Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives

doi:10.3390/ph6091082

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Pharmaceuticals 2013, 6(9), 1082-1093; doi:10.3390/ph6091082

Article

Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives

Hiroto Fujita¹, Yuri Imaizumi¹, Yuuya Kasahara¹, Shunsuke Kitadume¹, Hiroaki Ozaki^1,2, Masayasu Kuwahara^1,2,* and Naoki Sugimoto^3,4

¹ Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan ² Division of Molecular Science, Faculty of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan ³ Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan ⁴ Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan

* Author to whom correspondence should be addressed.

Received: 1 July 2013; in revised form: 11 August 2013 / Accepted: 26 August 2013 / Published: 29 August 2013

(This article belongs to the Special Issue Aptamer-Based Therapeutics)

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Abstract: We recently selected DNA aptamers that bind to camptothecin (CPT) and CPT derivatives from a 70-mer oligodeoxyribonucleotide (ODN) library using the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method. The target-binding activity of the obtained 70-mer CPT-binding DNA aptamer, termed CA-70, which contains a 16-mer guanine (G)-core motif (G₃TG₃TG₃T₂G₃) that forms a three-tiered G-quadruplex, was determined using fluorescence titration. In this study, truncated fragments of CA-70 that all have the G-core motif, CA-40, -20, -19, -18A, -18B, -17, and -16, were carefully analyzed. We found that CA-40 retained the target-binding activity, whereas CA-20, -19, and -18B exhibited little or no binding activities. Further, not only CA-18A but also the shorter length fragments CA-17 and -16 clearly retained the binding activity, indicating that tail strands of the G-quadruplex structure can significantly affect the target binding of G-quadruplex DNA aptamers. Further analyses using circular dichroism (CD) spectroscopy and fluorescence polarization (FP) assay were conducted to investigate the structure and affinity of G-quadruplex DNA aptamers.

Keywords: DNA aptamer; G-quadruplex; camptothecin (CPT); circular dichroism (CD) spectroscopy; fluorescence titration; fluorescence polarization (FP) assay

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MDPI and ACS Style

Fujita, H.; Imaizumi, Y.; Kasahara, Y.; Kitadume, S.; Ozaki, H.; Kuwahara, M.; Sugimoto, N. Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives. Pharmaceuticals 2013, 6, 1082-1093.

AMA Style

Fujita H, Imaizumi Y, Kasahara Y, Kitadume S, Ozaki H, Kuwahara M, Sugimoto N. Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives. Pharmaceuticals. 2013; 6(9):1082-1093.

Chicago/Turabian Style

Fujita, Hiroto; Imaizumi, Yuri; Kasahara, Yuuya; Kitadume, Shunsuke; Ozaki, Hiroaki; Kuwahara, Masayasu; Sugimoto, Naoki. 2013. "Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives." Pharmaceuticals 6, no. 9: 1082-1093.

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