Slower Motions and Dramatic Conformational Populations Present in A:G Mismatched DNA Phosphates

Abstract Mismatches such as A:G base pairs arise in DNA primarily due to improper nucleotide incorporation during replication as well as formation of a heteroduplex. Repair of these mismatches and prevention of deleterious mutations is vital to an organism’s survival. Mismatch Repair (MMR) is the primary repair pathway for general DNA mismatches and follows replication to maintain genomic integrity; however, some details of mismatch recognition are unknown. Repair invariably requires precise and localized DNA–protein interactions and binding processes that depend on the specific properties, such as conformational structure and dynamics, of the repair protein and the damaged dsDNA substrate. Therefore, it is likely that the conformational properties of damaged, mismatched or modified DNAs will be different than canonical duplexed DNA. The work herein demonstrates a dramatic shift in time scale of motions and conformational populations for the phosphate flanking an A:G mismatched base pair. 31P NMR results show the motions are in the intermediate time scale (10–3 s), which is orders of magnitude slower than prior results (10–5–10–9 s), and the population of the BII substate shifts to ∼ 99%. These perturbations could be utilized in a phosphate tracking mechanism during indirect readout by repair enzymes such as MutS.