Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives
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, t...
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MDPI AG
2013-08-01
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| Series: | Pharmaceuticals |
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| Online Access: | http://www.mdpi.com/1424-8247/6/9/1082 |
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| author | Naoki Sugimoto Masayasu Kuwahara Yuuya Kasahara Shunsuke Kitadume Hiroaki Ozaki Yuri Imaizumi Hiroto Fujita |
| author_facet | Naoki Sugimoto Masayasu Kuwahara Yuuya Kasahara Shunsuke Kitadume Hiroaki Ozaki Yuri Imaizumi Hiroto Fujita |
| author_sort | Naoki Sugimoto |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-10T04:45:39Z |
| format | Article |
| id | doaj.art-923a849ab45d404fbd68132d7fec0d7c |
| institution | Directory Open Access Journal |
| issn | 1424-8247 |
| language | English |
| last_indexed | 2024-12-10T04:45:39Z |
| publishDate | 2013-08-01 |
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| spelling | doaj.art-923a849ab45d404fbd68132d7fec0d7c2022-12-22T02:01:46ZengMDPI AGPharmaceuticals1424-82472013-08-01691082109310.3390/ph6091082Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin DerivativesNaoki SugimotoMasayasu KuwaharaYuuya KasaharaShunsuke KitadumeHiroaki OzakiYuri ImaizumiHiroto FujitaWe 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.http://www.mdpi.com/1424-8247/6/9/1082DNA aptamerG-quadruplexcamptothecin (CPT)circular dichroism (CD) spectroscopyfluorescence titrationfluorescence polarization (FP) assay |
| spellingShingle | Naoki Sugimoto Masayasu Kuwahara Yuuya Kasahara Shunsuke Kitadume Hiroaki Ozaki Yuri Imaizumi Hiroto Fujita Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives Pharmaceuticals DNA aptamer G-quadruplex camptothecin (CPT) circular dichroism (CD) spectroscopy fluorescence titration fluorescence polarization (FP) assay |
| title | Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives |
| title_full | Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives |
| title_fullStr | Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives |
| title_full_unstemmed | Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives |
| title_short | Structural and Affinity Analyses of G-Quadruplex DNA Aptamers for Camptothecin Derivatives |
| title_sort | structural and affinity analyses of g quadruplex dna aptamers for camptothecin derivatives |
| topic | DNA aptamer G-quadruplex camptothecin (CPT) circular dichroism (CD) spectroscopy fluorescence titration fluorescence polarization (FP) assay |
| url | http://www.mdpi.com/1424-8247/6/9/1082 |
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