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Double-stranded RNA bending by AU-tract sequences.

Alberto Marin-Gonzalez1, Clara Aicart-Ramos1, Mikel Marin-Baquero1

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The nucleotide sequence can bend double-stranded RNA (dsRNA). Alternating adenine-uracil sequences (AU-tracts) cause significant dsRNA helix bending, a finding confirmed by experiments.

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Area of Science:

  • Biophysics
  • Molecular Biology
  • RNA Structure

Background:

  • DNA structure is sequence-dependent, with adenine tracts (A-tracts) causing bending.
  • Sequence-dependent structural features of double-stranded RNA (dsRNA) are less understood.
  • Little attention has been paid to sequence-induced structural variations in dsRNA.

Purpose of the Study:

  • To investigate if nucleotide sequence can induce bending in dsRNA.
  • To identify specific sequence motifs responsible for dsRNA helix curvature.
  • To explore potential applications of sequence-controlled dsRNA structures.

Main Methods:

  • All-atom molecular dynamics simulations to model dsRNA behavior.
  • Identification of sequence motifs causing helix bending.
  • Experimental validation using atomic force microscopy (AFM).

Main Results:

  • A sequence motif of alternating adenine and uracil (AU-tracts) strongly bends the dsRNA helix.
  • Atomic force microscopy confirmed macroscopic curvature in dsRNA with phased AU-tract motifs.
  • Localized major groove compression and propeller twist at AU-tracts underlie the bending phenomenon.
  • Bending magnitude is tunable by altering AU-tract length.

Conclusions:

  • Nucleotide sequence can control dsRNA curvature.
  • AU-tracts are identified as a novel sequence motif for inducing dsRNA bending.
  • Sequence-directed dsRNA bending has potential applications in RNA nanotechnology and protein recognition.