Abstract
Base pair mismatches in DNA can erroneously be incorporated during replication, recombination, etc. Here, the influence of A…A mismatch in the context of 5′CAA·5′TAG sequence is explored using molecular dynamics (MD) simulation, umbrella sampling MD, circular dichroism (CD), microscale thermophoresis (MST) and NMR techniques. MD simulations reveal that the A…A mismatch experiences several transient events such as base flipping, base extrusion, etc. facilitating B–Z junction formation. A…A mismatch may assume such conformational transitions to circumvent the effect of nonisostericity with the flanking canonical base pairs so as to get accommodated in the DNA. CD and 1D proton NMR experiments further reveal that the extent of B–Z junction increases when the number of A…A mismatch in d(CAA)·d(T(A/T)G) increases (1–5). CD titration studies of d(CAA)·d(TAG)n=5 with the hZαADAR1 show the passive binding between the two, wherein, the binding of protein commences with B–Z junction recognition. Umbrella sampling simulation indicates that the mismatch samples anti…+ syn/+ syn…anti, anti…anti & + syn…+ syn glycosyl conformations. The concomitant spontaneous transitions are: a variety of hydrogen bonding patterns, stacking and minor or major groove extrahelical movements (with and without the engagement of hydrogen bonds) involving the mismatch adenines. These transitions frequently happen in anti…anti conformational region compared with the other three regions as revealed from the lifetime of these states. Further, 2D-NOESY experiments indicate that the number of cross-peaks diminishes with the increasing number of A…A mismatches implicating its dynamic nature. The spontaneous extrahelical movement seen in A…A mismatch may be a key pre-trapping event in the mismatch repair due to the accessibility of the base(s) to the sophisticated mismatch repair machinery.
Highlights
Base pair mismatches in DNA can erroneously be incorporated during replication, recombination, etc
The molecular dynamics simulation, umbrella sampling MD, circular dichroism, microscale thermophoresis and NMR experiments carried out here to investigate the conformational preference of the A...A mismatch in the CAA sequence indicate that A...A mismatch is highly dynamic in nature
Glycosyl torsion angles corresponding to A 8 and A 23 favor −syn conformation instead of the starting anti conformation after 150 ns (Supplementary Fig. S1A,B). These results indicate the formation of a local B–Z junction at the A8...A23 site
Summary
Base pair mismatches in DNA can erroneously be incorporated during replication, recombination, etc. Spontaneous and frequent transitions between base flipping, extrusion, stacking and a variety of hydrogen bond conformations are observed concomitant with the formation of B–Z junction during the MD and umbrella sampling simulations Such a dynamic nature of A...A mismatch is confirmed by the 2D-NOESY experiment, wherein, the number of proton-proton cross-peaks decreases with the increasing number of A...A mismatch. The B–Z junction formation further facilitates the binding with Z-DNA binding domain of human-ADAR1 (hZαADAR1) protein as seen in CD and microscale thermophoresis experiments Such an aberrant backbone conformational preference along with the extrahelical minor or major groove movement of the adenine(s) may be the key structural features responsible for the recognition of A...A mismatch by the repair proteins to initiate the chemical reaction
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