# Nucleic acid structure

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## DNA

### 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

## RNA

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

### Pseudoknots

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.

### Thermodynamics

$\displaystyle \Delta G^0 = -RT log K = \Delta H^0 - T\cdot\Delta S^0$ where $\displaystyle K=\frac{\rm [duplex]}{\rm [single-strand]^2}$

At the melting temperature, $\displaystyle T_m$ , $\displaystyle 2[{\rm duplex}] = [{\rm single-strand}]$ and from conservation of total RNA, $\displaystyle 2[{\rm duplex}] + [{\rm single-strand}] = [{\rm RNA}]_{total}$ . From this, we can derive that:

$\displaystyle T_m = \frac{\Delta H^0}{\Delta S^0 + R\cdot log[{\rm RNA}]_{total}}$