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PMID: 2156233 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Proton exchange and base-pair opening kinetics in 5'-d(CGCGAATTCGCG)-3' and related dodecamers.

Nucleic acids research ·Vol. 18 ·No. 4 ·1990-02-25 ·Pages 821-7

Moe JG, Russu IM

Abstract

We have used nuclear magnetic resonance (NMR) spectroscopy to measure the lifetimes of individual base-pairs in the palindromic DNA oligonucleotide 5'-d(CGCGAATTCGCG)-3' and in three other dodecamers with symmetrical base substitutions in the sites underlined. The resonances of the hydrogen-bonded imino protons in each of the substituted oligomers in the duplex form have been assigned using one dimensional nuclear Overhauser effect (1-D NOE) experiments. The lifetimes have been obtained from the dependence of selective longitudinal relaxation times and linewidths of the imino proton resonances on the concentration of base catalyst (Tris) at 25 degrees C and in the presence of 50 mM NaCl. The lifetimes of the central A.T base-pairs have been found to depend on base sequence. They are greatly increased in the dodecamer 5'-d(CGCAAATTTGCG)-3' which contains an A3T3 tract. The lifetimes of the central A.T base-pairs in 5'-d(CGCGAATTCGCG)-3', 5'-d(CGCTAATTAGCG)-3' and 5'-d(CGCCAATTGGCG)-3' are comparable. In all dodecamers, the lifetime of the A.T base-pair at the 5'-end of the AnTn tract is the shortest. The anomalous opening kinetics of the A.T base-pairs can be correlated to the bending properties of the corresponding sequences.

MeSH Terms
Base Composition Base Sequence DNA Kinetics Magnetic Resonance Spectroscopy/methods Molecular Sequence Data Oligodeoxyribonucleotides/chemical synthesis Protons Structure-Activity Relationship Tromethamine
Chemicals
Oligodeoxyribonucleotides Protons Tromethamine DNA
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Moe J G
Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06457.
Russu I M
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/18.4.821
Published
1990-02-25
Pages
821-7
Language
English
Region
England
NLM ID
0411011
PMCID
PMC330333
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/18.4.821 PMC Full Text View journal details
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