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Thermodynamics of RNA Internal Loops with a Guanosine-Guanosine Pair Adjacent to Another Noncanonical Pair

Burkard, Mark E. and Xia, Tianbing and Turner, Douglas H. (2001) Thermodynamics of RNA Internal Loops with a Guanosine-Guanosine Pair Adjacent to Another Noncanonical Pair. Biochemistry, 40 (8). pp. 2478-2483. ISSN 0006-2960. https://resolver.caltech.edu/CaltechAUTHORS:20170131-084422355

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Abstract

Thermodynamic parameters measured by optical melting are reported for formation of RNA duplexes containing tandem noncanonical pairs with at least one guanosine-guanosine (GG) pair. For selected sequences, imino proton NMR provides evidence that the desired duplex forms and that the structure of a GG pair adjacent to a noncanonical pair depends on context. A GG pair next to a different noncanonical pair is more stable than expected from measurements of adjacent GG pairs. This is likely due to an unfavorable stacking interaction between adjacent GG pairs, where areas of high negative charge probably overlap. The results suggest a model where tandem noncanonical pairs closed by two GC pairs are assigned the following free energy increments at 37 °C:  0.8 kcal/mol for adjacent GG pairs, 1.0 kcal/mol for GG next to UU, and −0.3 kcal/mol for all others. These values are adjusted by 0.65 kcal/mol for each closing AU pair.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/bi0012181DOIArticle
http://pubs.acs.org/doi/abs/10.1021/bi0012181PublisherArticle
http://pubs.acs.org/doi/suppl/10.1021/bi0012181Related ItemSupporting Information
Additional Information:© 2001 American Chemical Society. Received 30 May 2000. Published online 1 February 2001. Published in print 1 February 2001. We thank an anonymous reviewer for bringing to our attention water-inserted CU pairs. This work was supported by NIH Grant GM 22939. M.E.B. is a trainee in the Medical Scientist Training Program funded by NIH Grant T32 GM07356.
Funders:
Funding AgencyGrant Number
NIHGM 22939
NIH Predoctoral FellowshipT32 GM07356
Issue or Number:8
Record Number:CaltechAUTHORS:20170131-084422355
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170131-084422355
Official Citation:Thermodynamics of RNA Internal Loops with a Guanosine-Guanosine Pair Adjacent to Another Noncanonical Pair Mark E. Burkard, Tianbing Xia, and Douglas H. Turner Biochemistry 2001 40 (8), 2478-2483 DOI: 10.1021/bi0012181
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:73852
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:31 Jan 2017 17:18
Last Modified:03 Oct 2019 16:32

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