Fluorescence-Based Study of Oligonucleotide Interactions With Recombinant Proteins: Insulin, Interferon α2-β, Somatotropin, and Their Receptors

Authors

  • Oleksandr Nuzhnyi The Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Ukraine
  • Roman Nikolaiev The Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Ukraine https://orcid.org/0000-0001-7606-9918
  • Zenovii Tkachuk The Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Ukraine

DOI:

https://doi.org/10.20535/ibb.2024.8.3.304238

Keywords:

interferon, interferon receptor, insulin, insulin receptor, somatotropin, oligonucleotide, protein-ligand interaction, spectroscopy

Abstract

Background. Oligonucleotides (OLNs) can participate in a wide range of protein-ligand interactions and perform numerous cellular functions by forming structures that enable specific interactions with DNA, RNA, and proteins, what is crucial for many biological processes. Advances in understanding these interactions could lead to the development of new technologies for treating various diseases. However, the mechanism of interaction between proteins and OLNs is complex and still requires detailed study. More research is needed to fully elucidate this process and enhance our understanding of these biomolecular interactions.

Objective. The aim of this study was to synthesize, purify, and investigate the interaction of OLNs with recombinant signaling proteins interferon α2-β and insulin with their receptors and somatropin by assessing binding strength using fluorescence spectroscopy.

Methods. The interactions were analyzed using the Stern–Volmer equation in both general and modified forms, as well as the Hill equation. OLNs were synthesized via the solid-phase phosphoramidite method, purified through solid-phase extraction, and subsequently verified with a spectrophotometer.

Results. Fluorometric titration revealed that OLNs bind to proteins within the medium affinity range, forming non-fluorescent complexes, with the most active interactions observed with shorter OLN. Positive cooperative binding of interferon to G20 and T20, and negative cooperative binding of insulin to C20 and A20, were identified. Additionally, negative cooperative binding of somatropin to C20 was observed.

Conclusions. The study demonstrated the interaction between OLNs and recombinant signaling proteins and receptors through various binding mechanisms, which could potentially affect their conformation and biolo­gical activity. These findings have implications for the therapeutic use of OLNs in the context of signaling proteins and receptors.

References

Zarrintaj P, Seidi F, Youssefi Azarfam M, Khodadadi Yazdi M, Erfani A, Barani M, et al. Biopolymer-based composites for tissue engineering applications: A basis for future opportunities. Compos B Eng. 2023;258:110701. DOI: 10.1016/j.compositesb.2023.110701

Tkachuk Z. Multiantivirus compound, composition and method for treatment of virus diseases. United States patent US20120232129A1, published 16.04.2013. Available from: https://patents.google.com/patent/US20120232129A1/en

Tkachuk ZY, Rybalko SL, Zharkova LD, Starosila DB, Semernikova LI. Antiinfluenza activity of the drug Nuclex. Reports of the National Academy of Sciences of Ukraine, 2010:9:191-6.

Levchenko SM, Rebriev AV, Tkachuk VV, Dubey LV, Dubey IY, Tkachuk ZY. Studies on the interaction of oligoadenylates with proteins by MALDI-TOF mass spectrometry. Biopolym Cell. 2013;29(1):42-8. DOI: 10.7124/bc.000804

Agrawal DK, Schulman R. Modular protein-oligonucleotide signal exchange. Nucleic Acids Res. 2020;48(12):6431-44. DOI: 10.1093/nar/gkaa405

Mátyus L, Szöllősi J, Jenei A. Steady-state fluorescence quenching applications for studying protein structure and dynamics. J Photochem Photobiol B. 2006;83(3):223-36. DOI: 10.1016/j.jphotobiol.2005.12.017

Peacock J, Jaynes JB. Using competition assays to quantitatively model cooperative binding by transcription factors and other ligands. Biochim Biophys Acta Gen Subj. 2017;1861(11 Pt A):2789-801. DOI: 10.1016/j.bbagen.2017.07.024

Wilce J, Vivian J, Wilce M. Oligonucleotide binding proteins: the occurrence of dimer and multimer formation. In: Protein Dimerization and Oligomerization in Biology. Springer, New York, NY, 2012;747:91-104. DOI: 10.1007/978-1-4614-3229-6_6

Terada C, Kawamoto S, Yamayoshi A, Yamamoto T. Chemistry of therapeutic oligonucleotides that drives interactions with biomolecules. Pharmaceutics. 2022;14(12):2647. DOI: 10.3390/pharmaceutics14122647

Gabrielsen OS, Matre V, Bergholtz S. Protein–oligonucleotide interactions. In: Meyers RA, Schöneich C, editors. Encyclopedia of analytical chemistry: applications, theory, and instrumentation. Hoboken: Wiley; 2000. DOI: 10.1002/9780470027318.a1628

Crooke ST, Vickers TA, Liang XH. Phosphorothioate modified oligonucleotide-protein interactions. Nucleic Acids Res. 2020;48(10):5235-53. DOI: 10.1093/nar/gkaa299

Kong LZ, Kim SM, Wang C, Lee SY, Oh SC, Lee S, et al. Understanding nucleic acid sensing and its therapeutic applications. Exp Mol Med. 2023;55(11):2320-31. DOI: 10.1038/s12276-023-01118-6

Tachas G, Dobie K, Jain R, Belyea C, Heffernan M. Modulation of growth hormone receptor expression and insulin-like growth factor expression. Patent EP2492282A1, published 29.08.2012.

Ayhan-Sahin B, Apaydın ZE, Obakan-Yerlikaya P, Arisan ED, Coker-Gurkan A. Synthesis and characterization of novel ssDNA X-aptamers targeting Growth Hormone Releasing Hormone (GHRH). PLoS One. 2022;17(1):e0260144. DOI: 10.1371/journal.pone.0260144

Downloads

Published

2024-10-06

How to Cite

1.
Nuzhnyi O, Nikolaiev R, Tkachuk Z. Fluorescence-Based Study of Oligonucleotide Interactions With Recombinant Proteins: Insulin, Interferon α2-β, Somatotropin, and Their Receptors. Innov Biosyst Bioeng [Internet]. 2024Oct.6 [cited 2024Nov.21];8(3):50-9. Available from: https://ibb.kpi.ua/article/view/304238

Issue

Section

Articles