Mapping of T7 RNA polymerase active site with novel reagents – oligonucleotides with reactive dialdehyde groups

Tunitskaya, V. L.; Rusakova, E. E.; Memelova, L. V.; Kochetkov, S. N.; Aerschot, Arthur Van; Herdewijn, Piet; Efimtseva, Ekaterina V.; Ermolinsky, Boris S.; Mikhailov, Sergey N.

doi:10.1016/s0014-5793(98)01625-1

Cited by 24 publications

(14 citation statements)

References 17 publications

(31 reference statements)

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“…ODNs containing 3'aldehyde groups were prepared on modified support. 15A) [63]. The ODN-aldehyde was conjugated to alkaline phosphatase to obtain the ODN-enzyme conjugate that showed unaltered hybridisation properties.…”

Section: Conjugation Via Reductive Amination Hydrazone or Oxime Linkagementioning

confidence: 99%

Chemical Strategies for Oligonucleotide-Conjugates Synthesis

Defrancq

Singh²,

Spinelli

2008

COC

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Oligonucleotide conjugates have found numerous applications in the field of diagnostics and therapeutics. Structurally diverse oligonucleotide conjugates have been prepared and evaluated for various applications. Research efforts have focused on the development of synthetic procedures to accomplish efficient oligonucleotide conjugation with different target molecules. Both on-support and solution-phase coupling procedures have been used to conjugate oligonucleotides. This review gives an account of major synthetic approaches available to prepare covalent oligonucleotide conjugates with diverse target molecules.

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Section: Conjugation Via Reductive Amination Hydrazone or Oxime Linkagementioning

confidence: 99%

Chemical Strategies for Oligonucleotide-Conjugates Synthesis

Defrancq

Singh²,

Spinelli

2008

COC

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“…It was shown that modified ON formed stable complexes with complementary DNA ( Tm= 0-3°C) [93]. DNA duplexes bearing extra dialdehyde groups were used for affinity modification of T7 RNA polymerase [94] and restriction-modification enzymes EcoRII and MvaI [93,95]. The data obtained revealed the localization of DNA-binding sites of these enzymes.…”

Section: Oligonucleotides Containing Disac-charide Nucleosidesmentioning

confidence: 99%

“…To study T7 RNA polymerase and its mutants, modified ON duplexes, containing the T7 RNA polymerase promoter and five transcript base pairs were used [94]. It was shown that duplexes bearing 2 -O--D-ribofuranosylcytidine or its oxidized derivative were competitive inhibitors of T7 RNA polymerase, the values of binding constants being 2-3.5 times lower than in the case of the reference unmodified duplex.…”

Section: Oligonucleotides Containing Disac-charide Nucleosidesmentioning

confidence: 99%

“…It was shown that duplexes bearing 2 -O--D-ribofuranosylcytidine or its oxidized derivative were competitive inhibitors of T7 RNA polymerase, the values of binding constants being 2-3.5 times lower than in the case of the reference unmodified duplex. Much higher yield up to 50% of such conjugation was observed in the case of T7 RNA polymerase [94]. The developed methods of introduction of extra functional groups into ON, such as cis-diol and aldehyde groups, open new possibilities for functionalization of nucleic acids.…”

Section: Oligonucleotides Containing Disac-charide Nucleosidesmentioning

confidence: 99%

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Disaccharide Nucleosides and their Incorporation into Oligonucleotides

Efimtseva¹,

Kulikova²,

Mikhailov³

2007

COC

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The review summarizes structural features, biological activity and synthetic methods of disaccharide nucleosides. In the first part the structures of natural disaccharide nucleosides are presented. The consequent part deals with general methods of synthesis of these compounds -formation of new N-and O-glycosidic bonds. Recent achievements in the preparation of disaccharide nucleosides from natural nucleosides are discussed. The last part is devoted to the synthesis and properties of oligonucleotides containing disaccharide nucleosides.Disaccharide nucleosides belong to an important group of natural compounds forming poly(ADP-ribose) and found in tRNA, antibiotics, and other physiologically active compounds. To date about a hundred disaccharide nucleoside and related derivatives have been isolated from various natural sources. These compounds contain an extra carbohydrate residue linked to one of the nucleoside hydroxyl groups via an O-glycosidic bond. The presence of a disaccharide residue and a heterocyclic base makes their properties similar to those of carbohydrates and nucleosides. These compounds manifest a broad spectrum of biological (including antibacterial, fungicidal, herbicidal, antitumour and antiviral) activities. The review by Lerner [1] published in 1991 provides a detailed description of the structures of disaccharide nucleoside antibiotics and the approaches to their synthesis. Some of the published data on the synthesis of complex nucleoside antibiotics were summarized by Knapp [2]. Since that time, many new publications devoted to this problem have appeared in the current literature. In our recent publiccations physicochemical properties [3], structure and general synthetic approaches to the synthesis [4] of disaccharide nucleosides were reviewed. Here we describe structural peculiarities of disaccharide nucleosides and summarize our recent data on their synthesis and incorporation into oligonucleotides (ONs). NATURAL DISACCHARIDE NUCLEOSIDESThe structures of disaccharide nucleosides are extremely diverse [5,6] and their elucidation is a rather complicated task. In addition to a heterocyclic base and two mono-saccharide residues, these compounds contain various functional substituents, such as acyl and alkyl groups as well as phosphate and sulfate residues, fatty acids, amino acids, peptides and additional sugars. Their degradation by acid and alkaline hydrolysis or methanolysis, periodate oxidation and subsequent reduction yields fragments the structures of which can be established by physicochemical methods. At present, the structures of many complex antibiotics are determined mainly by NMR spectroscopy and mass spectrometry.According to their structure natural disaccharide nucleosides may be divided into three main groups. Disaccharide nucleosides belonging to the first two groups contain natural purine nucleoside. In the first group additional ribofuranosyl residue is attached via O-glycosidic bond to the adenosine or guanosine. Most of these derivatives were found in biopolymers. 2 (3 )-O-...

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“…Oligonucleotides 148 containing a dialdehyde group in the 2 H -position were used for the study of protein-NA interactions with restriction endonuclease EcoRII, DNA-methyltransferases EcoRII, 371 MvaI (see Refs 372 ± 374) and T7 RNA polymerase. 373,375 The use of modified oligonucleotides permits one to inhibit the enzyme activity without any effect on the ability of enzymes to bind the NA substrate. The interaction of oligonucleotides 148 with enzymes occurs in a selective manner and involves the e-amino groups of lysine.…”

Section: B Studies Of Dna7protein Interactionsmentioning

confidence: 99%

Nucleosides and oligonucleotides containing 2'-reactive groups: synthesis and applications

Zatsepin¹,

Романова²,

Oretskaya³

2004

Russ. Chem. Rev.

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The known methods for the synthesis of 2 The known methods for the synthesis of 2 H -functional--functionalised nucleosides, oligonucleotides and their conjugates are sys-ised nucleosides, oligonucleotides and their conjugates are systematised. The applications of 2 tematised. The applications of 2 H -modified nucleosides and -modified nucleosides and oligonucleotides are discussed. The bibliography includes 451 oligonucleotides are discussed. The bibliography includes 451 references references. .

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Mapping of T7 RNA polymerase active site with novel reagents – oligonucleotides with reactive dialdehyde groups

Cited by 24 publications

References 17 publications

Chemical Strategies for Oligonucleotide-Conjugates Synthesis

Chemical Strategies for Oligonucleotide-Conjugates Synthesis

Disaccharide Nucleosides and their Incorporation into Oligonucleotides

Nucleosides and oligonucleotides containing 2'-reactive groups: synthesis and applications

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