by DNA glycosylases. Repair of these potentially mutagenic or lethal lesions is carried out by apurinic/apyrimidinic (AP) endonucleases. To test current models of AP site recognition, we examined the effects of site-specific DNA structural modifications and an F266A mutation on incision and protein-DNA complex formation by the major human AP endonuclease, Ape. Changing the ring component of the abasic site from a neutral tetrahydrofuran (F) to a positively charged pyrrolidine had only a 4-fold effect on the binding capacity of Ape. A non-polar 4-methylindole base analog opposite F had a <2-fold effect on the incision activity of Ape and the human protein was unable to incise or specifically bind 'bulged' DNA substrates. Mutant Ape F266A protein complexed with F-containing DNA with only a 6-fold reduced affinity relative to wild-type protein. Similar studies are described using Escherichia coli AP endonucleases, exonuclease III and endonuclease IV. The results, in combination with previous findings, indicate that the ring structure of an AP site, the base opposite an AP site, the conformation of AP-DNA prior to protein binding and the F266 residue of Ape are not critical elements in targeted recognition by AP endonucleases.

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Section: Structures Of Abasic Sites As Determined By Quantum Chemistrysupporting

confidence: 84%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Elements in abasic site recognition by the major human and Escherichia coli apurinic/apyrimidinic endonucleases

Erzberger

Barsky

Schärer

et al. 1998

Nucleic Acids Research

135

View full text Add to dashboard Cite

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“…The aldehydic form, however, represents Ͻ1% of the mixture (Manoharan et al, 1988;Wilde et al, 1989). In many studies (Millican et al, 1984;Takeshita et al, 1987), this intrinsic instability of the abasic site is avoided using a 3-hydroxy-3 (hydroxymethyl) tetrahydrofuran analog, and this choice has also been made in the present modeling study. The reader is also referred to a recent NMR study of abasic bulges, which was also carried out with a tetrahydrofuran analog (Lin et al, 1998).…”

Section: Introductionmentioning

confidence: 99%

Abasic Sites in Duplex DNA: Molecular Modeling of Sequence-Dependent Effects on Conformation

Ayadi

Coulombeau

Lavery

1999

Biophysical Journal

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Molecular modeling calculations using JUnction Minimization of Nucleic Acids (JUMNA) have been used to study sequence effects on the conformation of abasic sites within duplex DNA. We have considered lesions leading to all possible unpaired bases (X), adenine, guanine, cytosine, or thymine contained within two distinct sequence contexts, CXC and GXG. Calculations were carried out on DNA 11-mers using extensive conformational search techniques to locate the most stable abasic conformations and using Poisson-Boltzmann corrected electrostatics to account for solvation effects. The results, which are in very good agreement with available experimental data, point to strong sequence effects on both the position of the unpaired base (intra or extrahelical) and on the overall curvature induced by the abasic lesion. For CXC, unpaired purines are found to lie within the helix, while unpaired pyrimidines are either extrahelical or in equilibrium between the intra and extrahelical forms. For GXG, all unpaired bases lead to intrahelical forms, but with marked, sequence-dependent differences in induced curvature.

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“…Thus, when the polymerase stalls at a DNA lesion at a replication fork, the efficiency of nucleotide insertion is compromised, and the effect may extend to several 5'-downstream nucleotides. [10,11] When a natural AP site or a tetrahydrofuran derivative (used frequently as a model abasic site because of its good stability; [12] Figure 1 a) is bypassed, dAMP is preferentially inserted, followed by dGMP (deoxyguanosine monophosphate) and dCMP (deoxycytidine monophosphate) or dTMP. [8,9] Structural studies of AP site-containing DNA duplexes show that these duplexes maintain B-DNA geometry, with only localized perturbations at the lesion site increasing DNA flexibility.…”

mentioning

confidence: 99%

Thermodynamic Impact of Abasic Sites on Simulated Translesion DNA Synthesis

Malina

Brabec

2014

Chemistry A European J

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Loss of a base in DNA and the creation of an abasic (apurinic/apyrimidinic, AP) site is a frequent lesion that may occur spontaneously, or as a consequence of the action of DNA-damaging agents. The AP lesion is mutagenic or lethal if not repaired. We report a systematic thermodynamic investigation by differential scanning calorimetry on the evolution, during primer extension, of a model AP site in chemically simulated DNA translesion synthesis. Incorporation of dAMP (deoxyadenosine monophosphate), as well as dTMP (deoxythymidine monophosphate), opposite an AP site is enthalpically unfavorable, although incorporation of dTMP is more enthalpically unfavorable than that of dAMP. This finding is in a good agreement with experimental data showing that AP sites block various DNA polymerases of eukaryotic and prokaryotic origin and that, if bypassed, dAMP is preferentially inserted, whereas insertion of dTMP is less likely. The results emphasize the importance of thermodynamic contributions to the insertion of nucleotides opposite an AP site by DNA polymerases.

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Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/apyrimidinic endonucleases.

Cited by 393 publications

References 28 publications

Elements in abasic site recognition by the major human and Escherichia coli apurinic/apyrimidinic endonucleases

Elements in abasic site recognition by the major human and Escherichia coli apurinic/apyrimidinic endonucleases

Abasic Sites in Duplex DNA: Molecular Modeling of Sequence-Dependent Effects on Conformation

Thermodynamic Impact of Abasic Sites on Simulated Translesion DNA Synthesis

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