O⁶-carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine

Area of Science:

• Molecular Biology
• Structural Biology
• Cancer Research

Background:

• N-Nitrosation of glycine derivatives forms O(6)-carboxymethylguanine (O(6)-CMG), a DNA adduct found in human colon tissue.
• O(6)-CMG is associated with diets high in red and processed meats, suggesting a link to colorectal cancer induction.
• O(6)-CMG is predicted to be mutagenic, potentially causing G-to-A mutations and increasing cancer risk.

Purpose of the Study:

• To investigate the structural versatility of O(6)-CMG in DNA base-pairing.
• To determine the DNA structure of a dodecamer containing O(6)-CMG at a different sequence context than previously reported.
• To compare O(6)-CMG pairing modes with thymine under various conditions.

Main Methods:

• X-ray crystallography was employed to determine the DNA dodecamer structure.
• Four crystal forms were obtained using different solvent ions (Sr(2+), Ba(2+), Mg(2+), K(+)/Na(+)) and Hoechst 33258.
• Structural analysis focused on the base-pairing interactions of O(6)-CMG with thymine.

Main Results:

• O(6)-CMG formed alternative pairing modes with thymine, differing from previously reported Watson-Crick-like pairing.
• A 'high-wobble' pairing mode was observed, involving thymine displacement into the major groove and hydrogen bonding with O(6)-CMG's carboxyl group.
• A water molecule mediated hydrogen bonds between thymine O(2) and O(6)-CMG's amino group, stabilizing the wobble pair.
• These alternative pairing modes were consistent across different crystallization conditions.

Conclusions:

• O(6)-CMG exhibits versatility in DNA base pairing, forming at least two distinct types of pairs with thymine.
• The observed pairing modes include a Watson-Crick-like interaction and a novel 'high-wobble' interaction.
• The DNA sequence context likely influences which pairing mode O(6)-CMG adopts, impacting its mutagenic potential.