Structural alignments of (+)- and (-)-trans-anti-benzo[a]pyrene-dG adducts. Positioned at a DNA template-primer junction

Monique Cosman, Brian E. Hingerty, Nicholas E. Geacintov, Suse Broyde, Dinshaw J. Patel

Research output: Contribution to journalArticle

Abstract

The structural features of a chemically modified DNA template strand may promote error-prone DNA synthesis during replication. The resulting higher incidence of mutations, in turn, can eventually lead to tumor initiation. Structural insights into this process can be monitored by studying chemically modified base adducts of defined stereochemistry positioned site-specifically at a single strand-duplex template-primer junction. We have used a NMR-molecular mechanics approach to obtain the solution conformations of the covalent adducts derived from trans additions at the [BP]C10 position of the highly tumorigenic (+)-anti-benzo[a]pyrene diol epoxide [(+)-anti-BPDE] and nontumorigenic (-)-anti-benzo-[a]pyrene diol epoxide [(-)-anti-BPDE] to the N2 position of guanine [(+) and (-)-trans-anti-[BP]dG, respectively] in the d(A1-A2-C3-[BP]G4-C5-T6-A7-C8-C9-A10-T11-C12-C13)·d(G14-G15-A16-T17-G18- G19-T20-A21-G22) 13/9-mer DNA sequence. The modified 13-mer strand constitutes the template strand, while the complementary 9-mer strand constitutes a primer which has been synthesized from the 3′-end of the template toward the 5′-end up to the base preceding, but not including, the modified guanine. The modified guanine (denoted by [BP]dG4) is positioned at the junction site between the single-stranded and duplex segments. Structural features of the (+)-trans-anti-[BP]dG 13/9-mer have been determined by incorporating proton-proton distances defined by lower and upper bounds deduced from. NOESY spectra as restraints in molecular mechanics computations in torsion angle space. The 3′-side duplex segment retains a minimally perturbed B-DNA conformation with all nine base pairs in Watson-Crick hydrogen-bonded alignments. Conformational heterogeneity is detected at the single-stranded d(A1-A2-C3) segment located 5′ to the modified (+)-trans-anti-[BP]dG lesion which contrasts with an unperturbed alignment of these same residues in the unmodified control 13/9-mer. The modified guanine adopts a syn glycosidic torsion angle, is displaced into the major groove, and no longer stacks over the adjacent dC5·dG22 base pair. Such a base displacement is accompanied by stacking of one face of the pyrenyl ring with the dC5·dG22 base pair located on the duplex segment proximate to the modified guanine, while the other face of BP is exposed to solvent. The orientations elucidated for the modified guanine and benzo[a]pyrenyl rings in the (+)-trans-anti-[BP]dG template-primer junction contrasts with orientations previously reported for the same adduct when positioned opposite either a dC base [Cosman, M., et al. (1992) Proc. Natl. Acad Sci. U.S.A. 89, 1914-1918] or a deletion site [Cosman, M., et al. (1994) Biochemistry 33, 11507-11517] at the duplex level. The NMR spectra of the stereoisomeric (-)-trans-anti-[BP]dG 13/9-mer are characterized by very broad and overlapped resonances for the protons located at the lesion site and for the single-strand and duplex segments flanking this site as well as by the presence of exchange cross peaks. This result indicates conformational heterogeneity for the strand and duplex segments on either side of the lesion site in the (-)-trans-anti-[BP]dG 13/9-mer precluding characterization of the structural alignment of this lesion when positioned at the template-primer junction. The different spectral and structural patterns associated with the stereoisomeric (+)- and (-)-trans-anti-[BP]dG 13/9-mers should help to define the interrelationship between the conformations of site-specific and stereochemically defined covalent DNA adducts at template-primer junction sites and their effects on the action of polymerases in the cell.

Original languageEnglish (US)
Pages (from-to)15334-15350
Number of pages17
JournalBiochemistry
Volume34
Issue number46
StatePublished - 1995

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DNA Primers
Benzo(a)pyrene
Guanine
DNA
Base Pairing
Conformations
Protons
Molecular mechanics
Epoxy Compounds
Mechanics
varespladib methyl
Torsional stress
Molecular Computers
Nuclear magnetic resonance
B-Form DNA
Biochemistry
Stereochemistry
DNA Adducts
DNA sequences
antineoplaston A10

ASJC Scopus subject areas

  • Biochemistry

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Structural alignments of (+)- and (-)-trans-anti-benzo[a]pyrene-dG adducts. Positioned at a DNA template-primer junction. / Cosman, Monique; Hingerty, Brian E.; Geacintov, Nicholas E.; Broyde, Suse; Patel, Dinshaw J.

In: Biochemistry, Vol. 34, No. 46, 1995, p. 15334-15350.

Research output: Contribution to journalArticle

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title = "Structural alignments of (+)- and (-)-trans-anti-benzo[a]pyrene-dG adducts. Positioned at a DNA template-primer junction",
abstract = "The structural features of a chemically modified DNA template strand may promote error-prone DNA synthesis during replication. The resulting higher incidence of mutations, in turn, can eventually lead to tumor initiation. Structural insights into this process can be monitored by studying chemically modified base adducts of defined stereochemistry positioned site-specifically at a single strand-duplex template-primer junction. We have used a NMR-molecular mechanics approach to obtain the solution conformations of the covalent adducts derived from trans additions at the [BP]C10 position of the highly tumorigenic (+)-anti-benzo[a]pyrene diol epoxide [(+)-anti-BPDE] and nontumorigenic (-)-anti-benzo-[a]pyrene diol epoxide [(-)-anti-BPDE] to the N2 position of guanine [(+) and (-)-trans-anti-[BP]dG, respectively] in the d(A1-A2-C3-[BP]G4-C5-T6-A7-C8-C9-A10-T11-C12-C13)·d(G14-G15-A16-T17-G18- G19-T20-A21-G22) 13/9-mer DNA sequence. The modified 13-mer strand constitutes the template strand, while the complementary 9-mer strand constitutes a primer which has been synthesized from the 3′-end of the template toward the 5′-end up to the base preceding, but not including, the modified guanine. The modified guanine (denoted by [BP]dG4) is positioned at the junction site between the single-stranded and duplex segments. Structural features of the (+)-trans-anti-[BP]dG 13/9-mer have been determined by incorporating proton-proton distances defined by lower and upper bounds deduced from. NOESY spectra as restraints in molecular mechanics computations in torsion angle space. The 3′-side duplex segment retains a minimally perturbed B-DNA conformation with all nine base pairs in Watson-Crick hydrogen-bonded alignments. Conformational heterogeneity is detected at the single-stranded d(A1-A2-C3) segment located 5′ to the modified (+)-trans-anti-[BP]dG lesion which contrasts with an unperturbed alignment of these same residues in the unmodified control 13/9-mer. The modified guanine adopts a syn glycosidic torsion angle, is displaced into the major groove, and no longer stacks over the adjacent dC5·dG22 base pair. Such a base displacement is accompanied by stacking of one face of the pyrenyl ring with the dC5·dG22 base pair located on the duplex segment proximate to the modified guanine, while the other face of BP is exposed to solvent. The orientations elucidated for the modified guanine and benzo[a]pyrenyl rings in the (+)-trans-anti-[BP]dG template-primer junction contrasts with orientations previously reported for the same adduct when positioned opposite either a dC base [Cosman, M., et al. (1992) Proc. Natl. Acad Sci. U.S.A. 89, 1914-1918] or a deletion site [Cosman, M., et al. (1994) Biochemistry 33, 11507-11517] at the duplex level. The NMR spectra of the stereoisomeric (-)-trans-anti-[BP]dG 13/9-mer are characterized by very broad and overlapped resonances for the protons located at the lesion site and for the single-strand and duplex segments flanking this site as well as by the presence of exchange cross peaks. This result indicates conformational heterogeneity for the strand and duplex segments on either side of the lesion site in the (-)-trans-anti-[BP]dG 13/9-mer precluding characterization of the structural alignment of this lesion when positioned at the template-primer junction. The different spectral and structural patterns associated with the stereoisomeric (+)- and (-)-trans-anti-[BP]dG 13/9-mers should help to define the interrelationship between the conformations of site-specific and stereochemically defined covalent DNA adducts at template-primer junction sites and their effects on the action of polymerases in the cell.",
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TY - JOUR

T1 - Structural alignments of (+)- and (-)-trans-anti-benzo[a]pyrene-dG adducts. Positioned at a DNA template-primer junction

AU - Cosman, Monique

AU - Hingerty, Brian E.

AU - Geacintov, Nicholas E.

AU - Broyde, Suse

AU - Patel, Dinshaw J.

PY - 1995

Y1 - 1995

N2 - The structural features of a chemically modified DNA template strand may promote error-prone DNA synthesis during replication. The resulting higher incidence of mutations, in turn, can eventually lead to tumor initiation. Structural insights into this process can be monitored by studying chemically modified base adducts of defined stereochemistry positioned site-specifically at a single strand-duplex template-primer junction. We have used a NMR-molecular mechanics approach to obtain the solution conformations of the covalent adducts derived from trans additions at the [BP]C10 position of the highly tumorigenic (+)-anti-benzo[a]pyrene diol epoxide [(+)-anti-BPDE] and nontumorigenic (-)-anti-benzo-[a]pyrene diol epoxide [(-)-anti-BPDE] to the N2 position of guanine [(+) and (-)-trans-anti-[BP]dG, respectively] in the d(A1-A2-C3-[BP]G4-C5-T6-A7-C8-C9-A10-T11-C12-C13)·d(G14-G15-A16-T17-G18- G19-T20-A21-G22) 13/9-mer DNA sequence. The modified 13-mer strand constitutes the template strand, while the complementary 9-mer strand constitutes a primer which has been synthesized from the 3′-end of the template toward the 5′-end up to the base preceding, but not including, the modified guanine. The modified guanine (denoted by [BP]dG4) is positioned at the junction site between the single-stranded and duplex segments. Structural features of the (+)-trans-anti-[BP]dG 13/9-mer have been determined by incorporating proton-proton distances defined by lower and upper bounds deduced from. NOESY spectra as restraints in molecular mechanics computations in torsion angle space. The 3′-side duplex segment retains a minimally perturbed B-DNA conformation with all nine base pairs in Watson-Crick hydrogen-bonded alignments. Conformational heterogeneity is detected at the single-stranded d(A1-A2-C3) segment located 5′ to the modified (+)-trans-anti-[BP]dG lesion which contrasts with an unperturbed alignment of these same residues in the unmodified control 13/9-mer. The modified guanine adopts a syn glycosidic torsion angle, is displaced into the major groove, and no longer stacks over the adjacent dC5·dG22 base pair. Such a base displacement is accompanied by stacking of one face of the pyrenyl ring with the dC5·dG22 base pair located on the duplex segment proximate to the modified guanine, while the other face of BP is exposed to solvent. The orientations elucidated for the modified guanine and benzo[a]pyrenyl rings in the (+)-trans-anti-[BP]dG template-primer junction contrasts with orientations previously reported for the same adduct when positioned opposite either a dC base [Cosman, M., et al. (1992) Proc. Natl. Acad Sci. U.S.A. 89, 1914-1918] or a deletion site [Cosman, M., et al. (1994) Biochemistry 33, 11507-11517] at the duplex level. The NMR spectra of the stereoisomeric (-)-trans-anti-[BP]dG 13/9-mer are characterized by very broad and overlapped resonances for the protons located at the lesion site and for the single-strand and duplex segments flanking this site as well as by the presence of exchange cross peaks. This result indicates conformational heterogeneity for the strand and duplex segments on either side of the lesion site in the (-)-trans-anti-[BP]dG 13/9-mer precluding characterization of the structural alignment of this lesion when positioned at the template-primer junction. The different spectral and structural patterns associated with the stereoisomeric (+)- and (-)-trans-anti-[BP]dG 13/9-mers should help to define the interrelationship between the conformations of site-specific and stereochemically defined covalent DNA adducts at template-primer junction sites and their effects on the action of polymerases in the cell.

AB - The structural features of a chemically modified DNA template strand may promote error-prone DNA synthesis during replication. The resulting higher incidence of mutations, in turn, can eventually lead to tumor initiation. Structural insights into this process can be monitored by studying chemically modified base adducts of defined stereochemistry positioned site-specifically at a single strand-duplex template-primer junction. We have used a NMR-molecular mechanics approach to obtain the solution conformations of the covalent adducts derived from trans additions at the [BP]C10 position of the highly tumorigenic (+)-anti-benzo[a]pyrene diol epoxide [(+)-anti-BPDE] and nontumorigenic (-)-anti-benzo-[a]pyrene diol epoxide [(-)-anti-BPDE] to the N2 position of guanine [(+) and (-)-trans-anti-[BP]dG, respectively] in the d(A1-A2-C3-[BP]G4-C5-T6-A7-C8-C9-A10-T11-C12-C13)·d(G14-G15-A16-T17-G18- G19-T20-A21-G22) 13/9-mer DNA sequence. The modified 13-mer strand constitutes the template strand, while the complementary 9-mer strand constitutes a primer which has been synthesized from the 3′-end of the template toward the 5′-end up to the base preceding, but not including, the modified guanine. The modified guanine (denoted by [BP]dG4) is positioned at the junction site between the single-stranded and duplex segments. Structural features of the (+)-trans-anti-[BP]dG 13/9-mer have been determined by incorporating proton-proton distances defined by lower and upper bounds deduced from. NOESY spectra as restraints in molecular mechanics computations in torsion angle space. The 3′-side duplex segment retains a minimally perturbed B-DNA conformation with all nine base pairs in Watson-Crick hydrogen-bonded alignments. Conformational heterogeneity is detected at the single-stranded d(A1-A2-C3) segment located 5′ to the modified (+)-trans-anti-[BP]dG lesion which contrasts with an unperturbed alignment of these same residues in the unmodified control 13/9-mer. The modified guanine adopts a syn glycosidic torsion angle, is displaced into the major groove, and no longer stacks over the adjacent dC5·dG22 base pair. Such a base displacement is accompanied by stacking of one face of the pyrenyl ring with the dC5·dG22 base pair located on the duplex segment proximate to the modified guanine, while the other face of BP is exposed to solvent. The orientations elucidated for the modified guanine and benzo[a]pyrenyl rings in the (+)-trans-anti-[BP]dG template-primer junction contrasts with orientations previously reported for the same adduct when positioned opposite either a dC base [Cosman, M., et al. (1992) Proc. Natl. Acad Sci. U.S.A. 89, 1914-1918] or a deletion site [Cosman, M., et al. (1994) Biochemistry 33, 11507-11517] at the duplex level. The NMR spectra of the stereoisomeric (-)-trans-anti-[BP]dG 13/9-mer are characterized by very broad and overlapped resonances for the protons located at the lesion site and for the single-strand and duplex segments flanking this site as well as by the presence of exchange cross peaks. This result indicates conformational heterogeneity for the strand and duplex segments on either side of the lesion site in the (-)-trans-anti-[BP]dG 13/9-mer precluding characterization of the structural alignment of this lesion when positioned at the template-primer junction. The different spectral and structural patterns associated with the stereoisomeric (+)- and (-)-trans-anti-[BP]dG 13/9-mers should help to define the interrelationship between the conformations of site-specific and stereochemically defined covalent DNA adducts at template-primer junction sites and their effects on the action of polymerases in the cell.

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