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Oligonucleotide derivatives in nucleic acid hybridization analysis. III. Synthesis and investigation of properties of oligonucleotides, bearing bifunctional non-nucleotide insertion

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Abstract

Non-nucleotide phosporamidites were synthetized, having a branching backbone with different positions for functional groups. Phosphoramidite monomers obtained contain intercalator moiety, 6-chloro-2-methoxyacridine, and additional hydroxyl residue protected with dimethoxytrityl group or with the tert-butyldimethylsilyl group for post-synthetic modification. Oligothymidilates containing one or more modified units in different positions of the sequence were synthesized. The melting point and thermodynamic parameters of the formation of complementary duplexes formed by modified oligonucleotides were defined (change in enthalpy and entropy). The introduction of intercalating residue causes a significant stabilization of DNA duplexes. It is shown that the efficiency of the fluorescence of acridine residue in the oligonucleotide conjugate significantly changes upon hybridization with DNA.

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Abbreviations

CEP-2:

cyanoethoxy diisopropylaminophosphinyl

DMAP:

4-N,N-dimethylaminopyridine

DIPEA:

diisopropylethylamine

DMTr:

dimethoxytrityl

TBDMS:

tret-butyldimethylsilyl

TEA:

triethylamine

Tz:

1H-tetrazole

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Authors and Affiliations

  1. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, pr. Akademika Lavrent’eva 8, Novosibirsk, 630090, Russia

    M. S. Kupryushkin & D. V. Pyshnyi

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  1. M. S. Kupryushkin
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  2. D. V. Pyshnyi
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Correspondence to D. V. Pyshnyi.

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Original Russian Text © M.S. Kupryushkin, D.V. Pyshnyi, 2012, published in Bioorganicheskaya Khimiya, 2012, Vol. 38, No. 6, pp. 706–720.

The prefix “d” in the notation of oligodeoxyribonucleotides is omitted.

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Kupryushkin, M.S., Pyshnyi, D.V. Oligonucleotide derivatives in nucleic acid hybridization analysis. III. Synthesis and investigation of properties of oligonucleotides, bearing bifunctional non-nucleotide insertion. Russ J Bioorg Chem 38, 625–638 (2012). https://doi.org/10.1134/S106816201206009X

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  • DOI: https://doi.org/10.1134/S106816201206009X

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