The characterization of abasic sites in DNA heteroduplexes by site specific labeling with carbon-13

Manoharan, Muthiah; Ransom, Stephen C.; Mazumder, Abhijit; Gerlt, J.A.; Wilde, Joyce A.; Withka, Jane; Bolton, Philip H.

doi:10.1021/ja00213a044

Cited by 88 publications

(76 citation statements)

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“…2. The NMR results are consistent with our prior observations (8,11) of essentially equal amounts of the ␣ and ␤ forms.…”

Section: Resultssupporting

confidence: 92%

“…The abasic site is an equilibrium mixture of ␣-(I), and ␤-(II) hemiacetals (2-deoxy-D-erythro-pentofuranoses), of aldehyde (III), and of hydrated aldehyde (IV), as depicted below. The hemiacetal forms predominate with about 1% aldehyde being present (8,11). The strand cleavage at the 3Ј side of the abasic site catalyzed by UV endonuclease V of bacteriophage T4 or endonuclease III of Escherichia coli occurs via a syn ␤-elimination reaction (9,10,12).…”

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confidence: 99%

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Refined Solution Structure of a DNA Heteroduplex Containing an Aldehydic Abasic Site

Goljer

Kumar

Bolton

1995

Journal of Biological Chemistry

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“…2. The NMR results are consistent with our prior observations (8,11) of essentially equal amounts of the ␣ and ␤ forms.…”

Section: Resultssupporting

confidence: 92%

mentioning

confidence: 99%

Refined Solution Structure of a DNA Heteroduplex Containing an Aldehydic Abasic Site

Goljer

Kumar

Bolton

1995

Journal of Biological Chemistry

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“…This mechanism served as a foundation to establish the mechanistic basis for bypassing DNA lesions such as AP sites, catalyzed by Dpo4. Notably, natural AP sites exist as an uneven mixture of four species, with the equilibrium favoring the two anomeric hemiacetals over the two open chain aldehydes (19,20). However, the aldehydic forms are subject to ␤-elimination and subsequent scission of the DNA backbone, producing a heterogeneous mixture of DNA substrates.…”

Section: Resultsmentioning

confidence: 99%

Mechanism of Abasic Lesion Bypass Catalyzed by a Y-family DNA Polymerase

Fiala

Hypes²,

Suo

2007

Journal of Biological Chemistry

113

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The 3 million-base pair genome of Sulfolobus solfataricus likely undergoes depurination/depyrimidination frequently in vivo. These unrepaired abasic lesions are expected to be bypassed by Dpo4, the only Y-family DNA polymerase from S. solfataricus. Interestingly, these error-prone Y-family enzymes have been shown to be physiologically vital in reducing the potentially negative consequences of DNA damage while paradoxically promoting carcinogenesis. Here we used Dpo4 as a model Y-family polymerase to establish the mechanistic basis for DNA lesion bypass. While showing efficient bypass, Dpo4 paused when incorporating nucleotides directly opposite and one position downstream from an abasic lesion because of a drop of several orders of magnitude in catalytic efficiency. Moreover, in disagreement with a previous structural report, Dpo4-catalyzed abasic bypass involves robust competition between the A-rule and the lesion loop-out mechanism and is governed by the local DNA sequence. Analysis of the strong pause sites revealed biphasic kinetics for incorporation indicating that Dpo4 primarily formed a nonproductive complex with DNA that converted slowly to a productive complex. These strong pause sites are mutational hot spots with the embedded lesion even affecting the efficiency of five to six downstream incorporations. Our results suggest that abasic lesion bypass requires tight regulation to maintain genomic stability.

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“…Despite the biologically significant roles of abasic sites as intermediates in the repair of damaged cells and as a mutagenic and carcinogenic lesion, only recently has detailed structural information on this lesion become available through several independent NMR studies on modified oligomeric duplexes (8)(9)(10)(11). The common goal of these NMR studies has been to characterize the structural distortion induced by an abasic site within a duplex.…”

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confidence: 99%

Influence of abasic and anucleosidic sites on the stability, conformation, and melting behavior of a DNA duplex: correlations of thermodynamic and structural data.

Vesnaver

Chang

Eisenberg

et al. 1989

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

120

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We report a complete thermodynamic characterization of the impact of abasic and anucleosidic lesions on the stability, conformation, and melting behavior of a DNA duplex. The requisite thermodynamic data were obtained by using a combination of spectroscopic and calorimetric techniques to investigate helix-to-coil transitions in a family of DNA duplexes of the form d(CGCATGAGTACGC)-d(GCGTA-CXCATGCG), where X corresponds to a thymidine residue in the parent Watson-Crick duplex and to an abasic or anucleosidic site in the modified duplexes. The data derived from these studies reveal that incorporation of an abasic site into a DNA duplex dramatically reduces the duplex stability, transition enthalpy, and transition entropy. The magnitudes of these lesion-induced effects are greater than one would expect based on simple nearest-neighbor considerations. Nearly identical thermodynamic data are obtained when the modified duplex contains an anucleosidic site rather than an abasic site. This observation suggests that the thermodynamic impact of these lesions primarily results from removal of the base rather than the sugar ring. Significantly, the melting cooperativities of the abasic and anucleosidic derivatives are identical with each other and with the corresponding unmodified Watson-Crick parent duplex. This result suggests that the phosphodiester backbone, rather than the base-sugar network, serves as the primary propagation path for the communication of cooperative melting effects. We propose molecular interpretations for the thermodynamic data based on the structural picture that has emerged from the NMR studies of Patel and coworkers on the same family of modified and unmodified DNA duplexes

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The characterization of abasic sites in DNA heteroduplexes by site specific labeling with carbon-13

Cited by 88 publications

References 0 publications

Refined Solution Structure of a DNA Heteroduplex Containing an Aldehydic Abasic Site

Refined Solution Structure of a DNA Heteroduplex Containing an Aldehydic Abasic Site

Mechanism of Abasic Lesion Bypass Catalyzed by a Y-family DNA Polymerase

Influence of abasic and anucleosidic sites on the stability, conformation, and melting behavior of a DNA duplex: correlations of thermodynamic and structural data.

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