Nucleic acid structure

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B-form DNA

  • radius: 100 nm
  • pitch: 340 nm/turn
  • minor groove angle: 137.5078°
  • Twist angle of 34.7°
  • frequency: 10.4 bases/turn
  • The roll and tilt angles vary by a few degrees depending on the basepairs. The dinucleotide AA (or TT) causes significant variations in the roll and tilt angles


The extra 2'-OH usually prevents formation of the B-form helix found in DNA.

A-form RNA

  • 11 bases/turn
  • The basepair stacks are tilted and displaced with respect to the axis of the helix


RNA is normally assumed by folding algorithms to fold without pseudoknots. A non-pseudoknotted structure in parenthesis format would close all parenthesis in order, i.e. [()]. A pseudoknot has the form [(]). In a pseudoknot, the knotted region the "()" pairing cannot exceed 9 or 10 basepairs. This constraint is because of the helical structure of RNA which forms 10 or 11 basepairs per turn. With a full turn, the two strands of the pseudoknot would form a true knot which is physically and biologically unrealistic.