Imino proton exchange and base-pair kinetics in RNA duplexes

K. Snoussi, J. L. Leroy

Research output: Contribution to journalArticle

Abstract

Using NMR magnetization transfer from water and ammonia-catalyzed exchange of the imino proton, we have measured the base-pair lifetimes and the dissociation constants of six RNA duplexes: [r(CGCGAUCGCG)]2, [r(CGCGAAUUCGCG)]2, [r(CCUUUCGAAAGG)]2, [r(CGCACGUGCG)]2, [r(GGU8-C C)·r(GGA8CC)], and [poly(rA)·poly(rU)], and we compare them with those of their DNA homologues. As predicted by a two-state (closed/open) model of the pair, the imino proton exchange times decrease linearly vs. the inverse of catalyst concentration. As in DNA duplexes, base pairs open one at a time, and the kinetics is in most cases insensitive to the nature of the adjacent residues. The lifetime of the r(G·C) pairs, 40 to 50 ms, is longer than that of the equivalent in the corresponding oligodeoxynucleotides, and the dissociation constants, about 10-7, are slightly smaller. The r(A·U) opening and closing rates are much larger than those of the d(A·T) pairs, but the stabilities are comparable.

Original languageEnglish (US)
Pages (from-to)8898-8904
Number of pages7
JournalBiochemistry®
Volume40
Issue number30
DOIs
StatePublished - Jul 31 2001
Externally publishedYes

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Base Pairing
Protons
Poly A-U
RNA
Kinetics
Oligodeoxyribonucleotides
DNA
Ammonia
Magnetization
Nuclear magnetic resonance
Catalysts
Water
2'-deoxythymidylyl-(3'-5')-2'-deoxyadenosine

ASJC Scopus subject areas

  • Biochemistry

Cite this

Imino proton exchange and base-pair kinetics in RNA duplexes. / Snoussi, K.; Leroy, J. L.

In: Biochemistry®, Vol. 40, No. 30, 31.07.2001, p. 8898-8904.

Research output: Contribution to journalArticle

Snoussi, K. ; Leroy, J. L. / Imino proton exchange and base-pair kinetics in RNA duplexes. In: Biochemistry®. 2001 ; Vol. 40, No. 30. pp. 8898-8904.
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