Nucleic acid structure
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
[math]\displaystyle{ \Delta G^0 = -RT log K = \Delta H^0 - T\cdot\Delta S^0 }[/math] where [math]\displaystyle{ K=\frac{\rm [duplex]}{\rm [single-strand]^2} }[/math]
At the melting temperature, [math]\displaystyle{ T_m }[/math], [math]\displaystyle{ 2[{\rm duplex}] = [{\rm single-strand}] }[/math] and from conservation of total RNA, [math]\displaystyle{ 2[{\rm duplex}] + [{\rm single-strand}] = [{\rm RNA}]_{total} }[/math]. From this, we can derive that:
[math]\displaystyle{ T_m = \frac{\Delta H^0}{\Delta S^0 + R\cdot log[{\rm RNA}]_{total}} }[/math]
You can experimentally find the melting curve and extract the values of [math]\displaystyle{ \Delta H^0 }[/math] and [math]\displaystyle{ \Delta S^0 }[/math] from which you can get [math]\displaystyle{ \Delta G^0 }[/math]. The Freier-Turner rules shows the incremental [math]\displaystyle{ \Delta G^0 }[/math] of stacking another basepair to the end of another pair. The top row shows the 5' basepair, the left column shows the 3' basepair, and the values are in kcal/mol. For example, a GC basepair followed by a CG basepair has -3.4 kcal/mol. This data was calculated for the folding of RNA at 37°C.
| GU | UG | AU | UA | CG | GC | |
| GU | -0.5 | -0.6 | -0.5 | -0.7 | -1.5 | -1.3 |
| UG | -0.5 | -0.5 | -0.7 | -0.5 | -1.5 | -0.9 |
| AU | -0.5 | -0.7 | -0.9 | -1.1 | -1.8 | -2.3 |
| UA | -0.7 | -0.5 | -0.9 | -0.9 | -1.7 | -2.1 |
| CG | -1.9 | -1.3 | -2.1 | -2.3 | -2.9 | -3.4 |
| GC | -1.5 | -1.5 | -1.7 | -1.8 | -2.0 | -2.9 |
