Characterization of RNA hairpin loop stability

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 varies as a function of loop size but is almost independent of loop composition....

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Bibliographic Details
Published in:Nucleic acids research 1988-12, Vol.16 (24), p.11725-11735
Main Authors: GROEBE, D. R, UHLENBECK, O. C
Format: Article
Language:English
Subjects:
Analytical, structural and metabolic biochemistry
Base Composition
Base Sequence
Biological and medical sciences
Fundamental and applied biological sciences. Psychology
Nucleic Acid Conformation
Nucleic Acid Denaturation
Nucleic acids
Phylogeny
Rna, ribonucleoproteins
RNA, Ribosomal - chemical synthesis
RNA, Ribosomal - isolation & purification
Templates, Genetic
Thermodynamics
Transcription, Genetic
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Summary: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 varies 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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/16.24.11725