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Journal of Biomolecular Structure and Dynamics Volume 23, 2006 - Issue 5
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Original Articles

Hybridization of the Bridged Oligonucleotides with DNA: Thermodynamic and Kinetic Studies

Dmitrii V. Pyshnyi Institute of Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, Prospect Akad. Lavrentyeva 8, 630090, Novosibirsk, Russia; Novosibirsk State University, Pirogova St. 2, 630090, Novosibirsk, Russia
,
Alexander A. Lomzov Institute of Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, Prospect Akad. Lavrentyeva 8, 630090, Novosibirsk, Russia; Novosibirsk State University, Pirogova St. 2, 630090, Novosibirsk, Russia
,
Inna A. Pyshnaya Institute of Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, Prospect Akad. Lavrentyeva 8, 630090, Novosibirsk, Russia
&
Eugenia M. Ivanova Institute of Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, Prospect Akad. Lavrentyeva 8, 630090, Novosibirsk, Russia
Pages 567-579 | Received 21 Oct 2005, Published online: 15 May 2012

Citations (25)

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Alexander A. Lomzov, Vitaly V. Gorelov, Victor M. Golyshev, Tatiana V. Abramova & Dmitrii V. Pyshnyi. (2015) 139 Analysis of structure and thermodynamics of modified DNA duplexes using molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics 33:sup1, pages 90-91.
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Olga Nikolaevna Koroleva, Eugeniy Mikhailovich Volkov & Valeriy Lvovich Drutsa. (2011) Interaction of Escherichia coli RNA Polymerase with Artificial Promoters, Containing Nonnucleotide Spacers. Nucleosides, Nucleotides & Nucleic Acids 30:7-8, pages 667-679.
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Articles from other publishers (23)

Brennan Ashwood, Michael S. Jones, Yumin Lee, Joseph R. Sachleben, Andrew L. Ferguson & Andrei Tokmakoff. (2023) Molecular insight into how the position of an abasic site modifies DNA duplex stability and dynamics. Biophysical Journal.
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Ekaterina A. Gorbunova, Anna V. Epanchintseva, Dmitrii V. Pyshnyi & Inna A. Pyshnaya. (2023) Noncovalent Adsorption of Single-Stranded and Double-Stranded DNA on the Surface of Gold Nanoparticles. Applied Sciences 13:12, pages 7324.
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Anastasia A. Zamoskovtseva, Victor M. Golyshev, Valeria A. Kizilova, Georgiy Yu. Shevelev, Dmitrii V. Pyshnyi & Alexander A. Lomzov. (2022) Pairing nanoarchitectonics of oligodeoxyribonucleotides with complex diversity: concatemers and self-limited complexes. RSC Advances 12:11, pages 6416-6431.
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V. M. Golyshev, D. V. Pyshnyi & A. A. Lomzov. (2021) Calculation of Energy for RNA/RNA and DNA/RNA Duplex Formation by Molecular Dynamics Simulation. Molecular Biology 55:6, pages 927-940.
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Victor M. Golyshev, Dmitrii V. Pyshnyi & Alexander A. Lomzov. (2021) Effects of Phosphoryl Guanidine Modification of Phosphate Residues on the Structure and Hybridization of Oligodeoxyribonucleotides. The Journal of Physical Chemistry B 125:11, pages 2841-2855.
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Olga A. Krasheninina, Veniamin S. Fishman, Alexander A. Lomzov, Alexey V. Ustinov & Alya G. Venyaminova. (2020) Postsynthetic On-Column 2′ Functionalization of RNA by Convenient Versatile Method. International Journal of Molecular Sciences 21:14, pages 5127.
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Dale C. Guenther, Raymond G. Emehiser, Allison Inskeep, Saswata Karmakar & Patrick J. Hrdlicka. (2020) Impact of non-nucleotidic bulges on recognition of mixed-sequence dsDNA by pyrene-functionalized Invader probes. Organic & Biomolecular Chemistry 18:24, pages 4645-4655.
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E. S. Dyudeeva, M. S. Kupryushkin, A. A. Lomzov, I. A. Pyshnaya & D. V. Pyshnyi. (2020) Physicochemical Properties of the Phosphoryl Guanidine Oligodeoxyribonucleotide Analogs. Russian Journal of Bioorganic Chemistry 45:6, pages 709-718.
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Georgiy Yu. Shevelev, Evgeny L. Gulyak, Alexander A. Lomzov, Andrey A. Kuzhelev, Olesya A. Krumkacheva, Maxim S. Kupryushkin, Victor M. Tormyshev, Matvey V. Fedin, Elena G. Bagryanskaya & Dmitrii V. Pyshnyi. (2017) A Versatile Approach to Attachment of Triarylmethyl Labels to DNA for Nanoscale Structural EPR Studies at Physiological Temperatures. The Journal of Physical Chemistry B 122:1, pages 137-143.
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Rebekah J. Karadeema, Maria Stancescu, Tyler P. Steidl, Sophia C. Bertot & Dmitry M. Kolpashchikov. (2018) The owl sensor: a ‘fragile’ DNA nanostructure for the analysis of single nucleotide variations. Nanoscale 10:21, pages 10116-10122.
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Valentina M. Farzan, Mikhail L. Markelov, Alexander Yu. Skoblov, German A. Shipulin & Timofei S. Zatsepin. (2017) Specificity of SNP detection with molecular beacons is improved by stem and loop separation with spacers. The Analyst 142:6, pages 945-950.
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Alexander A. Lomzov, Yury N. Vorobjev & Dmitrii V. Pyshnyi. (2015) Evaluation of the Gibbs Free Energy Changes and Melting Temperatures of DNA/DNA Duplexes Using Hybridization Enthalpy Calculated by Molecular Dynamics Simulation. The Journal of Physical Chemistry B 119:49, pages 15221-15234.
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Dale C. Guenther, Saswata Karmakar & Patrick J. Hrdlicka. (2015) Bulged Invader probes: activated duplexes for mixed-sequence dsDNA recognition with improved thermodynamic and kinetic profiles. Chemical Communications 51:81, pages 15051-15054.
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Yann Tonin, Anne-Marie Heckel, Ilya Dovydenko, Mariya Meschaninova, Caroline Comte, Alya Venyaminova, Dmitrii Pyshnyi, Ivan Tarassov & Nina Entelis. (2014) Characterization of chemically modified oligonucleotides targeting a pathogenic mutation in human mitochondrial DNA. Biochimie 100, pages 192-199.
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Natalia A. Lebedeva, Nadejda I. Rechkunova, Alexander A. Ishchenko, Murat Saparbaev & Olga I. Lavrik. (2013) The mechanism of human tyrosyl-DNA phosphodiesterase 1 in the cleavage of AP site and its synthetic analogs. DNA Repair 12:12, pages 1037-1042.
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M. S. Kupryushkin & D. V. Pyshnyi. (2012) Oligonucleotide derivatives in nucleic acid hybridization analysis. III. Synthesis and investigation of properties of oligonucleotides, bearing bifunctional non-nucleotide insertion. Russian Journal of Bioorganic Chemistry 38:6, pages 625-638.
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A. A. Lomzov & D. V. Pyshnyi. (2012) Considering the oligonucleotide secondary structures in thermodynamic and kinetic analysis of DNA duplex formation. Biophysics 57:1, pages 19-34.
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M. R. Kabilov & D. V. Pyshnyi. (2011) Analytical consideration of the selectivity of oligonucleotide hybridization. Journal of Biophysical Chemistry 02:02, pages 75-91.
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E. V. Dmitrienko, E. A. Khomyakova, I. A. Pyshnaya, A. G. Bragin, V. E. Vedernikov & D. V. Pyshnyi. (2010) Oligonucleotide derivatives in the hybridization analysis of nucleic acids: II. Isothermal signal amplification in DNA analysis by minisequencing. Russian Journal of Bioorganic Chemistry 36:6, pages 734-745.
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I. A. Pyshnaya, O. A. Vinogradova, M. R. Kabilov, E. M. Ivanova & D. V. Pyshnyi. (2009) Bridged oligonucleotides as molecular probes for investigation of enzyme-substrate interaction and allele-specific analysis of DNA. Biochemistry (Moscow) 74:9, pages 1009-1020.
Crossref
Nikita A. Kuznetsov, Alexandr D. Milov, Vladimir V. Koval, Rimma I. Samoilova, Yuri A. Grishin, Dmitry G. Knorre, Yuri D. Tsvetkov, Olga S. Fedorova & Sergei A. Dzuba. (2009) PELDOR study of conformations of double-spin-labeled single- and double-stranded DNA with non-nucleotide inserts. Physical Chemistry Chemical Physics 11:31, pages 6826.
Crossref
Ernesto Carrillo-Nava, Yamilet Mejía-Radillo & Hans-Jürgen Hinz. (2008) Dodecamer DNA Duplex Formation Is Characterized by Second-Order Kinetics, Positive Activation Energies, and a Dependence on Sequence and Mg 2+ Ion Concentration . Biochemistry 47:50, pages 13153-13157.
Crossref
A. A. Lomzov, I. A. Pyshnaya, E. M. Ivanova & D. V. Pyshnyi. (2006) Thermodynamic parameters for calculating the stability of complexes of bridged oligonucleotides. Doklady Biochemistry and Biophysics 409:1, pages 211-215.
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