Dynamic conformational states of DNA containing T·T or BrdU·T mispaired bases: wobble H-bond pairing versus cross-strand inter-atomic contacts

Abstract

The dynamic structure of 11-mer DNA duplexes of different sequences with or without homopyrimidine (T·T, or BrdU·T) mismatches was studied by molecular dynamics (MD) simulations on a time scale from 200 ps to 1 ns. The conformational analysis suggests that in mismatched duplexes the formation of classical T·T wobble H-bonding pairing is nearest-neighbor sequence-dependent and, in most cases, three-centered H-bonds and numerous alternative close cross-strand interatomic contacts exist. Thus, in duplex W1, where the central triplet is 5′d(CTA)·d(TTG), two wobble conformations W↑ (αβ) and W↓ (βα) are formed and exchange rapidly at 300 K. In contrast, when the central triplet is 5′d(TTT)·d(ATA) (W2 duplex) wobble conformations are rarely observed at 300 K, and the T·T mispair most often adopts a “twisted” conformation with one largely persistent normal H-bond, plus a stable cross-strand contact involving a T flanking base. However, at elevated temperature (400 K) the same W2 duplex shows frequent exchange between the two classical wobble conformations (αβ↔βα), as is in the case when the central triplet is 5′d(TBrdUT)·d(ATA) (W3 duplex at 300 K). It is suggested that in the W2 sequence, restrictions due to thymine-methyl/π interactions prevent the formation of wobble pairing and thermal activation energy, and/or the chemical replacement of T by BrdU are required in order for the T(BrdU)·T mismatch to adopt and exchange between wobble conformations. The specific short and/or long-lived (double/triple) cross-strand dynamic interactions in W1, W2 and W3 duplexes are throughout characterized. These frequent atomic encounters exemplify possible inter-strand charge transfer pathways in the studied DNA molecules.

Figure 3D structure snapshots of wobble and frequent overlapping conformers formed within the W3 central triplet during 200 ps MD: α’+ ϒ’. H-bonds (magenta) and close cross-strand contacts, Å (orange).