Base sequence effects in bending induced by bulky carcinogen-DNA adducts: experimental and computational analysis

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Covalent binding of bulky mutagens like benzo[a]pyrene diol epoxide (BPDE) to DNA can distort DNA structure.
• BPDE adducts can alter DNA-protein interactions crucial for replication and transcription.
• Stereoisomers of BPDE, specifically (+)- and (-)-anti-BPDE, exhibit differential tumorigenicity, suggesting distinct biological impacts.

Purpose of the Study:

• To investigate the impact of stereoisomeric BPDE-N(2)-dG adducts on DNA bending.
• To determine how DNA sequence context influences the bending induced by these adducts.
• To correlate DNA bending with potential differential processing by cellular enzymes.

Main Methods:

• Synthesis of oligonucleotides containing single (+)- and (-)-trans-anti-[BP]-N(2)-dG adducts at specific positions.
• Assessment of DNA bending using native polyacrylamide gel electrophoresis to measure changes in mobility.
• Estimation of global DNA bending using a sequence-specific three-dimensional model to extract base-pair step parameters.

Main Results:

• (+)-trans-anti-[BP]-N(2)-dG adducts induce significantly greater DNA bending than their (-) enantiomers, irrespective of the surrounding DNA sequence.
• The presence of A-T base pairs flanking the adduct site allows for local flexibility, indicating conformational heterogeneity.
• Computed gel mobilities suggest that DNA exhibits enhanced flexibility in gels compared to aqueous solutions.

Conclusions:

• Stereochemistry of BPDE adducts dictates the extent of DNA bending.
• DNA sequence context, particularly flanking A-T base pairs, influences local DNA flexibility around adducts.
• Differential DNA bending caused by BPDE stereoisomers may underlie their distinct biological effects on DNA replication, transcription, and repair.