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Interaction between thrombin and oligonucleotide RA36 is a two-stage process.

Olga M Antipova1, Georgy M Solius2, Dmitry Y Panteleev3

  • 1Apto-Pharm Ltd, Kolomensky dr., 13A, 115564, Moscow, Russia; Chemistry Department, Lomonosov Moscow State University, Leninskie Gory 1-40, 119991, Moscow, Russia.

Biochemical and Biophysical Research Communications
|December 10, 2019
PubMed
Summary

Oligonucleotide RA36 has two G-quadruplex modules that bind thrombin differently. This study resolves discrepancies in reported thrombin:RA36 binding affinities using electrophoretic mobility shift assay.

Keywords:
Dissociation constantElectrophoretic mobility shift assayOligonucleotideRA36Thrombin

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biophysical Chemistry

Background:

  • Oligonucleotide RA36 features two G-quadruplex modules, each with potential thrombin-binding capacity.
  • Previous studies reported a single, widely varying dissociation constant for the thrombin:RA36 complex, creating a data discrepancy.
  • The differing functional activities of the two modules suggest distinct binding characteristics.

Purpose of the Study:

  • To investigate the interaction between oligonucleotide RA36 and thrombin.
  • To resolve discrepancies in previously reported binding affinities for the thrombin:RA36 complex.
  • To elucidate the binding mechanism of RA36 to thrombin.

Main Methods:

  • Electrophoretic mobility shift assay (EMSA) was employed to study the interaction.
  • The binding kinetics and affinities of RA36 modules to thrombin were analyzed.

Main Results:

  • The interaction between RA36 and thrombin was confirmed to be a two-stage process.
  • Each G-quadruplex module within RA36 exhibits distinct affinities for thrombin.
  • These differential affinities explain the wide range of dissociation constants reported in prior research.

Conclusions:

  • The binding of RA36 to thrombin is not a single event but a multi-stage interaction.
  • The two G-quadruplex modules of RA36 possess unique binding characteristics towards thrombin.
  • This study clarifies the complex binding behavior of RA36 and thrombin, resolving previous inconsistencies.