Characterization of RNA hairpin loop stability

Duncan R. Groebe; Olke C. Uhlenbeck

doi:10.1093/nar/16.24.11725

Characterization of RNA hairpin loop stability

Duncan R. Groebe^*, Olke C. Uhlenbeck

^*Corresponding author for this work

Molecular Biosciences

Research output: Contribution to journal › Article › peer-review

174 Scopus citations

Abstract

Fifteen RNA hairpins that share the same stem sequence and have homopolymer loops of A, C and U residues which vary in length from three to nine nucleotides were synthesized and their thermal stabilities determined. T_m varys as a function of loop size but is almost independent of loop composition. Loops of four or five nucleotides are found to be the most stable loop size. This is consistent with the observation that four-membered loops are the most prevalent loop size in 16S-like RNAs. The contribution of each loop to hairpin stability was calculated by subtracting the known contribution of the helical stem. These data should be useful for predicting the stability of other hairpins.

Original language	English (US)
Pages (from-to)	11725-11735
Number of pages	11
Journal	Nucleic acids research
Volume	16
Issue number	24
DOIs	https://doi.org/10.1093/nar/16.24.11725
State	Published - Dec 23 1988

Funding

ACKNOWLEDGMENTS We thank Mr. Jerry Haney for his assistance in this study. This work was supported by a grant from the National Institutes of Health (GM36944).

ASJC Scopus subject areas

Genetics

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10.1093/nar/16.24.11725

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abstract = "Fifteen RNA hairpins that share the same stem sequence and have homopolymer loops of A, C and U residues which vary in length from three to nine nucleotides were synthesized and their thermal stabilities determined. Tm varys as a function of loop size but is almost independent of loop composition. Loops of four or five nucleotides are found to be the most stable loop size. This is consistent with the observation that four-membered loops are the most prevalent loop size in 16S-like RNAs. The contribution of each loop to hairpin stability was calculated by subtracting the known contribution of the helical stem. These data should be useful for predicting the stability of other hairpins.",

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AU - Groebe, Duncan R.

AU - Uhlenbeck, Olke C.

N1 - Funding Information: ACKNOWLEDGMENTS We thank Mr. Jerry Haney for his assistance in this study. This work was supported by a grant from the National Institutes of Health (GM36944).

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N2 - Fifteen RNA hairpins that share the same stem sequence and have homopolymer loops of A, C and U residues which vary in length from three to nine nucleotides were synthesized and their thermal stabilities determined. Tm varys as a function of loop size but is almost independent of loop composition. Loops of four or five nucleotides are found to be the most stable loop size. This is consistent with the observation that four-membered loops are the most prevalent loop size in 16S-like RNAs. The contribution of each loop to hairpin stability was calculated by subtracting the known contribution of the helical stem. These data should be useful for predicting the stability of other hairpins.

AB - Fifteen RNA hairpins that share the same stem sequence and have homopolymer loops of A, C and U residues which vary in length from three to nine nucleotides were synthesized and their thermal stabilities determined. Tm varys as a function of loop size but is almost independent of loop composition. Loops of four or five nucleotides are found to be the most stable loop size. This is consistent with the observation that four-membered loops are the most prevalent loop size in 16S-like RNAs. The contribution of each loop to hairpin stability was calculated by subtracting the known contribution of the helical stem. These data should be useful for predicting the stability of other hairpins.

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Characterization of RNA hairpin loop stability

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