Nucleic acid structure: Difference between revisions
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(New page: ==General== ==DNA== ===B 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 angle...) |
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==DNA== | ==DNA== | ||
===B DNA=== | ===B-form DNA=== | ||
* radius: 100 nm | * radius: 100 nm | ||
* pitch: 340 nm/turn | * pitch: 340 nm/turn | ||
| Line 11: | Line 11: | ||
==RNA== | ==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. | |||
[[Category:DNA]] [[Category:RNA]] | [[Category:DNA]] [[Category:RNA]] | ||
Revision as of 20:29, 23 August 2007
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.
