Oligonucleotide derivatives bearing reactive and stabilizing groups attached to C5 of deoxyuridine

Левина, А. С.; Tabatadse, David R.; Khalimskaya, L. M.; Prichodko, Tatjana A.; Shishkin, G. V.; Alexandrova, L. А.; Zarytova, Valentina P.

doi:10.1021/bc00023a003

Cited by 30 publications

(17 citation statements)

References 17 publications

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“…The desired 5-alkyloxymethyl substituted analogues 1 – 3 were then prepared by coupling with the corresponding 1-alcohol [51] and subsequent deprotection of the 4’-hydroxy group to provide targets 4 – 6 (Scheme 2).…”

Section: Resultsmentioning

confidence: 99%

Novel 5′-Norcarbocyclic Pyrimidine Derivatives as Antibacterial Agents

et al. 2018

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A series of novel 5′-norcarbocyclic derivatives of 5-alkoxymethyl or 5-alkyltriazolyl-methyl uracil were synthesized and the activity of the compounds evaluated against both Gram-positive and Gram-negative bacteria. The growth of Mycobacterium smegmatis was completely inhibited by the most active compounds at a MIC99 of 67 μg/mL (mc2155) and a MIC99 of 6.7–67 μg/mL (VKPM Ac 1339). Several compounds also showed the ability to inhibit the growth of attenuated strains of Mycobacterium tuberculosis ATCC 25177 (MIC99 28–61 μg/mL) and Mycobacterium bovis ATCC 35737 (MIC99 50–60 μg/mL), as well as two virulent strains of M. tuberculosis; a laboratory strain H37Rv (MIC99 20–50 μg/mL) and a clinical strain with multiple drug resistance MS-115 (MIC99 20–50 μg/mL). Transmission electron microscopy (TEM) evaluation of M. tuberculosis H37Rv bacterial cells treated with one of the compounds demonstrated destruction of the bacterial cell wall, suggesting that the mechanism of action for these compounds may be related to their interactions with bacteria cell walls.

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Section: Resultsmentioning

confidence: 99%

Novel 5′-Norcarbocyclic Pyrimidine Derivatives as Antibacterial Agents

et al. 2018

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“…Perfluoroarylazide derivatives of hexadecathymidylate were synthesized as described (Levina et al, 1993b). Molar extinc¬ tion coefficients (e) of oligonucleotides were estimated at 260 nm according to Cantor and Tinoco (1965).…”

Section: Methodsmentioning

confidence: 99%

“…Molar extinc¬ tion coefficients (e) of oligonucleotides were estimated at 260 nm according to Cantor and Tinoco (1965). For hexade¬ cathymidylate derivatives, this was calculated as a sum of e val¬ ues for unmodified oligonucleotide and the conjugated group (Levina et al, 1993b (1-12, 15-26) The reaction mixtures before and after piperidine treatment, respectively. (13, 14) A + G sequenc¬ ing reaction of strands II and III, respectively.…”

Section: Methodsmentioning

confidence: 99%

Sequence-Specific Photomodification of Single-Stranded and Double-Stranded DNA Fragments by Oligonucleotide Perfluoroarylazide Derivative

Левина¹,

Tabatadze²,

Dobrikov³

et al. 1996

Antisense and Nucleic Acid Drug Development

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A highly efficient, sequence-specific photomodification of single-stranded (ss) and double-stranded (ds) DNA fragments was carried out with a hexadecathymidilate derivative, R approximately p(T)16 (R-perfluoroarylazido group), using 27-base pair DNA fragments as a target [table: see text] The main points of modification were G7 and G24 of the A-rich strand of the ss target and G7 and G22 of the A-rich and T-rich strands, respectively, for the ds target. The extent of photomodification was 60%-77% for ss DNA and 10%-53% for ds DNA depending on the reaction conditions. Photomodification increased in buffer with a high ionic strength (1.0 M) and at low temperature (4 degrees C) when presumably the triplexes were more stable.

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“…This is an active intermediate which is able to provide a high yield of cross-links with both nucleic acids and proteins under a short (less than 1 min) irradiation, using commercially available UV-lamps. [47][48][49] The excellent cross-linking properties of perfluorated aryl azides relates to the higher reactivity of the respective nitrenes as compared to those of the unfluorinated aryl azides. 50 Secondly, the ATB group can be introduced at various nucleotide positions not involved in classical Watson-Crick base-pairing, namely, at the C5 of uridines, N7 of guanosines or C8 of adenosines, in addition to the 59-or 39-terminal phosphates (Fig.…”

Section: Derivatives Of Oligoribonucleotides Modified With Perfluorop...mentioning

confidence: 99%

Photoactivatable RNA derivatives as tools for studying the structural and functional organization of complex cellular ribonucleoprotein machineries

Graifer

Карпова

2013

RSC Adv.

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Ribonucleic acids (RNAs) are biopolymers that play key roles in many processes crucial for the life of cells.Functions of RNAs are generally mediated by their specific interactions with proteins and ribonucleoproteins (supramolecular RNA-protein complexes) that take place within complexes of RNA ligands with proteins or ribonucleoproteins. These interactions are defined by the molecular environment of the RNA ligand in the complex. A beneficial approach for studying such complexes involves site-directed crosslinking: RNA derivatives that contain chemically reactive groups form covalent bonds (cross-links) with those structural elements of the protein or ribonucleoprotein that neighbor the RNA ligand. Such RNA derivatives have been successfully used to study the interaction of messenger RNA (mRNA) with the protein synthesis machinery. By applying this approach to studies of the protein translation machinery of higher organisms, chemically reactive RNA derivatives have provided unique information that could not have been obtained by other approaches to date. This article presents a brief review of the types of RNA derivatives used as mRNA analogs, and their structures and synthesis, together with methods for identification of cross-linking targets. Furthermore, we summarize current data on mRNA interactions occurring during the course of protein synthesis in higher organisms.

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Oligonucleotide derivatives bearing reactive and stabilizing groups attached to C5 of deoxyuridine

Cited by 30 publications

References 17 publications

Novel 5′-Norcarbocyclic Pyrimidine Derivatives as Antibacterial Agents

Novel 5′-Norcarbocyclic Pyrimidine Derivatives as Antibacterial Agents

Sequence-Specific Photomodification of Single-Stranded and Double-Stranded DNA Fragments by Oligonucleotide Perfluoroarylazide Derivative

Photoactivatable RNA derivatives as tools for studying the structural and functional organization of complex cellular ribonucleoprotein machineries

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