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Chemical and structural characterization of interstrand cross-links formed between abasic sites and adenine residues in duplex DNA.

Price NE, Catalano MJ, Liu S, Wang Y, Gates KS - Nucleic Acids Res. (2015)

Bottom Line: A synthetic standard was prepared for the putative nucleoside cross-link remnant 6 in which the anomeric carbon of the 2-deoxyribose residue was connected to the exocyclic N(6)-amino group of dA.These findings establish the chemical structure of the dA-Ap cross-link released from duplex DNA and may provide methods for the detection of this lesion in cellular DNA.Both the nucleoside cross-link remnant 6: and the cross-link in duplex DNA were quite stable at pH 7 and 37°C, suggesting that the dA-Ap cross-link could be a persistent lesion with the potential to block the action of various DNA processing enzymes.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA.

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EXSY-2D-NMR of the H1″ spectral region for compound 6. Correlations between the isomers of 6 appear as contours at the intersecting lines between signals for the H1″ protons, indicating a dynamic equilibrium between the α-pyranose, β-pyranose, α-furanose and β-furanose isomers of the 2-deoxyribose adduct located at the exocyclic N6-amino group of the adenine residue.
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Figure 1: EXSY-2D-NMR of the H1″ spectral region for compound 6. Correlations between the isomers of 6 appear as contours at the intersecting lines between signals for the H1″ protons, indicating a dynamic equilibrium between the α-pyranose, β-pyranose, α-furanose and β-furanose isomers of the 2-deoxyribose adduct located at the exocyclic N6-amino group of the adenine residue.

Mentions: Proton NMR analysis revealed resonances for both dA and an additional 2-deoxyribose unit consistent with the anticipated structure 6 (Tables S1 and S2). The HMQC spectra allowed assignment of carbon-to-hydrogen connectivity. Multiple resonances were observed for the 2-deoxyribose adduct in the product. This was not unexpected, as 2-deoxyribose itself exists as an equilibrium mixture of the α-pyranose, β-pyranose, α-furanose and β-furanose isomers (Scheme 2) (32). Similarly, N-aryl-2-deoxyaminoriboside analogs exist as a mixture of cyclic forms, in which the pyranose isomers typically dominate (21,33–36). Thus, the observation of multiple resonances for the carbons and hydrogens of the 2-deoxyribose unit in the product suggested that the adduct was present as an equilibrium mixture of four possible isomers (α-pyranose, β-pyranose, α-furanose and β-furanose). A 2D-EXSY-NMR experiment that gives cross-peaks between sites that are in slow chemical exchange confirmed that the multiple resonances reflected an equilibrium mixture of 2-deoxyribose isomers in the product. For example, the H1″ signals from 5.6–6.3 ppm are a dynamic isomeric mixture of four separate signals (Figure 1).


Chemical and structural characterization of interstrand cross-links formed between abasic sites and adenine residues in duplex DNA.

Price NE, Catalano MJ, Liu S, Wang Y, Gates KS - Nucleic Acids Res. (2015)

EXSY-2D-NMR of the H1″ spectral region for compound 6. Correlations between the isomers of 6 appear as contours at the intersecting lines between signals for the H1″ protons, indicating a dynamic equilibrium between the α-pyranose, β-pyranose, α-furanose and β-furanose isomers of the 2-deoxyribose adduct located at the exocyclic N6-amino group of the adenine residue.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4402519&req=5

Figure 1: EXSY-2D-NMR of the H1″ spectral region for compound 6. Correlations between the isomers of 6 appear as contours at the intersecting lines between signals for the H1″ protons, indicating a dynamic equilibrium between the α-pyranose, β-pyranose, α-furanose and β-furanose isomers of the 2-deoxyribose adduct located at the exocyclic N6-amino group of the adenine residue.
Mentions: Proton NMR analysis revealed resonances for both dA and an additional 2-deoxyribose unit consistent with the anticipated structure 6 (Tables S1 and S2). The HMQC spectra allowed assignment of carbon-to-hydrogen connectivity. Multiple resonances were observed for the 2-deoxyribose adduct in the product. This was not unexpected, as 2-deoxyribose itself exists as an equilibrium mixture of the α-pyranose, β-pyranose, α-furanose and β-furanose isomers (Scheme 2) (32). Similarly, N-aryl-2-deoxyaminoriboside analogs exist as a mixture of cyclic forms, in which the pyranose isomers typically dominate (21,33–36). Thus, the observation of multiple resonances for the carbons and hydrogens of the 2-deoxyribose unit in the product suggested that the adduct was present as an equilibrium mixture of four possible isomers (α-pyranose, β-pyranose, α-furanose and β-furanose). A 2D-EXSY-NMR experiment that gives cross-peaks between sites that are in slow chemical exchange confirmed that the multiple resonances reflected an equilibrium mixture of 2-deoxyribose isomers in the product. For example, the H1″ signals from 5.6–6.3 ppm are a dynamic isomeric mixture of four separate signals (Figure 1).

Bottom Line: A synthetic standard was prepared for the putative nucleoside cross-link remnant 6 in which the anomeric carbon of the 2-deoxyribose residue was connected to the exocyclic N(6)-amino group of dA.These findings establish the chemical structure of the dA-Ap cross-link released from duplex DNA and may provide methods for the detection of this lesion in cellular DNA.Both the nucleoside cross-link remnant 6: and the cross-link in duplex DNA were quite stable at pH 7 and 37°C, suggesting that the dA-Ap cross-link could be a persistent lesion with the potential to block the action of various DNA processing enzymes.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA.

Show MeSH