title: Structural and affinity analyses of g-quadruplex DNA aptamers for camptothecin derivatives.
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.
authors.affiliation: Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan. mkuwa@gunma-u.ac.jp.
authors.forename: Hiroto
authors.initials: H
authors.lastname: Fujita
authors.forename: Yuri
authors.initials: Y
authors.lastname: Imaizumi
authors.forename: Yuuya
authors.initials: Y
authors.lastname: Kasahara
authors.forename: Shunsuke
authors.initials: S
authors.lastname: Kitadume
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Ozaki
authors.forename: Masayasu
authors.initials: M
authors.lastname: Kuwahara
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto