Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives
by
Hiroto Fujita 1, Yuri Imaizumi 1, Yuuya Kasahara 1, Shunsuke Kitadume 1, Hiroaki Ozaki 1,2, Masayasu Kuwahara 1,2,* and Naoki Sugimoto 3,4
Hiroto Fujita 1, Yuri Imaizumi 1, Yuuya Kasahara 1, Shunsuke Kitadume 1, 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.
Pharmaceuticals 2013, 6(9), 1082-1093; https://doi.org/10.3390/ph6091082
Received: 1 July 2013 / Revised: 11 August 2013 / Accepted: 26 August 2013 / Published: 29 August 2013
(This article belongs to the Special Issue Aptamer-Based Therapeutics)
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.
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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.
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