Coexistence of G-quadruplex and duplex domains within the secondary structure of 31-mer DNA thrombin-binding aptamer

Journal of Biomolecular Structure and Dynamics

Volumn 30, Issue 5, 2012, Pages 524-531

  Dolinnaya, N G ^a   Yuminova, A V ^a   Spiridonova, V A ^a   Arutyunyan, A M ^a   Kopylov, A M ^a  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

Circular dichroism; G quadruplex structure; Noncanonical DNA; Thrombin binding aptamer; Uv melting

Indexed keywords

APTAMER; DNA; DNA APTAMER; GUANINE QUADRUPLEX; OLIGODEOXYRIBONUCLEOTIDE; OLIGONUCLEOTIDE; THROMBIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CIRCULAR DICHROISM; MELTING POINT; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN UNFOLDING; TEMPERATURE; ULTRAVIOLET SPECTROSCOPY;

APTAMERS, NUCLEOTIDE; CIRCULAR DICHROISM; DNA; DNA-BINDING PROTEINS; G-QUADRUPLEXES; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; PHOTOELECTRON SPECTROSCOPY; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; THROMBIN;

EID: 84865630601     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2012.687518     Document Type: Article

References (37)

1. Arnott, S., Chandrasekaran, R., & Marttila, C.M. (1974). Structures for polyinosinic acid and polyguanylic acid. Biochemical Journal, 141, 537-543.
2. Bates, P.J., Kahlon, J.B., Thomas, S.D., Trent, J.O., & Miller, D.M. (1999). Antiproliferative activity of G-rich oligonucleotides correlates with protein binding. Journal of Biological Chemistry, 274, 26369-26377.
3. Bock, L.C., Griffin, L.C., Latham, J.A., Vermaas, E.H., & Toole, J.J. (1992). Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature, 355, 564-566.
4. Cantor, C.R., Warshaw, M.M., & Shapiro, H. (1970). Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers, 9, 1059-1077.
5. Dapiæ, V., Abdomeroviæ, V., Marrington, R., Peberdy, J., Rodger, A., Trent, J.O., & Bates, P.J. (2003). Biophysical and biological properties of quadruplex oligodeoxyribonucleotides. Nucleic Acids Research, 31, 2097-2107.
6. de Soultrait, V.R., Lozach, P.Y., Altmeyer, R., Tarrago-Litvak, L., Litvak, S., & Andreola, M.L. (2002). DNA aptamers derived from HIV-1 RNase H inhibitors are strong anti-integrase agents. Journal of Molecular Biology, 324, 195-203.
7. Di Giusto, D.A., Wlassoff, W.A., Gooding, J.J., Messerle, B. A., & King, G.C. (2005). Proximity extension of circular DNA aptamers with real-time protein detection. Nucleic Acids Research, 33, e64.
8. Gellert, M., Lipsett, M.N., & Davies, D.R. (1962). Helix formation by guanylic acid. Proceedings of the National Academy of Sciences USA, 48, 2013.2018.
9. Giraldo, R., Suzuki, M., Chapman, L., & Rhodes, D. (1994). Promotion of parallel DNA quadruplexes by a yeast telomere binding protein: A circular dichroism study. Proceedings of the National Academy of Sciences USA, 91, 7658-7662.
10. Gros, J., Rosu, F., Amrane, S., De Cian, A., Gabelica, V., Lacroix, L., & Mergny, J.-L. (2007). Guanines are a quartetf's best friend: Impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes. Nucleic Acids Research, 35, 3064-3075.
11. Huppert, J.L. (2008). Four-stranded nucleic acids: Structure, function and targeting of G-quadruplexes. Chemical Society Reviews, 37, 1375-1384.
12. Huppert, J.L., & Balasubramanian, S. (2005). Prevalence of quadruplexes in the human genome. Nucleic Acids Research, 33, 2908-2916.
13. Ikebukuro, K., Okumura, Y., Sumikara, K., & Karube, I. (2005). A novel method of screening thrombin-inhibiting DNA aptamers using an evolution-mimicking algorithm. Nucleic Acids Research, 33, e108.
14. Johnson, J.E., Smith, J.S., Kozak, M.L., & Johnson, F.B. (2008). In vivo veritas: Using yeast to probe the biological functions of G-quadruplexes. Biochimie, 90, 1250-1263.
15. Kelly, J.A., Feigon, J., & Yeates, T.O. (1996). Reconciliation of the X-ray and NMR structures of the thrombin-binding aptamer d(GGTTGGTGTGGTTGG). Journal of Molecular Biology, 256, 417-422.
16. Lech, C.J., Cheow Lim, J.K., Wen Lim, J.M., Amrane, S., Heddi, B., & Phan, A.T. (2011). Effect of site-specific guanine C8-modifications on an intramolecular DNA G-quadruplex. Biophysical Journal, 101, 1987-1998.
17. Macaya, R.F., Schultze, P., Smith, F.W., Roe, J.A., & Feigon, J. (1993). Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution. Proceedings of the National Academy of Sciences USA, 90, 3745-3749.
18. Macaya, R.F., Waldron, J.A., Beutel, B.A., Gao, H., Joesten, M.E., Yang, M., Cook, A.F. (1995). Structural and functional characterization of potent antithrombotic oligonucleotides possessing both quadruplex and duplex motifs. Biochemistry, 34, 4478-4492.
19. Mergny, J.-L., De Cian, A., Ghelab, A., Sacca, B., & Lacroix, L. (2005). Kinetics of tetramolecular quadruplexes. Nucleic Acids Research, 33, 81-94.
20. Nagatoishi, S., Tanaka, Y., & Tsumoto, K. (2007). Circular dichroism spectra demonstrate formation of the thrombinbinding DNA aptamer G-quadruplex under stabilizing-cation- deficient conditions. Biochemical and Biophysical Research Communications, 352, 812-817.
21. Olsen, C.M., Lee, H.-T., & Marky, L.A. (2009). Unfolding thermodynamics of intramolecular G-quadruplexes: Base sequence contributions of the loops. The Journal of Physical Chemistry B, 113, 2587-2595.
22. Padmanabhan, K., Padmanabhan, K.P., Ferrara, J.D., Sadler, J.E., & Tulinsky, A. (1993). The structure of alphathrombin inhibited by a 15-mer single-stranded DNA aptamer. Journal of Biological Chemistry, 268, 17651-17654.
23. Padmanabhan, K., & Tulinsky, A. (1996). An ambiguous structure of a DNA 15-mer thrombin complex. Acta Crystallographica. Section D, Biological Crystallographica, D52, 272-282.
24. Pasternak, A., Hernandez, F.J., Rasmussen, L.M., Vester, B., & Wengel, J. (2011). Improved thrombin binding aptamer by incorporation of a single unlocked nucleic acid monomer. Nucleic Acids Research, 39, 1155-1164.
25. Petraccone, L., Erra, E., Esposito, V., Randazzo, A., Mayol, L., Nasti, L., Giancola, C. (2004). Stability and structure of telomeric DNA sequences forming quadruplexes containing four G-tetrads with different topological arrangements. Biochemistry, 43, 4877-4884.
26. Phan, A.T., Kuryavyi, V., Ma, J.B., Faure, A., Andréola, M.L., & Patel, D.J. (2005). An interlocked dimeric parallelstranded DNA quadruplex: A potent inhibitor of HIV-1 integrase. Proceedings of the National Academy of Sciences USA, 102, 634-639.
27. Poniková, S., Tluèková, K., Antalík, M., Víglaský, V., & Hianik, T. (2011). The circular dichroism and differential scanning calorimetry study of the properties of DNA aptamer dimers. Biophysical Chemistry, 155, 29-35.
28. Reshetnikov, R.V., Sponer, J., Rassokhina, O.I., Kopylov, A. M., Tsvetkov, P.O., Makarov, A.A., & Golovin, A.V. (2011). Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process. Nucleic Acids Research, 39, 9789-9802.
29. Sasisekharan, V., Zimmerman, S., & Davies, D.R. (1975). The structure of helical 5'-guanosine monophosphate. Journal of Molecular Biology, 92, 171-174.
30. Schultze, P., Macaya, R.F., & Feigon, J. (1994). Threedimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG). Journal of Molecular Biology, 235, 1532-1547.
31. Sen, D., & Gilbert, W. (1990). A sodium-potassium switch in the formation of four-stranded G4-DNA. Nature, 344, 410-414.
32. Siddiqui-Jain, A., Grand, C.L., Bearss, D.J., & Hurley, L.H. (2002). Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proceedings of the National Academy of Sciences USA, 99, 11593-11598.
33. Sissi, C., Gatto, B., & Palumbo, M. (2011). The evolving world of protein-G-quadruplex recognition: A medicinal chemist's perspective. Biochimie, 93, 1219-1230.
34. Teng, Y., Girvan, A.C., Casson, L.K., Pierce, W.M.Jr, Qian, M., Thomas, S.D., & Bates, P.J. (2007). AS1411 alters the localization of a complex containing protein arginine methyltransferase 5 and nucleolin. Cancer Research, 67, 10491-10500.
35. Tran, P.L.T., Mergny, J.-L., & Alberti, P. (2011). Stability of telomeric G-quadruplexes. Nucleic Acids Research, 39, 3282-3294.
36. Tuesuwan, B., Kern, J.T., Thomas, P.W., Rodriguez, M., Li, J., David, W.M., & Kerwin, S.M. (2008). Simian virus 40 large T-antigen G-quadruplex DNA helicase inhibition by G-quadruplex DNA-interactive agents. Biochemistry, 47, 1896-1909.
37. Zhang, M.-L., Tong, X.-J., Fu, X.-H., Zhou, B.O., Wang, J., Liao, X.-H., Zhou, J.-Q. (2010). Yeast telomerase subunit Est1p has guanine quadruplex-promoting activity that is required for telomere elongation. Nature Structural and Molecular Biology, 17, 202-209.