Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond
Unravelling how mechanical information flows along B-DNA double helix by focusing on all the possible hexamer and octamer contexts around the CTAG tetranucleotide. Determination of the structural polymorphisms at the base level (shift, slide, and twist) and their connections with backbone sub-states, cation-DNA interaction, and Hydrogen bond formation. Fig. by Alexandra Balaceanu.
Balaceanu A, Buitrago D, Walther J, Hospital A, Dans PD, Orozco M.
Nucleic Acids Res 2019 May; 47: 4418.
We used extensive molecular dynamics simulations to study the structural and dynamic properties of the central d(TpA) step in the highly polymorphic d(CpTpApG) tetranucleotide. Contrary to the assumption of the dinucleotide-model and its nearest neighbours (tetranucleotide-model), the properties of the central d(TpA) step change quite significantly dependent on the next-to-nearest (hexanucleotide) sequence context and in a few cases are modulated by even remote neighbours (beyond next-to-nearest from the central TpA). Our results highlight the existence of previously undescribed dynamical mechanisms for the transmission of structural information into the DNA and demonstrate the existence of certain sequences with special physical properties that can impact on the global DNA structure and dynamics.
PubMed: 30957854. Doi: 10.1093/nar/gkz255. Free PMC article
