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Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Biophysics

Background:

  • Molecular modeling of RNA double helices relies on basepair parameters from crystal structures.
  • The non-canonical A:A w:wC basepair, with two Adenines in cis orientation, is frequently observed.
  • Bimodal Shear distribution of A:A w:wC basepairs, due to varied H-bonding, complicates parameter assignment, especially when stacked on G:U wobble pairs.

Purpose of the Study:

  • To investigate the structural behavior of the non-canonical A:A w:wC basepair in RNA double helices.
  • To elucidate the factors influencing the stability and conformational plasticity of A:A w:wC basepairs.
  • To explain the observed promiscuous nature and occasional structural plasticity of the A:A w:wC basepair.

Main Methods:

  • Molecular dynamics (MD) simulations of RNA double helices with GAG, UAG, and GAU sequence motifs.
  • Quantum chemical calculations for non-canonical A:A w:wC basepairs stacked on G:U W:WC basepairs.
  • Hybrid DFT-D and MP2 stacking energy analyses on dinucleotide step sequences.

Main Results:

  • MD simulations showed stable GAG motifs with negative Shear for A:A w:wC basepairs; other motifs were unstable.
  • Stacking energy analyses revealed that A:A::G:U dinucleotides favor negative Shear, consistent with crystal data.
  • A:A::U:G dinucleotides preferred structures with positive Shear, indicating sequence-dependent orientation preferences.

Conclusions:

  • Quantum chemical calculations explain the stability of GAG motifs in MD simulations.
  • A 'tug of war' between positive and negative Shears of the A:A w:wC basepair in GAU and UAG motifs induces conformational plasticity.
  • The study provides a comprehensive understanding of the A:A w:wC basepair's promiscuous nature and its role in structural plasticity.