Non-Equilibrium Capillary Electrophoresis of Equilibrium Mixtures-Based Affinity Separation and Selective Enrichment of a Long-Length DNA Aptamer
Kenta Hagiwara A , Yuuya Kasahara B , Hiroto Fujita A and Masayasu Kuwahara A C
+ Author Affiliations
- Author Affiliations
A Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
B National Institute of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.
C Corresponding author. Email: mkuwa@gunma-u.ac.jp
Australian Journal of Chemistry 69(10) 1102-1107 https://doi.org/10.1071/CH16272
Submitted: 1 May 2016 Accepted: 26 June 2016 Published: 13 July 2016
Abstract
Non-equilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) is a kinetic capillary electrophoresis method used for the affinity analysis of DNA binding to proteins or ligands as well as a rapid selection of DNA aptamers. However, long DNA strands (100-mer or more) are generally difficult to analyse by this method owing to their poor peak separation. Herein, we report optimized conditions (use of a neutral phosphate buffer with an ionic strength of 0.074 as a binding buffer and use of an 80-cm fused silica capillary with a 75-μm internal diameter) for the peak separation of a 100-mer thrombin-binding DNA aptamer-target complex and its consequent enrichment using the NECEEM-based capillary electrophoresis–systematic evolution of ligands by exponential enrichment (CE-SELEX) method.
References
[1] M. Geiger, A. L. Hogerton, M. T. Bowser, Anal. Chem. 2012, 84, 577.| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXhs1SlsrzM&md5=fe63b9e66473bf3504cc90d3b74a662cCAS | 22148626PubMed |
[2] I. O. Neaga, E. Bodoki, S. Hambye, B. Blankert, R. Oprean, Talanta 2016, 148, 247.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2MXhvVWnurfL&md5=a091451ae4f73dbfe1c7bffe3de3cb5dCAS | 26653446PubMed |
[3] P.-L. Chang, M.-M. Hsieh, T.-C. Chiu, Int. J. Environ. Res. Public Health 2016, 13, 409.
| Crossref | GoogleScholarGoogle Scholar |
[4] S. E. Deeb, H. Watzig, D. A. El-Hady, H. M. Albishri, C. S. de Griend, G. K. Scriba, Electrophoresis 2014, 35, 170.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXhvVWgurjK&md5=dc7a606dae1b875cc1543fa947b85e2dCAS | 24395663PubMed |
[5] T. Acunha, C. Ibanez, V. Garcia-Canas, C. Simo, A. Cifuentes, Electrophoresis 2016, 37, 111.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2MXhs1Slu7%2FF&md5=0a198920264f78a5b57e6572dca7c7b5CAS | 26256797PubMed |
[6] C. Giovannoli, C. Baggiani, L. Anfossi, G. Giraudi, Electrophoresis 2008, 29, 3349.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXhtVyrsL7M&md5=b10fd5dcafc1c711fb1d63d9a25e7381CAS | 18646281PubMed |
[7] B. C. Durney, C. L. Crihfield, L. A. Holland, Anal. Bioanal. Chem. 2015, 407, 6923.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2MXnvFeguro%3D&md5=09abfab10eccd8bc803952e526cd59bfCAS | 25935677PubMed |
[8] S. D. Mendonsa, M. T. Bowser, J. Am. Chem. Soc. 2004, 126, 20.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3sXpsFygtrg%3D&md5=f8da3821dbebf4058e431d62d27555b1CAS | 14709039PubMed |
[9] J. Tang, J. Xie, N. Shao, Y. Yan, Electrophoresis 2006, 27, 1303.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XjslyltLo%3D&md5=a266171b28c79188568199715d6bbc51CAS | 16518777PubMed |
[10] R. K. Mosing, S. D. Mendonsa, M. T. Bowser, Anal. Chem. 2005, 77, 6107.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXps1erurY%3D&md5=270d0476ae6a9f94bca95cdda3713589CAS | 16194066PubMed |
[11] S. D. Mendonsa, M. T. Bowser, J. Am. Chem. Soc. 2005, 127, 9382.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXkvVGksrk%3D&md5=ac4679a43be7ae63eb4019511ec3ff51CAS | 15984861PubMed |
[12] J. Yang, M. T. Bowser, Anal. Chem. 2013, 85, 1525.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XhvVahsrfL&md5=6bd3c6a04258fd0a51c1ad3016fde21eCAS | 23234289PubMed |
[13] M. Jing, M. T. Bowser, Anal. Chem. 2013, 85, 10761.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXhs1WltLfM&md5=8438877130fbe21fe68c4dcec8f10984CAS | 24125636PubMed |
[14] M. Berezovski, M. Musheev, A. Drabovich, S. N. Krylov, J. Am. Chem. Soc. 2006, 128, 1410.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XjvV2mug%3D%3D&md5=5dca3e03161a00cc978c5c174778d050CAS | 16448086PubMed |
[15] J. Tok, J. Lai, T. Leung, S. F. Li, Electrophoresis 2010, 31, 2055.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3cXnvFSisLw%3D&md5=bcb4022522180f24c6d87ed43091fb8fCAS | 20564698PubMed |
[16] Y. Kasahara, Y. Irisawa, H. Fujita, A. Yahara, H. Ozaki, S. Obika, M. Kuwahara, Anal. Chem. 2013, 85, 4961.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXnsVKrurw%3D&md5=ade3e163bb25bebc57086da4b4d5e8b4CAS | 23662585PubMed |
[17] Y. Kasahara, Y. Irisawa, H. Ozaki, S. Obika, M. Kuwahara, Bioorg. Med. Chem. Lett. 2013, 23, 1288.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXhvVGnsL4%3D&md5=dd8702d759d6a8ef20fe3ada3b27135aCAS | 23374873PubMed |
[18] K. Hagiwara, H. Fujita, Y. Kasahara, Y. Irisawa, S. Obika, M. Kuwahara, Mol. Biosyst. 2015, 11, 71.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2cXhslert73M&md5=13aa3effbf3bbb90e1b23e082cc77b58CAS | 25325213PubMed |
[19] M. Kuwahara, S. Obika, Artif. DNA PNA XNA 2013, 4, 39.
| Crossref | GoogleScholarGoogle Scholar | 24044051PubMed |
[20] M. Kanoatov, V. A. Galievsky, S. M. Krylova, L. T. Cherney, H. K. Jankowski, S. N. Krylov, Anal. Chem. 2015, 87, 3099.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2MXisF2jtLo%3D&md5=ca3e83e6b8bcc15cb3661c38815c6f00CAS | 25668425PubMed |
[21] L. S. Green, D. Jellinek, R. Jenison, A. Ostman, C. H. Heldin, N. Janjic, Biochemistry 1996, 35, 14413.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK28XmtlOksb8%3D&md5=e087fb5064287663902fc3a01d47952fCAS | 8916928PubMed |
[22] X. Lou, J. Qian, Y. Xiao, L. Viel, A. E. Gerdon, E. T. Lagally, P. Atzberger, T. M. Tarasow, A. J. Heeger, H. T. Soh, Proc. Natl. Acad. Sci. USA 2009, 106, 2989.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXivFyqtLc%3D&md5=e89d57f59c48f69a6411d80bf9c25002CAS | 19202068PubMed |
[23] H. W. Meng, J. M. Pagano, B. S. White, Y. Toyoda, I. M. Min, H. G. Craighead, D. Shalloway, J. T. Lis, K. Xiao, M. M. Jin, PLoS One 2014, 9, e93052.
| Crossref | GoogleScholarGoogle Scholar | 24675636PubMed |
[24] R. Welz, R. R. Breaker, RNA 2007, 13, 573.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXkt1Chtb4%3D&md5=e8a0f7aa5aa6a834341d265b0322121dCAS | 17307816PubMed |
[25] N. Sudarsan, E. R. Lee, Z. Weinberg, R. H. Moy, J. N. Kim, K. H. Link, R. R. Breaker, Science 2008, 321, 411.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXosVOrsLs%3D&md5=f9ba264fb106d9a39911fd6aad7163f7CAS | 18635805PubMed |
[26] E. R. Lee, K. F. Blount, R. R. Breaker, RNA Biol. 2009, 6, 187.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1MXmtV2mt7k%3D&md5=68e6468fbd3390ff25b2016877268127CAS | 19246992PubMed |
[27] J. Wang, Q. Gong, N. Maheshwari, M. Eisenstein, M. L. Arcila, K. S. Kosik, H. T. Soh, Angew. Chem. Int. Ed. Engl. 2014, 53, 4796.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2cXks1Witrw%3D&md5=ddcfc167c42340701aaa805e6366e179CAS | 24644057PubMed |
[28] D. M. Tasset, M. F. Kubik, W. Steiner, J. Mol. Biol. 1997, 272, 688.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK2sXntVKqt7k%3D&md5=25fcfb2034c6aa32fa3062121b8f7f6aCAS | 9368651PubMed |
[29] Y. Imaizumi, Y. Kasahara, H. Fujita, S. Kitadume, H. Ozaki, T. Endoh, M. Kuwahara, N. Sugimoto, J. Am. Chem. Soc. 2013, 135, 9412.
| Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXovFWls74%3D&md5=da982bdfdc42b0713f250227f381fe0eCAS | 23734784PubMed |
[30] M. Y. Zhou, S. E. Clark, C. E. Gomez-Sanchez, Biotechniques 1995, 19, 34.
| 1:CAS:528:DyaK2MXmsl2mu7o%3D&md5=a88aa25b6b202e5587a61717f06b1e57CAS | 7669292PubMed |
