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

Fujita H, Imaizumi Y, Kasahara Y, Kitadume S, Ozaki H, Kuwahara M, Sugimoto N - Pharmaceuticals (Basel) (2013)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan. mkuwa@gunma-u.ac.jp.

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.

No MeSH data available.


Chemical structures of analytes used in this study.
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pharmaceuticals-06-01082-f001: Chemical structures of analytes used in this study.

Mentions: Ultraviolet-visible (UV-vis) spectra were measured using a U-3000 spectrophotometer (Hitachi High Technologies Corporation, Tokyo, Japan). Fluorescence spectra and fluorescence polarization were measured with a LS-55 spectrofluorophotometer (Perkin Elmer Japan Co., Ltd., Kanagawa, Japan). CD spectra were acquired with a JASCO J-820 spectrometer equipped with thermoelectrically controlled cell holders (JASCO Corporation, Tokyo, Japan). ODNs used were purchased from GeneDesign Inc. (Osaka, Japan) (Table 1). (S)-(+)-Camptothecin (CPT), 9(10H)-acridone, fluorescein, and polyoxyethylene sorbitan monolaurate (TWEEN® 20) were purchased from Tokyo Chemical Industry Co., Ltd. (Tokyo, Japan). Riboflavin-5′-phosphate sodium (FMN) was purchased from Yamasa Corporation (Chiba, Japan). The seven-substituted camptothecin derivatives (CPT1 and CPT2) were synthesized from CPT according to the method reported in the literature [13] (Figure 1). 2-(Carboxymethyl)-9(10H)acridone was synthesized according to the method reported in the literature [16].


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

Fujita H, Imaizumi Y, Kasahara Y, Kitadume S, Ozaki H, Kuwahara M, Sugimoto N - Pharmaceuticals (Basel) (2013)

Chemical structures of analytes used in this study.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3818834&req=5

pharmaceuticals-06-01082-f001: Chemical structures of analytes used in this study.
Mentions: Ultraviolet-visible (UV-vis) spectra were measured using a U-3000 spectrophotometer (Hitachi High Technologies Corporation, Tokyo, Japan). Fluorescence spectra and fluorescence polarization were measured with a LS-55 spectrofluorophotometer (Perkin Elmer Japan Co., Ltd., Kanagawa, Japan). CD spectra were acquired with a JASCO J-820 spectrometer equipped with thermoelectrically controlled cell holders (JASCO Corporation, Tokyo, Japan). ODNs used were purchased from GeneDesign Inc. (Osaka, Japan) (Table 1). (S)-(+)-Camptothecin (CPT), 9(10H)-acridone, fluorescein, and polyoxyethylene sorbitan monolaurate (TWEEN® 20) were purchased from Tokyo Chemical Industry Co., Ltd. (Tokyo, Japan). Riboflavin-5′-phosphate sodium (FMN) was purchased from Yamasa Corporation (Chiba, Japan). The seven-substituted camptothecin derivatives (CPT1 and CPT2) were synthesized from CPT according to the method reported in the literature [13] (Figure 1). 2-(Carboxymethyl)-9(10H)acridone was synthesized according to the method reported in the literature [16].

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan. mkuwa@gunma-u.ac.jp.

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.

No MeSH data available.