Structural and Functional Characterization of Thrombin Binding Aptamer Minor Loop

Giuseppe Marson(1*), Manlio Palumbo(2), Claudia Sissi(3)

(1) Dept. of Pharmaceutical Sciences, v. Marzolo 5, 35131 Padova, Italy, Italy
(2) Dept. of Pharmaceutical Sciences, v. Marzolo 5, 35131 Padova, Italy, Italy
(3) Dept. of Pharmaceutical Sciences, v. Marzolo 5, 35131 Padova, Italy, Italy
(*) Corresponding author


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Abstract


The thrombin binding aptamer (29hTBA), identified with a SELEX approach, shows a significant affinity for the coagulation factor thrombin by recognizing the protein  Exosite II (heparin binding site). The structure of 29hTBA consists of a G-quadruplex core flanked by two partially paired terminal strands. Literature data underline that the structure and stability of intramolecular G-quadruplexes can be profoundly influenced by the length and composition of the loops. Here, we investigated the role of the minor loop (10-11) composition by introducing a single A-T mutation at position 11. A comparative structural investigation of the wild type and the mutant aptamers evidenced that this loop is not largely impairing the folding of the G-quadruplex core. Additionally, thrombin binding analysis suggested that this loop is not directly involved in protein binding at exosite II
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Keywords


Thrombin; Aptamer; G-quadruplex

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References


B. Gatto, M. Palumbo, C. Sissi, Nucleic Acid Aptamers Based on the G-Quadruplex Structure: Therapeutic and Diagnostic Potential, Current Medicinal Chemistry, Volume 16, 2009, Pages 1248-1265.

L. Bock, L. Griffin, J. Latham, E. Vermaas, J. Toole, Selection of single-stranded DNA molecules that bind and inhibit human Thrombin, Nature, Volume 355, 1992, Pages 564-566.

D.M. Tasset, M.F. Kubik, W. Steiner, Oligonucleotide inhibitors of human thrombin that bind distinct epitopes, J. Mol. Biol., Volume 272, 1997, Pages 688-698.

R.F. Macaya, P.Schultze, F.W. Smith, J.A. Roe, J. Feigon, Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution, Proc. Natl. Acad. Sci. U. S. A., Volume 90, 1993, Pages 3745-3749.

I. Smirnov, R.H. Shafer, Effect of loop sequence and size on DNA aptamer stability, Biochemistry, Volume 39, 2000, Pages 1462-1468.

F., Macaya, Structural and functional characterization of potent antithrombotic oligonucleotides possessing both quadruplex and duplex motif, Biochemistry, Volume 34, 1995, Pages 4478-4492.

S. Niedle, S. Balasubramanian, Quadruplex nucleic acids (The Royal Society of Chemistry, 2006, Pages 34-35).

J. Kypr, M. Vorlickova, Circular dichroism and conformational polymorphism of DNA, Nucleic Acid Research, Volume 37, 2009, Pages 1713-1725.

S. Nagatoishi, Y. Tanaka, K. Tsumoto, Circular dichroism spectra demonstrate formation of the thrombin-binding DNA aptamer G-quadruplex under stabilizing-cation-deficient conditions, Biochem. Biophys. Res. Commun., Volume 352, 2007, Pages 352, 812-7.

M. Tracy, T.M. Bryan, M.B. Jarstfer, Interrogation of G-quadruplex–protein interactions, Methods, Volume 43, 2007, Pages 332–339.


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