Skip to main content
SpringerLink
Log in

Reactive oligonucleotide derivatives as gene-targeted biologically active compounds and affinity probes

  • Published:
Genetica Aims and scope Submit manuscript

Abstract

Development of efficient methods for synthesis of oligonucleotides and oligonucleotide analogs has opened up the possibility of designing a broad spectrum of affinity reagents for specific modification of nucleic acids and proteins. These affinity reagents are used for investigation of the topology of ribosomes and nucleic acid polymerases. Oligonucleotides and their analogs are already used for suppression of specific gene expression and for elucidation of the physiological role of their products. Oligonucleotide derivatives appear to offer considerable promise as potential gene-targeted drugs such as antivirals and specific inhibitors of oncogene expression.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Abramova, T. T., Blinov, V. M., Vlassov, V. V., Gorn, V. V., Zarytova, V. F., Ivanova, E. M., Konevets, D. A., Plyasunova, O. A., Pokrovski, A. G., Sandakhchiev, L. S., Svinarchuk, F. P., Starostin, V. P. & Chaplygina, S. P., 1990. Inhibition of HIV reproduction in cell culture by antisense oligonucleotide derivatives. Doklady Acad. Nauk SSR 312: 1259–1262.

    Google Scholar 

  • Belikova, A. M., Zarytova, V. F. & Grineva, N. I., 1967. Synthesis of ribonucleosides and diribonucleoside phosphates containing 2-chloroethylamine and nitrogen mustard residues. Tetrahedron Lett. 3557–3562.

  • Boiziau, C., Boutorine, A. S., Loreau, N., Verspieren, P., Thuong, N. T. & Toulme, J. J., 1991. Effect of antisense oligonucleotides linked to alkylating agent on in vitro translation of rabbit β-globin and Trypanosoma brucei mRNAs. Nucleosides & Nucleotides (in press).

  • Boutorin, A.S., Gus'kova, L. V., Ivanova, E. M., Kobetz, N. D., Zarytova, V. F., Ryte, A. S., Yurchenko, L. V. & Vlassov, V. V., 1989. Synthesis of alkylating oligonucleotide derivatives containing cholesterol or phenazinium residues at the 3′-terminus and their interaction with DNA within mammalian cells. FEBS Lett. 254: 129–132.

    Google Scholar 

  • Brossalina, E. B., Demchenko, E. N., Vlassov, V. V. & Mamaev S. V., 1991a. Sequence-specific alkylation of dsDNA with derivatives of pyrimidine oligonucleotides conjugated to 2-chloroethylamine groups. Antisense Res. Devel. (in press).

  • Brossalina, E. B., Demchenko, E. N., Mamaev S. V. & Vlassov, V. V., 1991b. Interaction of alkylating derivatives of homopyrimidine and homopurine oligonucleotide with dsDNA. Antisense Res. Devel. (in press).

  • Chu, B. C. F. & Orgel, L. E., 1989. Inhibition of DNA synthesis by cross-linking the template to platinum-thiol derivatives of complementary oligodeoxynucleotides. Nucl. Acids Res. 17: 4783–4798.

    Google Scholar 

  • Cohen, J. S. (ed.), 1989. Oligonucleotides. Antisense Inhibitors of Gene Expression. MacMillan Press, London.

    Google Scholar 

  • Degols, G., Leonetti, J.-P. & Lebleu, B., 1991. Antisense oligonucleotides as pharmacological modulators of gene expression. In: R. L. Tuliano (ed.) Targeted Drug Delivery, Springer Verlag (in press).

  • Dervan, P. B., 1989. Oligonucleotide recognition of double-helical DNA by triple-helix formation. In: J. S. Cohen (ed.) Oligonucleotides. Antisense Inhibitors of Gene Expression. MacMillan Press, London, pp. 197–210.

    Google Scholar 

  • Goodchild, J., 1990. Conjugates of oligonucleotides and modified oligonucleotides: a review of their synthesis and properties. Bioconjugate Chem. 1: 165–191.

    Google Scholar 

  • Graifer, D. M., Zenkova, M. A., Malygin, A. A., Mamaev, S. V., Mundus, D. A. & Karpova, G. G., 1990. Identification of a site on 18S rRNA of human placenta ribosomes in the region of the mRNA binding center. J. Mol. Biol. 214: 121–128.

    Google Scholar 

  • Helene, C. & Toulme, J.-J., 1989. Control of gene expression by oligodeoxynucleotides covalently linked to intercalating agents and nucleic acid-cleaving reagents. J. S. Cohen (ed.) Oligonucleotides. Antisense Inhibitors of Gene Expression. MacMillan Press, London, pp. 137–172.

    Google Scholar 

  • Helene, C. & Toulme, J.-J., 1990. Specific regulation of gene expression by antisense, sense and antigene nucleic acids. Biochim. Biophys. Acta 1049: 99–125.

    Google Scholar 

  • Kabanov, A. V., Vinogradov, S. V., Ovcharenko, A. V., Krivinos, A. V., Melik-Nubarov, N. S., Kiselev, V. I. & Severin, E. S., 1990. A new class of antivirals: antisense oligonucleotides combined with a hydrophobic substituent effectively inhibit influenza virus reproduction and synthesis of virus-specific proteins in MDCK cells. FEBS Lett. 259: 327–330.

    Google Scholar 

  • Karpova, G. G., Knorre, D. G., Ryte, A. S. & Stephanovich, L. E., 1980. Selective alkylation of poly(A) tracts of RNA inside the cell with the derivatives of ethyl ester of oligothymidilate bearing 2-chloroethylamino group. FEBS Lett. 122: 21–24.

    Google Scholar 

  • Kean, J. M., Murakami, A., Blake, K. R., Cushman, C. D. & Miller, P. S., 1988. Photochemical cross-linking of psoralenderivatized oligonucleoside methylphosphonates to rabbit globin messenger RNA. Biochemistry 27: 9113–9121.

    Google Scholar 

  • Knorre, V. L., Perminova, L. V., Baranova, L. V., Godovokov, A. A., Savinkova, L. K. & Salganik, R. I., 1989a. Oligonucleotides with highly reactive groups selectively bound by E.coli RNA polymerase: identification of the enzyme subunits interacting with them, and the competitive inhibition of transcription. Izvestija Sibirskogo Otdelenija Akademii Nauk SSSR, biology issue, No 2: 98–104.

  • Knorre, D. G., Lavrik, O. I. & Nevinsky, G. A., 1988. Proteinnucleic acid interaction in reactions catalysed with DNA polymerases. Biochimie 70: 655–661.

    Google Scholar 

  • Knorre, D. G., Vlassov, V. V. & Zarytova, V. F., 1989b. Oligonucleotides linked to reactive groups. In: J. S. Cohen (ed) Oligonucleotides. Antisense Inhibitors of Gene Expression. MacMillan Press, London, pp. 173–196.

    Google Scholar 

  • Knorre, D. G., Vlassov, V. V., Zarytova, V. F. & Lebedev, A. V., 1989c. Reactive oligonucleotide derivatives as tools for site specific modification of biopolymers. In: M. B. Volpin (ed), Soviet Scientific Reviews. Harwood Academic Publishers Gmbh, Amsterdam, pp. 271–339.

    Google Scholar 

  • Knorre, D. G. & Vlassov, V. V., 1990. Antisense oligonucleotide derivatives as gene-targeted drugs. Biomed. Sci. 1: 334–343.

    Google Scholar 

  • Kolocheva, T. I., Nevinsky, G. A., Volchkova, V. A., Levina, A. S., Khomov, V. V. & Lavrik, O. I., 1989. DNA polymerase I (Klenow fragment): role of the structure and length of a template in enzyme recognition. FEBS Lett. 248: 97–100.

    Google Scholar 

  • Kutyavin, I. V., Podyminogin, M. A., Bazhina, Yu. N., Fedorova, O. S., Knorre, D. G., Levina, A. S., Mamaev, S. V. & Zarytova, V. F., 1988. N-(2-Hydroxyethyl)phenazinium derivatives of oligonucleotides as effectors of the sequence-specific modification of nucleic acids with reactive oligonucleotide derivatives. FEBS Lett. 238: 35–38.

    Google Scholar 

  • Lee, B. L., Blake, K. R. & Miller, P. S., 1988. Interaction of psoralen-derivatized oligodeoxyribonucleoside methylphosphonates with synthetic DNA containing a promoter for T7 RNA polymerase. Nucl. Acids Res. 16: 10681–10697.

    Google Scholar 

  • Lee, B. L., Murakami, A., Blake, K. R., Lin, S.-B. & Miller, P. S., 1987. Interaction of psoralen-derivatized oligodeoxyribonucleoside methylphosphonates with single-stranded DNA. Biochemistry 27: 3197–3203.

    Google Scholar 

  • Leonetti, J.-P., Degols, G. & Lebleu, B., 1990. Biological activity of oligonucleotide-poly (L-lysine) conjugates: mechanism of cell uptake. Bioconjugate Chem. 1: 149–153.

    Google Scholar 

  • Leonetti, J.-P., Machy, P., Degols, G., Lebleu, B. & Leserman, L., 1990. Antibody-targeted liposomes containing oligodeoxyribonucleotides complementary to viral RNA selectively inhibit viral replication. Proc. Natl. Acad. Sci. USA 87: 2448–2451.

    Google Scholar 

  • Liebhaber, S. A., Cash, F. E. & Shakin, S. H., 1984. Translationally associated helix-destabilizing activity in rabbit reticulocyte lysate. J. Biol. Chem. 259: 15597–15602.

    Google Scholar 

  • Letsinger, R. L., Zhang, G., Sun, D. K., Ikeuchi, T. & Sarin, P. S., 1989. Cholesteryl-conjugated oligonucleotides: synthesis, properties, and activity as inhibitors of replication of human immunodeficiency virus in cell culture. Proc. Natl. Acad. Sci. USA 86: 6553–6556.

    Google Scholar 

  • Melton, D. A. (ed.), 1988. Antisense RNA and DNA, New York: Cold Spring Harbor Laboratory Press.

    Google Scholar 

  • Miller, P. S., 1989. Non-ionic antisense oligonucleotides. In: J. S. Cohen (ed.) Oligonucleotides. Antisense Inhibitors of Gene Expression. MacMillan Press, London, pp. 79–95.

    Google Scholar 

  • Neckers, L. M., 1989. Antisense oligodeoxynucleotides as a tool for studying cell regulation: mechanism uptake and application to the study of oncogene function. In: J. S. Cohen (ed.) Oligonucleotides. Antisense Inhibitors of Gene Expression. MacMillan Press, London, pp. 211–231.

    Google Scholar 

  • Paoletti, C., 1988. Anti-sense oligonucleotides as potential antitumor agents: prospective views and preliminary results. Anticancer Design 2: 325–331.

    Google Scholar 

  • Pieles, U. & English, U., 1989. Psoralen covalently linked to oligodeoxyribonucleotides: synthesis, sequence specific recognition of DNA and photo-cross-linking to pyrimidine residues of DNA. Nucl. Acids Res. 17: 285–299.

    Google Scholar 

  • Pogodina, V. V., Frolova, T. V., Abramova, T. V., Vlassov, V. V., Ivanova, E. M., Kutiavin, I. V., Pletnev, A. G. & Yakubov, L. A., 1988. Derivatives of oligonucleotides complementary to the RNA of the Tick-borne encephalitis virus inhibit multiplication of the virus in cell culture. Doklady Akademii Nauk SSSR (Russ.) 301: 1257–1260.

    Google Scholar 

  • Pogodina, V. V., Frolova, T. V., Frolova, M. P., Abramova, T. V., Vlassov, V. V., Knorre, D. G., Pletnev, A. G. & Yakubov, L. A., 1989. Oligonucleotides complementary to the RNA of the Tickborne encephalitis virus prevents development of the infection in mice. Doklady Akademii Nauk SSSR (Russ.) 308: 237–239.

    Google Scholar 

  • Povsic, T. J. & Dervan, P. B., 1989. Triple helix formation by oligonucleotides on DNA extended to the physiological pH range. J. Am. Chem. Soc. 111: 3059–3061.

    Google Scholar 

  • Savinkova, P. K., Sokolenko, A. A., Gorn, V. V., Tulokhomov, I. I., Salganik, R. I., Sedova, V. M. & Vorob'ev, V. I., 1991. Binding by human RNA polymerase II of oligonucleotides identical to regulatory elements of eukaryotic gene promoters. Doklady Akad. Nauk SSSR 317: No. 6.

  • Shea, R. G., Marsters, J. C. & Bischofberger, N., 1990. Synthesis, hybridization properties and antiviral activity of lipid-oligodeoxynucleotide conjugates. Nucl. Acids Res. 18: 3777–3783.

    Google Scholar 

  • Salganic, R. I., Dianov, G. L., Ovchinnikova, L. P., Voronina, E. N., Kokoza, E. B. & Mazin, A. V., 1980. Gene-directed mutagenesis in bacteriophage T7 provided by polyalkylating RNAs complementary to selected DNA sites. Proc. Natl. Acad. Sci. U.S.A. 77: 2796–2800.

    Google Scholar 

  • Strobel, S. A. & Dervan, P. B., 1990. Site-specific cleavage of a yeast chromosome by oligonucleotide-directed triple-helix formation. Science 249: 73–75.

    Google Scholar 

  • Tidd, D. M., 1990. A potential role for antisense oligonucleotide analogues in the development of oncogene targeted cancer chemotherapy. Anticancer Res. 10: 1169–1182.

    Google Scholar 

  • Tsarev, I. G., Mustaev, A. A., Zaychikov, E. F., Alikina, T. Yu., Venyaminova, A. G. & Repkova, M. N., 1990. Highly selective affinity labelling of E.coli RNA polymerase promoter complex with reactive derivatives of oligonucleotide primers of various chemical specificities. Bioorg. Khim. (Russ.) 16: 765–779.

    Google Scholar 

  • Uhlmann, E. & Peyman, A., 1990. Antisense oligonucleotides: a new therapeutic principle. Chem. Rev. 90: 543–584.

    Google Scholar 

  • Vladimirov, S. N., Babkina, G. T., Venijaminova, A. G., Gimautdinova, O. I., Zenkova, M. A. & Karpova, G. G., 1990. Structural arrangement of the decoding site of E.coli ribisomes as revealed from the data on affinity labelling of ribosomes by analogs-of mRNA derivatives of oligoribonucleotides. Biochim. Biophys. Acta 1048: 245–256.

    Google Scholar 

  • Vlassov, V. V., Gorn, V. V., Ivanova, E. M., Kazakov, S. A. & Mamaev, S. V., 1983. Complementary addressed modification of oligonucleotide d(pGpGpCpGpGpA) with platinum derivative of oligonucleotide d(pTpCpCpGpCpCpTpTpT). FEBS Lett. 162: 286–289.

    Google Scholar 

  • Vlassov, V. V., Godovikov, A. A., Kobetz, N. D., Ryte, A. S., Yurchenko, L. V. & Bukrinskaya, A. G., 1986a. Nucleotide and oligonucleotide derivatives as enzyme and nucleic acid targeted irreversible inhibitors. Biochemical aspects. Advances in enzyme regulation 24: 301–320.

    Google Scholar 

  • Vlassov, V. V., Zaryotova, V. F., Kutiavin, I. V., Mamaev, S. V. & Podyminogin, M. A., 1986b. Complementary addressed modification and cleavage of a single stranded DNA fragment with alkylating oligonucleotide derivatives. Nucl. Acids. Res. 14: 4065–4076.

    Google Scholar 

  • Vlassov, V. V., Gaidamakov, S. A., Zarytova, V. F., Knorre, D. G., Levina, A. S., Nikonova, A. A., Podust, L. M. & Fedorova, O. S., 1988a. Sequence-specific modification of doublestranded DNA with alkylating oligodeoxyribonucleotide derivatives. Gene 72: p. 313–322.

    Google Scholar 

  • Vlassov, V. V., Zarytova, V. F., Kutyavin, I. V. & Mamaev, S. V., 1988b. Sequence-specific chemical modification of a hybrid bacteriophage M13 single-stranded DNA by alkylating oligonucleotide derivatives. FEBS Lett. 231: 352.

    Google Scholar 

  • Vlassov, V. V., Ivanova, E. M., Krendelev, Yu. D., Kutyavin, I. V., Ovander, M. N., Ryte, A. S., Svinarchuk, F. P. & Yakubov, L. A., 1989. Sendai virus envelopes and erythrocyte ghosts as membrane vehicles for transport of the reactive oligonucleotide derivatives into the cells. Biopolimery i Kletka 5: 52–58.

    Google Scholar 

  • Vlassov, V. V., Godovikov, A. A., Zarytova, V. F., Ivanova, E. M. & Nomokonova, N. Yu., 1990a. Arrest of immunoglobuline G translation mRNA in vitro with an alkylating antisense oligonucleotide derivative. Mol. Biologija (Russ.) 24: 173–178.

    Google Scholar 

  • Vlassov, V. V., Kobetz, N. D., Chernolovskaya, E. L., Demidova, S. G., Borissov, R. G. & Ivanova, E. M., 1990b. Sequence-specific chemical modification of chromatin DNA with reactive derivatives of oligonucleotides. Mol. Biol. Reports 14: 11–15.

    Google Scholar 

  • Vlassov, V. V. & Yurchenko, L. V., 1990. Mechanism of the translation inhibition by antisense oligonucleotides (a minireview). Mol. Biologiya (Russ.) 24: 1157–1161.

    Google Scholar 

  • Walder, R. Y. & Walder, J. A., 1988. Role of RNase H in hybridarrested translation by antisense oligonucleotides. Proc. Natl. Acad. Sci. USA 85: 5011–5015.

    Google Scholar 

  • Yakubov, L. A., Deeva, E. A., Zaryotova, V. F., Ivanova, E. M. Ryte, A. S., Yurchenko, L. V. & Vlassov, V. V., 1989. Mechanism of oligonucleotide uptake by cells: involvement of specific receptors. Proc. Natl. Acad. Sci. USA 86: 6454–6458.

    Google Scholar 

  • Zarytova, V. F., Kutiavin, I. V., Mamaev, S. V. & Podyminogin, M. A., 1990. Effective and selective modification of a single-stranded DNA fragment with alkylating oligonucleotide derivatives in the presence of N-(2-hydroxyethyl)phenazinium oligonucleotide derivatives as effectors. Bioorgan. Khimija (USSR) 16: 1653–1660.

    Google Scholar 

  • Zenkova, M. A., Karpova, G. G., Levina, A. S., Mamaev, S. V. & Soloviev, V. V., 1990. Complementary addressed alkylation of the E.coli 16S rRNA with 2′, 3′-0-[4-N-methyl-N-(chloroethyl)-amino]benzylidene derivatives of oligodeoxyribonucleotides. IV. Identification of 16S rRNA binding sites with benzylidene derivatives of d(pACCTTGTT)rA, d(pTTACGACT)rU, d(pTTTGCTCCCC)rA. Bioorg. Khimiya (Russ.) 16: 788–800.

    Google Scholar 

  • Zon, G., 1989. Pharmaceutical considerations. In: J. S. Cohen (ed.) Oligonucleotides Antisense Inhibitors of Gene Expression. MacMillan Press, London, pp. 233–247.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Siberian Division of the USSR Academy of Sciences, Institute of Bioorganic Chemistry, 630090, Novosibirsk, USSR

    D. G. Knorre & V. V. Vlassov

Authors
  1. D. G. Knorre
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. V. V. Vlassov
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Knorre, D.G., Vlassov, V.V. Reactive oligonucleotide derivatives as gene-targeted biologically active compounds and affinity probes. Genetica 85, 53–63 (1991). https://doi.org/10.1007/BF00056106

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00056106

Key words

Search

Navigation