Spontaneous and frequent conformational dynamics induced by A...A mismatch in d(CAA)•d(TAG) duplex

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 hZ alpha(ADAR1) 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.

Automated summary

The study investigates the influence of A...A mismatch in DNA, revealing that it may experience various transient events during B-Z junction formation, and could adapt to the DNA environment through conformational transitions. Experimental results also show that an increase in the number of A...A mismatches deepens the extent of B-Z junction, and the protein binding process commences with B-Z junction recognition.