Analysis of the stability and flexibility of RNA complexes containing bulge loops of different sizes.

@article{Macchion2008AnalysisOT,
  title={Analysis of the stability and flexibility of RNA complexes containing bulge loops of different sizes.},
  author={Boel Nystr{\"o}m Macchion and Roger Str{\"o}mberg and Lennart Nilsson},
  journal={Journal of biomolecular structure & dynamics},
  year={2008},
  volume={26 2},
  pages={
          163-73
        }
}
Molecular dynamics simulations of RNA molecules consisting of an antisense oligonucleotide forming a complex with a target strand thereby creating an internal bulge-loop with 3, 4, or 5 nucleotides have been performed with and without O2' methylation of the antisense strand. The methylation influences minor groove hydration, in particular near guanines but also around the methylated O2', and it also reduces the flexibility of both RNA strands. A G.U wobble pair adjacent to the bulge-loop is… CONTINUE READING
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