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.
This is an open access article distributed under the
Creative Commons Attribution License which permits unrestricted use, distribution,
and reproduction in any medium, provided the original work is properly cited.
Export to BibTeX
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.
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.
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.