Nucleic Acids Research, 1994, Vol. 22, No. 5 835-841
© 1994
RNA |
On the use of phasing experiments to measure helical repeat and bulge loop-associated twist in RNA
Department of Chemistry, Johns Hopkins University Baltimore, MD 21218, USA
*To whom correspondence should be addressed
Received October 5, 1993. Revised January 19, 1994. Accepted January 19, 1994.
In a phasing experiment, two bends are introduced into a long duplex RNA or DNA and the number of base pairs between them varied. When electrophoresed in a gel, the set of molecules may show a periodic variation in mobility that contains information about the twist associated with the bends and the intervening helix. We show how a set of three phasing experiments can be used to extract this information, and apply it to an RNA helix bend at the bulge sequence A2. The bulge introduces a negative (left-handed) twist of {small tilde}30°; at low temperatures, It is mostly confined to the 5' side of the bulge. The apparent helical repeat of random sequence RNA measured In these experiments was 10.2±0.1 base pairs, an unexpectedly low value. It Is likely that moderate curvature of the RNA helix axis (30-40° over 80 bp) has affected the measurement.
+Present address: Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  X. Zheng and P. C. Bevilacqua Straightening of bulged RNA by the double-stranded RNA-binding domain from the protein kinase PKR PNAS, December 8, 2000; (2000) 11355798. [Abstract] [Full Text]
|
|
|
|
|
|
X. Zheng and P. C. Bevilacqua Straightening of bulged RNA by the double-stranded RNA-binding domain from the protein kinase PKR PNAS, December 19, 2000; 97(26): 14162 - 14167. [Abstract] [Full Text] [PDF]
|
|