Next Article in Journal
Molecular Insights in Psychiatry
Previous Article in Journal
The Role of Epigenetics in Primary Biliary Cholangitis
Article

Modulation of Aptamer–Ligand-Binding by Complementary Oligonucleotides: A G-Quadruplex Anti-Ochratoxin A Aptamer Case Study

1
A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia
2
Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
3
Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
*
Author to whom correspondence should be addressed.
Academic Editors: Aldo Galeone, Veronica Esposito and Antonella Virgilio
Int. J. Mol. Sci. 2022, 23(9), 4876; https://doi.org/10.3390/ijms23094876
Received: 28 March 2022 / Revised: 21 April 2022 / Accepted: 24 April 2022 / Published: 28 April 2022
Short oligonucleotides are widely used for the construction of aptamer-based sensors and logical bioelements to modulate aptamer–ligand binding. However, relationships between the parameters (length, location of the complementary region) of oligonucleotides and their influence on aptamer–ligand interactions remain unclear. Here, we addressed this task by comparing the effects of short complementary oligonucleotides (ssDNAs) on the structure and ligand-binding ability of an aptamer and identifying ssDNAs’ features that determine these effects. Within this, the interactions between the OTA-specific G-quadruplex aptamer 1.12.2 (5′-GATCGGGTGTGGGTGGCGTAAAGGGA GCATCGGACA-3′) and 21 single-stranded DNA (ssDNA) oligonucleotides complementary to different regions of the aptamer were studied. Two sets of aptamer–ssDNA dissociation constants were obtained in the absence and in the presence of OTA by isothermal calorimetry and fluorescence anisotropy, respectively. In both sets, the binding constants depend on the number of hydrogen bonds formed in the aptamer–ssDNA complex. The ssDNAs’ having more than 23 hydrogen bonds with the aptamer have a lower aptamer dissociation constant than for aptamer–OTA interactions. The ssDNAs’ having less than 18 hydrogen bonds did not affect the aptamer–OTA affinity. The location of ssDNA’s complementary site in the aptamer affeced the kinetics of the interaction and retention of OTA-binding in aptamer–ssDNA complexes. The location of the ssDNA site in the aptamer G-quadruplex led to its unfolding. In the presence of OTA, the unfolding process was longer and takes from 20 to 70 min. The refolding in the presence of OTA was possible and depends on the length and location of the ssDNA’s complementary site. The location of the ssDNA site in the tail region led to its rapid displacement and wasn’t affecting the G-qaudruplex’s integrity. It makes the tail region more perspective for the development of ssDNA-based tools using this aptamer. View Full-Text
Keywords: aptamers; G-quadruplex; DNA–DNA interactions; isothermal microcalorimetry; fluorescence anisotropy; circular dichroism; ochratoxin A aptamers; G-quadruplex; DNA–DNA interactions; isothermal microcalorimetry; fluorescence anisotropy; circular dichroism; ochratoxin A
Show Figures

Figure 1

MDPI and ACS Style

Samokhvalov, A.V.; Safenkova, I.V.; Eremin, S.A.; Bonchuk, A.N.; Maksimenko, O.G.; Sluchanko, N.N.; Zherdev, A.V.; Dzantiev, B.B. Modulation of Aptamer–Ligand-Binding by Complementary Oligonucleotides: A G-Quadruplex Anti-Ochratoxin A Aptamer Case Study. Int. J. Mol. Sci. 2022, 23, 4876. https://doi.org/10.3390/ijms23094876

AMA Style

Samokhvalov AV, Safenkova IV, Eremin SA, Bonchuk AN, Maksimenko OG, Sluchanko NN, Zherdev AV, Dzantiev BB. Modulation of Aptamer–Ligand-Binding by Complementary Oligonucleotides: A G-Quadruplex Anti-Ochratoxin A Aptamer Case Study. International Journal of Molecular Sciences. 2022; 23(9):4876. https://doi.org/10.3390/ijms23094876

Chicago/Turabian Style

Samokhvalov, Alexey V., Irina V. Safenkova, Sergei A. Eremin, Artem N. Bonchuk, Oksana G. Maksimenko, Nikolai N. Sluchanko, Anatoly V. Zherdev, and Boris B. Dzantiev. 2022. "Modulation of Aptamer–Ligand-Binding by Complementary Oligonucleotides: A G-Quadruplex Anti-Ochratoxin A Aptamer Case Study" International Journal of Molecular Sciences 23, no. 9: 4876. https://doi.org/10.3390/ijms23094876

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop