Structural and affinity analyses of G-quadruplex DNA aptamers for camptothecin derivatives

Pharmaceuticals

Volumn 6, Issue 9, 2013, Pages 1082-1093

  Fujita, Hiroto ^a   Imaizumi, Yuri ^a   Kasahara, Yuuya ^a   Kitadume, Shunsuke ^a   Ozaki, Hiroaki ^a   Kuwahara, Masayasu ^a   Sugimoto, Naoki ^b  

^a GUNMA UNIVERSITY   (Japan)

^b KONAN UNIVERSITY   (Japan)

Author keywords

Camptothecin (CPT); Circular dichroism (CD) spectroscopy; DNA aptamer; Fluorescence polarization (FP) assay; Fluorescence titration; G quadruplex

Indexed keywords

APTAMER; CAMPTOTHECIN; CAMPTOTHECIN DERIVATIVE; DNA; DNA FRAGMENT; GUANINE; GUANINE QUADRUPLEX; OLIGODEOXYRIBONUCLEOTIDE;

ARTICLE; BINDING AFFINITY; CIRCULAR DICHROISM; DNA BINDING; FLUORESCENCE POLARIZATION; PEPTIDE LIBRARY; PROTEIN DNA BINDING; PROTEIN MOTIF; PROTEIN STRUCTURE; PROTEIN TARGETING; STRUCTURE ANALYSIS;

EID: 84883438095     PISSN: None     EISSN: 14248247     Source Type: Journal    
DOI: 10.3390/ph6091082     Document Type: Article

References (30)

1. Ellington, A.D.; Szostak, J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346, 818-822.
2. Tuerk, C.; Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249, 505-510.
3. Ellington, A.D.; Szostak, J.W. Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures. Nature 1992, 355, 850-852.
4. Sissi, C.; Gatto, B.; Palumbo, M. The evolving world of protein-G-quadruplex recognition: a medicinal chemist's perspective. Biochimie 2011, 93, 1219-1230.
5. Hamon, F.; Faverie, A.; Renaud, F.A.; Hamon, F.; Di Primo, C.; Largy, E.; Dausse, E.; Delaurière, L.; Landras-Guetta, C.; Toulmé, J.J.; et al. Nucleic acids targeted to drugs: SELEX against a quadruplex ligand. Biochimie 2011, 93, 1357-1367.
6. Tucker, W.O.; Shum, K.T.; Tanner, J.A. G-quadruplex DNA aptamers and their ligands: Structure, function and application. Curr. Pharm. Des. 2012, 18, 2014-2026.
7. Nadai, M.; Sattin, G.; Palù, G.; Palumbo, M.; Richter, S.N. Clerocidin-mediated DNA footprinting discriminates among different G-quadruplex conformations and detects tetraplex folding in a duplex environment. Biochim. Biophys. Acta 2013, 1830, 4660-4668.
8. Gatto, B.; Palumbo, M.; Sissi, C. Nucleic acid aptamers based on the G-quadruplex structure: therapeutic and diagnostic potential. Curr. Med. Chem. 2009, 16, 1248-1265.
9. Smirnov, I.V.; Shafer, R.H. Electrostatics dominate quadruplex stability. Biopolymers 2007, 85, 91-101.
10. Nagatoishi, S.; Isono, N.; Tsumoto, K.; Sugimoto, N. Loop residues of thrombin-binding DNA aptamer impact G-quadruplex stability and thrombin binding. Biochimie 2011, 93, 1231-1238.
11. Nagatoishi, S.; Sugimoto, N. Interaction of water with the G-quadruplex loop contributes to the binding energy of G-quadruplex to protein. Mol. Biosyst. 2012, 8, 2766-2770.
12. Pramanik, S.; Nagatoishi, S.; Sugimoto, N. DNA tetraplex structure formation from human telomeric repeat motif (TTAGGG):(CCCTAA) in nanocavity water pools of reverse micelles. Chem. Commun. 2012, 48, 4815-4817.
13. Imaizumi, Y.; Kasahara, Y.; Fujita, H.; Kitadume, S.; Ozaki, H.; Endoh, T.; Kuwahara, M.; Sugimoto, N. Efficacy of base-modification on target binding of small molecule DNA aptamers. J. Am. Chem. Soc. 2013, 135, 9412-9419.
14. McLuckie, K.I.; Waller, Z.A.; Sanders, D.A.; Alves, D.; Rodriguez, R.; Dash, J.; McKenzie, G.J.; Venkitaraman, A.R.; Balasubramanian, S. G-quadruplex-binding benzo[a]phenoxazines down-regulate c-KIT expression in human gastric carcinoma cells. J. Am. Chem. Soc. 2011, 133, 2658-2663.
15. Hurley, L.H.; von Hoff, D.D.; Siddiqui-Jain, A.; Yang, D. Drug targeting of the c-MYC promoter to repress gene expression via a G-quadruplex silencer element. Semin. Oncol. 2006, 33, 498-512.
16. Shoji, A.; Hasegawa, T.; Kuwahara, M.; Ozaki, H.; Sawai, H. Chemico-enzymatic synthesis of a new fluorescent-labeled DNA by PCR with a thymidine nucleotide analogue bearing an acridone derivative. Bioorg. Med. Chem. Lett. 2007, 17, 776-779.
17. Beno, I.; Rosenthal, K.; Levitine, M.; Shaulov, L.; Haran, T.E. Sequence-dependent cooperative binding of p53 to DNA targets and its relationship to the structural properties of the DNA targets. Nucleic Acids Res. 2011, 39, 1919-1932.
18. Nagesh, N.; Sharma, V.K.; Ganesh, K.A.; Lewis, E.A. Effect of Ionic Strength on Porphyrin Drugs Interaction with Quadruplex DNA Formed by the Promoter Region of C-myc and Bcl2 Oncogenes. J. Nucleic Acids 2010, 2010, 146418.
19. Jecklin, M.C.; Schauer, S.; Dumelin, C.E.; Zenobi, R. Label-free determination of protein-ligand binding constants using mass spectrometry and validation using surface plasmon resonance and isothermal titration calorimetry. J. Mol. Recognit. 2009, 22, 319-329.
20. Ruta, J.; Perrier, S.; Ravelet, C.; Fize, J.; Peyrin, E. Noncompetitive fluorescence polarization aptamer-based assay for small molecule detection. Anal. Chem. 2009, 81, 7468-7473.
21. Mohanty, J.; Barooah, N.; Dhamodharan, V.; Harikrishna, S.; Pradeepkumar, P.I.; Bhasikuttan, A.C. Thioflavin T as an efficient inducer and selective fluorescent sensor for the human telomeric G-quadruplex DNA. J. Am. Chem. Soc. 2013, 135, 367-376
22. Chen, S.B.; Shi, Q.X.; Peng, D.; Huang, S.Y.; Ou, T.M.; Li, D.; Tan, J.H.; Gu, L.Q.; Huang, Z.S. The role of positive charges on G-quadruplex binding small molecules: Learning from bisaryldiketene derivatives. Biochim Biophys Acta 2013, 1830, 5006-5013.
23. Shi, S.; Huang, H.L.; Gao, X.; Yao, J.L.; Lv, C.Y.; Zhao, J.; Sun, W.L.; Yao, T.M.; Ji, L.N. A comparative study of the interaction of two structurally analogous ruthenium complexes with human telomeric G-quadruplex DNA. J. Inorg. Biochem. 2013, 121, 19-27.
24. SantaLucia, J., Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 1998, 95, 1460-1465.
25. Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31, 3406-3415.
26. Sen, D.; Gilbert, W. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 1988, 334, 364-366.
27. Giri, B.; Smaldino, P.J.; Thys, R.G.; Creacy, S.D.; Routh, E.D.; Hantgan, R.R.; Lattmann, S.; Nagamine, Y.; Akman, S.A. Vaughn, J.P. G4 resolvase 1 tightly binds and unwinds unimolecular G4-DNA. Nucleic Acids Res. 2011, 39, 7161-7178.
28. Kasahara, Y.; Irisawa, Y.; Fujita, H.; Yahara, A.; Ozaki, H.; Obika, S.; Kuwahara, M. Capillary electrophoresis-systematic evolution of ligands by exponential enrichment selection of base-and sugar-modified DNA aptamers: target binding dominated by 2'-O,4'-C-methylene-bridged/locked nucleic acid primer. Anal. Chem. 2013, 85, 4961-4967.
29. Seenisamy, J.; Rezler, E.M.; Powell, T.J.; Tye, D.; Gokhale, V.; Joshi, C.S. Siddiqui-Jain, A.; Hurley, L.H. The dynamic character of the G-quadruplex element in the c-MYC promoter and modification by TMPyP4. J. Am. Chem. Soc. 2004, 126, 8702-8709.
30. Kang, H.J.; Park, H.J. Novel molecular mechanism for actinomycin D activity as an oncogenic promoter G-quadruplex binder. Biochemistry 2009, 48, 7392-7398.