Influence of two bulge loops on the stability of RNA duplexes.
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Author(s)
Crowther, Claire V.
Jones, Laura E.
Morelli, Jessica N.
Mastrogiacomo, Eric M.
Porterfield, Claire A.
Kent, Jessica L.
Serra, Martin J.
Date Issued
March 2017
Abstract
53 RNA duplexes containing two single nucleotide bulge loops were optically melted in 1M NaCl in order to determine the thermodynamic parameters ΔH°, ΔS°, ΔG°37, and TM for each duplex. Because of the large number of possible combinations and lack of sequence effects observed previously, we limited our initial investigation to adenosine bulges, the most common naturally occurring bulge. For example, the following duplexes were investigated: 5′ GGCAXYAGGC 5′ GGCAXY GCC 5′ GGC XYAGCC CCG YX CCG CCG YXACGG CCGAXY CGG The identity of XY (where XY are Watson Crick base pairs) and the total number of base pairs in the terminal and central stems were varied. As observed for duplexes with a single bulge loop, the effect of the two bulge loops on duplex stability is primarily influenced by non-nearest neighbor interactions. In particular, the stability of the stems influences the destabilization of the duplex by the inserted bulge loops. The model proposed to predict the influence of multiple bulge loops on duplex stability suggests that the destabilization of each bulge is related to the stability of the adjacent stems. A database of RNA secondary structures was examined to determine the naturally occurring abundance of duplexes containing multiple bulge loops. Of the 2,000 examples found in the database, over 65% of the two bulge loops occur within 3 base pairs of each other. A database of RNA 3-dimensional structures was examined to determine the structure of duplexes containing two single nucleotide bulge loops. The structures of the bulge loops are described.
Journal
RNA
Department
Biochemistry
Citation
Crowther, C.V., Jones, J.E., and Morelli, Jessica N., et al. (2017). Influence of two bulge loops on the stability of RNA duplexes. RNA 23(2): 217-228. doi: 10.1261/rna.056168.116
Publisher
Cold Spring Harbor Laboratory Press
Version of Article
Published article
Embargo
This version of the article is available for viewing to the public after March 2018.
DOI
10.1261/rna.056168.116
ISSN
1355-8382
e1469-9001
Rights
This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date. After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
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