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Structural alignments of (+)- and (-)-trans-anti-benzo[a]pyrene-dG adducts positioned at a DNA template-primer
M Cosman1, B E Hingerty, N E Geacintov
1Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA.
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-A 21-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.(ABSTRACT TRUNCATED AT 400 WORDS)
Insights
Chemically modified DNA, specifically benzo[a]pyrene diol epoxide adducts, can cause mutations leading to cancer. Understanding the structural changes at the DNA junction site reveals how these mutations occur.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- Chemically modified DNA can lead to mutations and tumor initiation.
- Studying base adducts at DNA junctions provides insights into error-prone synthesis.
- Benzo[a]pyrene diol epoxide (BPDE) is a known carcinogen that forms adducts with DNA.
Purpose of the Study:
- To determine the solution conformations of DNA containing specific benzo[a]pyrene adducts.
- To investigate how these adducts affect DNA structure at a template-primer junction.
- To understand the structural basis for mutation induction by BPDE.
Main Methods:
- Nuclear Magnetic Resonance (NMR) spectroscopy to define structural restraints.
- Molecular mechanics computations to determine DNA conformations.
- Site-specific incorporation of BPDE adducts into DNA sequences.
Main Results:
- The tumorigenic (+)-anti-BPDE adduct induces significant structural changes at the DNA junction.
- The modified guanine adopts a syn glycosidic torsion angle and is displaced into the major groove.
- The pyrene ring of the adduct stacks with an adjacent base pair, while another face is exposed to solvent.
Conclusions:
- Structural alterations caused by BPDE adducts can promote error-prone DNA synthesis.
- The specific conformation of the adduct influences its mutagenic potential.
- These findings contribute to understanding the mechanism of chemical carcinogenesis.