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PMID: 7524072 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 91 ·No. 20 ·1994-09-27 ·Pages 9218-22

Walter AE, Turner DH, Kim J, Lyttle MH, Müller P, Mathews DH, Zuker M

Abstract

An RNA model system consisting of an oligomer binding to a 4-nt overhang at the 5' end of a hairpin stem provides thermodynamic parameters for helix-helix interfaces. In a sequence-dependent manner, oligomers bind up to 1000-fold more tightly adjacent to the hairpin stem than predicted for binding to a free tetramer at 37 degrees C. For the interface (/) in [formula: see text] additional free energy change, delta delta G 37 degrees, for binding is roughly the nearest-neighbor delta G 37 degrees for propagation of an uninterrupted helix of equivalent sequence, CGGC. When X and Z are omitted, the delta delta 37 degrees is even more favorable by approximately 1 kcal/mol (1 cal = 4.184J). On average, predictions of 11 RNA secondary structures improve from 67 to 74% accuracy by inclusion of similar stacking contributions.

MeSH Terms
Animals Base Sequence Calorimetry Introns Molecular Sequence Data Nucleic Acid Conformation Oligoribonucleotides/chemistry Phylogeny RNA/chemistry,genetics RNA, Bacterial/chemistry RNA, Fungal/chemistry Rats Structure-Activity Relationship
Chemicals
Oligoribonucleotides RNA, Bacterial RNA, Fungal RNA
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Walter A E
Department of Chemistry, University of Rochester, NY 14627-0216.
Turner D H
Kim J
Lyttle M H
Müller P
Mathews D H
Zuker M
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.91.20.9218
Published
1994-09-27
Pages
9218-22
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC44783
Subset
IM
Grants
NIGMS NIH HHS · GM22939 · United States
External Links
PubMed source DOI: 10.1073/pnas.91.20.9218 PMC Full Text View journal details
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