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Articles

Bimodular thrombin aptamers with two types of non-covalent locks

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Pages 559-577 | Received 07 Jan 2021, Accepted 25 Mar 2021, Published online: 13 Apr 2021

References

  • Odeh, F.; Nsairat, H.; Alshaer, W.; Ismail, M. A.; Esawi, E.; Qaqish, B.; Bawab, A. A.; Ismail, S. I. Aptamers Chemistry: chemical Modifications and Conjugation Strategies. Molecules 2019, 25, 3. DOI: 10.3390/molecules25010003.
  • Gelinas, A. D.; Davies, D. R.; Janjic, N. Embracing Proteins: structural Themes in Aptamer-Protein Complexes. Curr. Opin. Struct. Biol. 2016, 36, 122–132. DOI: 10.1016/j.sbi.2016.01.009.
  • Zhang, Y.; Lai, B. S.; Juhas, M. Recent Advances in Aptamer Discovery and Applications. Molecules 2019, 24, 941. DOI: 10.3390/molecules24050941.
  • Zavyalova, E. Kopylov, A. DNA Aptamer-Based Molecular Nanoconstructions and Nanodevices for Diagnostics and Therapy. In Nanostructures for the Engineering of Cells, Tissues and Organs; Grumezesku, A., Ed.; Elsevier: Chennai, 2018; pp 249–290
  • Vorobyeva, M.; Vorobjev, P.; Venyaminova, A. Multivalent Aptamers: versatile Tools for Diagnostic and Therapeutic Applications. Molecules 2016, 2112, 1613. DOI: 10.3390/molecules21121613.
  • Hasegawa, H.; Taira, K.; Sode, K.; Ikebukuro, K. Improvement of Aptamer Affinity by Dimerization. Sensors (Basel) 2008, 8, 1090–1098. DOI: 10.3390/s8021090.
  • Kim, Y.; Cao, Z.; Tan, W. Molecular Assembly for High-Performance Bivalent Nucleic Acid Inhibitor. Proc. Natl. Acad. Sci. U S A. 2008, 105, 5664–5669. DOI: 10.1073/pnas.0711803105.
  • Trajkovski, M.; Primoz, S.; Plavec, J. Cation Localization and Movement within DNA Thrombin Binding Aptamer in Solution. Org. Biomol. Chem. 2009, 7, 4677–4684. DOI: 10.1039/B914783G.
  • Ponzo, I.; Moller, F.; Daub, H.; Matscheko, N. A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding. Molecules 2019, 24, 2877. DOI: 10.3390/molecules24162877.
  • Zavyalova, E.; Tagiltsev, G.; Reshetnikov, R.; Arutyunyan, A.; Kopylov, A. Cation Coordination Alters the Conformation of a Thrombin-Binding G-Quadruplex DNA Aptamer That Affects Inhibition of Thrombin. Nucleic Acid Ther. 2016, 26, 299–308. DOI: 10.1089/nat.2016.0606.
  • Ponzo, I.; Moller, F.; Daub, H.; Matscheko, N. Stability and Binding Properties of a Modified Thrombin Binding Aptamer. Biophys. J. 2008, 94, 2, 562–569. DOI: 10.1529/biophysj.107.117382.
  • Zavyalova, E.; Golovin, A.; Pavlova, G.; Kopylov, A. Development of Antithrombotic Aptamers: From Recognizing Elements to Drugs. Curr. Pharm. Des. 2016, 22, 5163–5176. DOI: 10.2174/1381612822666161004163409.
  • Hsu, C.; Chang, H.; Chen, C.; Wei, S.; Shiang, Y.; Huang, C. Highly Efficient Control of Thrombin Activity by Multivalent Nanoparticles. Chemistry 2011, 17, 10994–11000. DOI: 10.1002/chem.201101081.
  • Musumeci, D.; Montesarchio, D. Polyvalent Nucleic Acid Aptamers and Modulation of Their Activity: A Focus on the Thrombin Binding Aptamer. Pharmacol. Ther. 2012, 136, 202–215. DOI: 10.1016/j.pharmthera.2012.07.011.
  • Zavyalova, E.; Kopylov, A. G-Quadruplexes and i-Motifs as Scaffolds for Molecular Engineering of DNA Aptamers. In G-Quadruplex Structures, Formation and Role in Biology; Santos, H., Ed. Nova Publishers: New York, 2016; pp 53–80
  • Alhadrami, H. A.; Chinnappan, R.; Eissa, S.; Rahamn, A. A.; Zourob, M. High Affinity Truncated DNA Aptamers for the Development of Fluorescence Based Progesterone Biosensors. Anal. Biochem. 2017, 525, 78–84. DOI: 10.1016/j.ab.2017.02.014.
  • Ueki, R.; Ueki, A.; Kanda, N.; Sando, S. Oligonucleotide-Based Mimetics of Hepatocyte Growth Factor. Angew. Chem. Int. Ed. Engl. 2016, 55, 579–582. DOI: 10.1002/anie.201508572.
  • Poniková, S.; Tlučková, K.; Antalík, M.; Víglaský, V.; Hianik, T. The Circular Dichroism and Differential Scanning Calorimetry Study of the Properties of DNA Aptamer Dimers. Biophys. Chem. 2011, 155, 29–35. DOI: 10.1016/j.bpc.2011.02.004.
  • Alieva, R. R.; Zavyalova, E. G.; Tashlitsky, V. N.; Kopylov, A. M. Quantitative Characterization of Oligomeric State of G-Quadruplex Antithrombin Aptamers by Size Exclusion HPLC. Mend. Commun. 2019, 29, 424–425. DOI: 10.1016/j.mencom.2019.07.023.
  • Han, X.; Wang, E.; Cui, Y.; Lin, Y.; Chen, H.; An, R.; Liang, X.; Komiyama, M. The Staining Efficiency of Cyanine Dyes for Single-Stranded DNA is Enormously Dependent on Nucleotide Composition. Electrophoresis 2019, 40, 1708–1714. DOI: 10.1002/elps.201800445.
  • Zavyalova, E. G.; Legatova, V. A.; Alieva, R. S.; Zalevsky, A. O.; Tashlitsky, V. N.; Arutyunyan, A. M.; Kopylov, A. M. Putative Mechanisms Underlying High Inhibitory Activities of Bimodular DNA Aptamers to Thrombin. Biomolecules 2019, 9, 41. DOI: 10.3390/biom9020041.
  • Vorlíčková, M.; Kejnovská, I.; Bednářová, K.; Renčiuk, D.; Kypr, J. Circular Dichroism Spectroscopy of DNA: From Duplexes to Quadruplexes. Chirality 2012, 24, 691–698. DOI: 10.1002/chir.22064.
  • Dolinnaya, N. G.; Yuminova, A. V.; Spiridonova, V. A.; Arutyunyan, A. M.; Kopylov, A. M. Coexistence of G-Quadruplex and Duplex Domains within the Secondary Structure of 31-Mer DNA Thrombin-Binding Aptamer. J. Biomol. Struct. Dyn. 2012, 30, 524–531. DOI: 10.1080/07391102.2012.687518.
  • Macaya, R. F.; Schultze, P.; Smith, F. W.; Roe, J. A.; Feigon, J. Thrombin-Binding DNA Aptamer Forms a Unimolecular Quadruplex Structure in Solution. Proc. Natl. Acad. Sci. U S A 1993, 90, 3745–3749. DOI: 10.1073/pnas.90.8.3745.
  • Ishizuka, T.; Yamashita, A.; Asada, Y.; Xu, Y. Studying DNA G-Quadruplex Aptamer by 19F NMR. ACS Omega. 2017, 2, 8843–8848. DOI: 10.1021/acsomega.7b01405.
  • Ida, R.; Wu, G. Direct NMR Detection of Alkali Metal Ions Bound to G-Quadruplex DNA. J. Am. Chem. Soc. 2008, 130, 3590–3602. DOI: 10.1021/ja709975z.
  • Steinert, H. S.; Rinnenthal, J.; Schwalbe, H. Individual Basepair Stability of DNA and RNA Studied by NMR-Detected Solvent Exchange. Biophys. J. 2012, 102, 2564–2574. DOI: 10.1016/j.bpj.2012.03.074.
  • Jaroszewski, J. W.; Clausen, V.; Cohen, J. S.; Dahl, O. NMR Investigations of Duplex Stability of Phosphorothioate and Phosphorodithioate DNA Analogues Modified in Both Strands. Nucleic Acids Res. 1996, 24, 829–834. DOI: 10.1093/nar/24.5.829.
  • Zavyalova, E.; Golovin, A.; Pavlova, G.; Kopylov, A. Module-Activity Relationship of G-Quadruplex Based DNA Aptamers for Human Thrombin. Curr. Med. Chem. 2013, 20, 4836–4843. DOI: 10.2174/09298673113206660283.
  • Ji, W. S. J.; Tan, Q.; Gu, L. Single-Molecule Detection of Folding and Unfolding of the G-Quadruplex Aptamer in a Nanopore Nanocavity. Nucleic Acids Res. 2009, 37, 972–982. DOI: 10.1093/nar/gkn968.
  • Cho, M.-S.; Kim, Y.-W.; Han, S.-Y.; Min, K.-I.; Rahman, M. D. A.; Shim, Y.-B.; Ban, C.-I. Detection for Folding of the Thrombin Binding Aptamer Using Label-Free Electrochemical Methods. BMB Rep. 2008, 41, 126–131. DOI: 10.5483/bmbrep.2008.41.2.126.
  • Hong, E. S.; Yoon, H.-J.; Kim, B.; Yim, Y.-H.; So, H.-Y.; Shin, S. K. Mass-Spectrometric Studies of Alkali Metal Ion Binding on Thrombin-Binding Aptamer DNA. J. Am. Soc. Mass Spectrom. 2010, 2, 1245–1255. DOI: 10.1016/j.jasms.2010.03.035.
  • Rajendran, A.; Endo, M.; Hidaka, K.; Tran, P. L. T.; Mergny, J.-L.; Sugiyama, H. Controlling the Stoichiometry and Strand Polarity of a Tetramolecular G-Quadruplex Structure by Using a DNA Origami Frame. Nucleic Acids Res. 2013, 41, 8738–8747. DOI: 10.1093/nar/gkt592.
  • Bhattacharyya, D.; Mirihana, G.; Basu, S. Metal Cations in G-Quadruplex Folding and Stability. Front. Chem. 2016, 4, 38 DOI: 10.3389/fchem.2016.00038.
  • O'Shannessy, D. J.; Brigham-Burke, M.; Soneson, K. K.; Hensley, P.; Brooks, I. Determination of rate and equilibrium binding constants for macromolecular interactions using surface plasmon resonance: use of nonlinear least squares analysis methods. Anal. Biochem. 1993, 212, 457–468. DOI: 10.1006/abio.1993.1355.

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