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. 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.
15 references, click to expand
-
Conformation of the anticodon loop intRNA.Nature. 1967 Aug 19;215(5103):817-21 PMID: 6049728
-
Thermodynamic studies of RNA stability.J Biomol Struct Dyn. 1984 Mar;1(5):1229-42 PMID: 6086053
-
Stability of RNA hairpin loops: A 6 -C m -U 6 .J Mol Biol. 1973 Feb 5;73(4):483-96 PMID: 4715013
-
Free energy of imperfect nucleic acid helices. II. Small hairpin loops.J Mol Biol. 1973 Feb 5;73(4):497-511 PMID: 4715014
-
Sequences of controlling regions of the lactose operon.Cold Spring Harb Symp Quant Biol. 1974;38:845-55 PMID: 4598642
-
Destabilization of secondary structure in 16S ribosomal RNA by dimethylation of two adjacent adenosines.Nucleic Acids Res. 1981 Sep 11;9(17):4413-22 PMID: 7029465
-
A carbon-13 nuclear magnetic resonance study of the 3'-terminus of 16S ribosomal RNA of Escherichia coli specifically labeled with carbon-13 in the methylgroups of the m6(2)Am6(2)A sequence.Nucleic Acids Res. 1982 Jul 24;10(14):4237-45 PMID: 6750555
-
Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp.Biochemistry. 1983 Jan 18;22(2):256-63 PMID: 6824629
-
Effects of terminal mismatches on RNA stability: thermodynamics of duplex formation for ACCGGGp, ACCGGAp, and ACCGGCp.Biochemistry. 1985 Jul 16;24(15):3987-91 PMID: 2413881
-
Comparative anatomy of 16-S-like ribosomal RNA.Prog Nucleic Acid Res Mol Biol. 1985;32:155-216 PMID: 3911275
-
Hairpin and duplex formation of the DNA octamer d(m5C-G-m5C-G-T-G-m5C-G) in solution. An NMR study.Nucleic Acids Res. 1986 May 27;14(10):4187-96 PMID: 3714474
-
Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid.Biochemistry. 1987 Jul 14;26(14):4554-8 PMID: 2444250
-
Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates.Nucleic Acids Res. 1987 Nov 11;15(21):8783-98 PMID: 3684574
-
CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes.Proc Natl Acad Sci U S A. 1988 Mar;85(5):1364-8 PMID: 2449689
-
Association of complementary oligoribonucleotides in aqueous solution.Biochemistry. 1968 Sep;7(9):3164-78 PMID: 4879239
Contact
No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong
Qilu Normal University · Genelibs Bioinformatics Lab
750 Shunhua Rd, Jinan
2F, Bldg F, University Science Park
Tel: 0531-88819269
WeChat Official Account
Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.
Business Email
E-mail: [email protected]
Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2
