The use of BrCN for assembling modified DNA duplexes and DNA-RNA hybrids; comparison with water-soluble carbodiimide.

Nucleic acids research ·Vol. 19 ·No. 11 ·1991-06-11 ·Pages 3067-72

Dolinnaya NG, Sokolova NI, Ashirbekova DT, Shabarova ZA

Abstract

Both cyanogen bromide (BrCN) and 1-ethyl-3-(3'-dimethylaminopropyl) carbodiimide may be used as coupling reagents for the template-directed assembly of DNA duplexes containing the sugar-phosphate backbone modification. Both reagents show similar ligation site structure-specific trend. Practical recommendations are given for selection of the condensing reagent depending on the properties of the duplex. Based on 31P NMR spectroscopy data, a scheme is suggested for BrCN activation of the nucleotide phosphomonoester group. Using both condensing reagents, we studied the condensation of oligonucleotides containing ribo-segments (from mononucleotide residue to full sequence) on the DNA template. Efficiency of the chemical ligation of RNA oligomers was shown to be much lower than that of DNA analogues. The coupling yield depends on the position of the RNA segment in the hybrid duplexes and on the position of the phosphate group in the nick.

MeSH Terms

Base Sequence Carbodiimides/chemistry Cyanogen Bromide/chemistry DNA/chemistry Electrophoresis, Polyacrylamide Gel Magnetic Resonance Spectroscopy Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Heteroduplexes RNA/chemistry Templates, Genetic

Chemicals

Carbodiimides Nucleic Acid Heteroduplexes RNA DNA Cyanogen Bromide

Authors & Affiliations

4 authors, click to expand affiliations / ORCID

Dolinnaya N G

Belozersky Laboratory of Molecular Biology, Moscow State University, USSR.

Sokolova N I

Ashirbekova D T

Shabarova Z A

References (10)

10 references, click to expand

Structural and kinetic aspects of chemical reactions in DNA duplexes. Information on DNA local structure obtained from chemical ligation data.
Nucleic Acids Res. 1991 Jun 11;19(11):3073-80 PMID: 2057363
Chemical reactions within DNA duplexes. Cyanogen bromide as an effective oligodeoxyribonucleotide coupling agent.
FEBS Lett. 1988 May 9;232(1):153-5 PMID: 2835262
Site-directed modification of DNA duplexes by chemical ligation.
Nucleic Acids Res. 1988 May 11;16(9):3721-38 PMID: 3375071
Template-directed polymerization of oligoadenylates using cyanogen bromide.
Biochemistry. 1986 Nov 18;25(23):7423-30 PMID: 3801421
Nonenzymic joining of oligoadenylates on a polyuridylic acid template.
Science. 1976 Apr 2;192(4234):53-4 PMID: 1257755
DNA-like duplexes with repetitions. III. Efficient template-guided chemical polymerization of d(TGGCCAAGCTp).
Nucleic Acids Res. 1981 Nov 11;9(21):5747-61 PMID: 6273807
The reactivity of phosphomono-and phosphodiester groups in oligonucleotides.
Nucleic Acids Res. 1978 Apr;5(4):1253-72 PMID: 206874
Polynucleotide block polymers consisting of a DNA.RNA hybrid joined to a DNA.DNA duplex. Synthesis and characterization of dGn.rCidCk duplexes.
J Biol Chem. 1979 Jun 25;254(12):5410-6 PMID: 447659
A colorimetric method for monitoring activation of Sepharose by cyanogen bromide.
Biochem Biophys Res Commun. 1978 Sep 14;84(1):7-14 PMID: 728136
Proton NMR studies on the covalently linked RNA-DNA hybrid r(GCG)d(TATACGC). Assignment of proton resonances by application of the nuclear Overhauser effect.
Nucleic Acids Res. 1983 Aug 25;11(16):5717-38 PMID: 6193486

Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

0305-1048

DOI

10.1093/nar/19.11.3067

Published

1991-06-11

Pages

3067-72

Language

English

Region

England

NLM ID

0411011

PMCID

PMC328272

Subset

External Links

PubMed source DOI: 10.1093/nar/19.11.3067 PMC Full Text View journal details

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The use of BrCN for assembling modified DNA duplexes and DNA-RNA hybrids; comparison with water-soluble carbodiimide.

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