Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond | Zendy

Alexandra Balaceanu | Zendy; Diana Buitrago | Zendy; Jürgen Walther | Zendy; Adam Hospital | Zendy; Pablo D. Dans | Zendy; Modesto Orozco | Zendy

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Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond

Author(s) -

Alexandra Balaceanu,

Diana Buitrago,

Jürgen Walther,

Adam Hospital,

Pablo D. Dans,

Modesto Orozco

Publication year - 2019

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkz255

Subject(s) - biology , context (archaeology) , dna , modulation (music) , computational biology , genetics , sequence (biology) , molecular dynamics , biophysics , biological system , physics , paleontology , quantum mechanics , acoustics

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.

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