Nucleic acid structure

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===Pseudoknots===
===Pseudoknots===
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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.
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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. <tt>[()]</tt>. A pseudoknot has the form <tt>[(])</tt>. In a pseudoknot, the knotted region the "<tt>()</tt>" 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.
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===Thermodynamics===
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<math>\Delta G^0 = -RT log K = \Delta H^0 - T\cdot\Delta S^0</math> where <math>K=\frac{\rm [duplex]}{\rm [single-strand]^2}</math>
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At the melting temperature, <math>T_m</math>, <math>2[{\rm duplex}] = [{\rm single-strand}]</math> and from conservation of total RNA, <math>2[{\rm duplex}] + [{\rm single-strand}] = [{\rm RNA}]_{total}</math>. From this, we can derive that:
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<math>T_m = \frac{\Delta H^0}{\Delta S^0 + R\cdot log[{\rm RNA}]_{total}}</math>
[[Category:DNA]] [[Category:RNA]]
[[Category:DNA]] [[Category:RNA]]

Revision as of 10:08, 24 August 2007

Contents

General

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

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

At the melting temperature, Tm, 2[duplex] = [single − strand] and from conservation of total RNA, 2[duplex] + [single − strand] = [RNA]total. From this, we can derive that:

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

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