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Chemical ligation as a method for the assembly of double-stranded nucleic acids: Modifications and local structure studies

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Chemical ligation as a method for the assembly of double-stranded nucleic acids: Modifications and local structure studies

Auteurs : N. G. Dolinnaya [Russie] ; Z. A. Shabarova [Russie]

Source :

Russian Chemical Bulletin [ 1066-5285 ] ; 1996-08-01.

RBID : ISTEX:0A9ED4AFC95F8568EEEF5769C3048C521D60A1C2

English descriptors

Abstract

Abstract: A new procedure was developed as an alternative to the enzymatic assembly of natural and modified double-stranded DNAs using chemical reagent (chemical ligation). BrCN was suggested as an efficient coupling reagent, which induces superfast reactions in DNA duplexes. The physicochemical properties and the structure of new types of DNA duplexes, which are the substrates for chemical ligation, with breaks in phosphodiester chains, including concatemers, were studied. Chemical ligation was applied to prepare biologically active 17–200 base-pair double-stranded DNAs and DNA-RNA block-copolymers, to incorporate various modifications into DNA duplexes including pyrophosphate and phosphoramidate unnatural internucleotide bonds. The unique possibilities of this approach were demonstrated in the development of methods for circularization of oligodeoxy ribonucleotides and assembly of branched DNAs. The structural-kinetic concept of chemicalligation was created and the relationship between the reactivity of interacting groups and sequence-dependent local conformation of the ligation site in B-DNA was established. The lesser efficiency of chemical ligation of RNA fragments in comparison to that of DNA analogs was demonstrated and rationalized. This approach was used as a sensitive monitor of a stable double helix formation and third-strand binding to a DNA duplex.

Url:

https://api.istex.fr/ark:/67375/1BB-GR70375T-R/fulltext.pdf

DOI: 10.1007/BF01457755

Affiliations:

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Le document en format XML

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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA hybrid duplexes</term>
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<term>branched DNAs</term>
<term>chemical ligation</term>
<term>circular DNAs</term>
<term>concatemeric DNAs</term>
<term>modified DNA duplexes</term>
<term>sequence dependent conformation of B-DNA</term>
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<keywords scheme="Teeft" xml:lang="en"><term>Adduct</term>
<term>Analog</term>
<term>Aqueous medium</term>
<term>August</term>
<term>Bioorg</term>
<term>Bioorgan</term>
<term>Brcn</term>
<term>Chem</term>
<term>Chemical assembly</term>
<term>Chemical ligation</term>
<term>Chemical reactions</term>
<term>Chemical reagent</term>
<term>Chemical shifts</term>
<term>Circularization</term>
<term>Complementary template</term>
<term>Complex formation</term>
<term>Concatemeric</term>
<term>Concatemeric complexes</term>
<term>Concatemeric systems</term>
<term>Condensation product</term>
<term>Conformation</term>
<term>Derivative</term>
<term>Dna</term>
<term>Dolinnaya</term>
<term>Double helix</term>
<term>Duplex</term>
<term>Efficient methods</term>
<term>Engl</term>
<term>Febs letters</term>
<term>General regularities</term>
<term>Helix</term>
<term>Hybrid</term>
<term>Hydroxyl</term>
<term>Hydroxyl group</term>
<term>Hydroxyl groups</term>
<term>Initial oligonucleotide</term>
<term>Internucleotide</term>
<term>Internucleotide bond</term>
<term>Internucleotide bonds</term>
<term>Khim</term>
<term>Kinetic parameters</term>
<term>Ligation</term>
<term>Ligation product</term>
<term>Ligation products</term>
<term>Ligation site</term>
<term>Linear precursor</term>
<term>Local conformation</term>
<term>Local structure</term>
<term>Major product</term>
<term>Molecular biology</term>
<term>More reactive</term>
<term>Mutual orientation</term>
<term>Nauk sssr</term>
<term>Nucleic</term>
<term>Nucleic acid</term>
<term>Nucleic acids</term>
<term>Nucleotide</term>
<term>Nucleotide residue</term>
<term>Nucleotide residues</term>
<term>Nucleotide sequence</term>
<term>Oligomer</term>
<term>Oligomers</term>
<term>Oligonucleotide</term>
<term>Oligonucleotide duplexes</term>
<term>Oligonucleotide synthesis</term>
<term>Oligonucleotides</term>
<term>Oretskaya</term>
<term>Phosphate</term>
<term>Phosphate group</term>
<term>Phosphate groups</term>
<term>Phosphodiester</term>
<term>Phosphodiester bond</term>
<term>Phosphodiester bonds</term>
<term>Phosphoramidate bonds</term>
<term>Physicochemical properties</term>
<term>Precursor</term>
<term>Pyrimidine</term>
<term>Pyrimidine strands</term>
<term>Pyrophosphate</term>
<term>Pyrophosphate bond</term>
<term>Rate constants</term>
<term>Reaction products</term>
<term>Reaction site</term>
<term>Reactive</term>
<term>Reagent</term>
<term>Regularity</term>
<term>Ribonucleotide residues</term>
<term>Same time</term>
<term>Secondary structure</term>
<term>Shabarova</term>
<term>Side reaction</term>
<term>Sokolova</term>
<term>Straight line</term>
<term>Thermal stability</term>
<term>Thermodynamic parameters</term>
<term>Third chain</term>
<term>Transl</term>
<term>Triple helices</term>
<term>Tsytovich</term>
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<front><div type="abstract" xml:lang="en">Abstract: A new procedure was developed as an alternative to the enzymatic assembly of natural and modified double-stranded DNAs using chemical reagent (chemical ligation). BrCN was suggested as an efficient coupling reagent, which induces superfast reactions in DNA duplexes. The physicochemical properties and the structure of new types of DNA duplexes, which are the substrates for chemical ligation, with breaks in phosphodiester chains, including concatemers, were studied. Chemical ligation was applied to prepare biologically active 17–200 base-pair double-stranded DNAs and DNA-RNA block-copolymers, to incorporate various modifications into DNA duplexes including pyrophosphate and phosphoramidate unnatural internucleotide bonds. The unique possibilities of this approach were demonstrated in the development of methods for circularization of oligodeoxy ribonucleotides and assembly of branched DNAs. The structural-kinetic concept of chemicalligation was created and the relationship between the reactivity of interacting groups and sequence-dependent local conformation of the ligation site in B-DNA was established. The lesser efficiency of chemical ligation of RNA fragments in comparison to that of DNA analogs was demonstrated and rationalized. This approach was used as a sensitive monitor of a stable double helix formation and third-strand binding to a DNA duplex.</div>
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Chemical ligation as a method for the assembly of double-stranded nucleic acids: Modifications and local structure studies

Chemical ligation as a method for the assembly of double-stranded nucleic acids: Modifications and local structure studies

Source :

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

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Pour mettre un lien sur cette page dans le réseau Wicri