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Journal of Analytical Methods in Chemistry
Volume 2015, Article ID 137489, 8 pages
http://dx.doi.org/10.1155/2015/137489
Research Article

Single-Round Patterned DNA Library Microarray Aptamer Lead Identification

1Human Effectiveness Directorate, 711 Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
2The Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, MD 20817, USA
3Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USA
4UES Inc., 4401 Dayton-Xenia Road, Dayton, Dayton, OH 45433, USA

Received 12 November 2014; Revised 22 April 2015; Accepted 27 April 2015

Academic Editor: Chih-Ching Huang

Copyright © 2015 Jennifer A. Martin et al. 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.

Linked References

  1. A. D. Ellington and J. W. Szostak, “In vitro selection of RNA molecules that bind specific ligands,” Nature, vol. 346, no. 6287, pp. 818–822, 1990. View at Publisher · View at Google Scholar · View at Scopus
  2. C. Tuerk and L. Gold, “Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase,” Science, vol. 249, no. 4968, pp. 505–510, 1990. View at Publisher · View at Google Scholar · View at Scopus
  3. R. Stoltenburg, C. Reinemann, and B. Strehlitz, “SELEX-a (r)evolutionary method to generate high-affinity nucleic acid ligands,” Biomolecular Engineering, vol. 24, no. 4, pp. 381–403, 2007. View at Publisher · View at Google Scholar · View at Scopus
  4. S. D. Jayasena, “Aptamers: an emerging class of molecules that rival antibodies in diagnostics,” Clinical Chemistry, vol. 45, no. 9, pp. 1628–1650, 1999. View at Google Scholar · View at Scopus
  5. S. C. B. Gopinath, “Methods developed for SELEX,” Analytical and Bioanalytical Chemistry, vol. 387, no. 1, pp. 171–182, 2007. View at Publisher · View at Google Scholar · View at Scopus
  6. M. V. Berezovski, M. U. Musheev, A. P. Drabovich, J. V. Jitkova, and S. N. Krylov, “Non-SELEX: selection of aptamers without intermediate amplification of candidate oligonucleotides,” Nature Protocols, vol. 1, no. 3, pp. 1359–1369, 2006. View at Publisher · View at Google Scholar · View at Scopus
  7. N. Savory, K. Abe, K. Sode, and K. Ikebukuro, “Selection of DNA aptamer against prostate specific antigen using a genetic algorithm and application to sensing,” Biosensors and Bioelectronics, vol. 26, no. 4, pp. 1386–1391, 2010. View at Publisher · View at Google Scholar · View at Scopus
  8. M. Cho, Y. Xiao, J. Nie et al., “Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 35, pp. 15373–15378, 2010. View at Publisher · View at Google Scholar · View at Scopus
  9. M. Platt, W. Rowe, D. C. Wedge, D. B. Kell, J. Knowles, and P. J. R. Day, “Aptamer evolution for array-based diagnostics,” Analytical Biochemistry, vol. 390, no. 2, pp. 203–205, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. C. G. Knight, M. Platt, W. Rowe et al., “Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape,” Nucleic Acids Research, vol. 37, no. 1, article e6, 2009. View at Publisher · View at Google Scholar · View at Scopus
  11. R. Asai, S. I. Nishimura, T. Aita, and K. Takahashi, “In Vitro selection of DNA aptamers on chips using a method for generating point mutations,” Analytical Letters, vol. 37, no. 4, pp. 645–656, 2004. View at Publisher · View at Google Scholar · View at Scopus
  12. J. R. Collett, J. C. Eun, and A. D. Ellington, “Production and processing of aptamer microarrays,” Methods, vol. 37, no. 1, pp. 4–15, 2005. View at Publisher · View at Google Scholar · View at Scopus
  13. E. J. Cho, J. R. Collett, A. E. Szafranska, and A. D. Ellington, “Optimization of aptamer microarray technology for multiple protein targets,” Analytica Chimica Acta, vol. 564, no. 1, pp. 82–90, 2006. View at Publisher · View at Google Scholar · View at Scopus
  14. E. Katilius, C. Flores, and N. W. Woodbury, “Exploring the sequence space of a DNA aptamer using microarrays,” Nucleic Acids Research, vol. 35, no. 22, pp. 7626–7635, 2007. View at Publisher · View at Google Scholar · View at Scopus
  15. S. E. Osborne and A. D. Ellington, “Nucleic acid selection and the challenge of combinatorial chemistry,” Chemical Reviews, vol. 97, no. 2, pp. 349–370, 1997. View at Publisher · View at Google Scholar · View at Scopus
  16. J. M. Carothers, S. C. Oestreich, J. H. Davis, and J. W. Szostak, “Informational complexity and functional activity of RNA structures,” Journal of the American Chemical Society, vol. 126, no. 16, pp. 5130–5137, 2004. View at Publisher · View at Google Scholar · View at Scopus
  17. Y. Chushak and M. O. Stone, “In silico selection of RNA aptamers,” Nucleic Acids Research, vol. 37, no. 12, article e87, 2009. View at Publisher · View at Google Scholar · View at Scopus
  18. J. H. Davis and J. W. Szostak, “Isolation of high-affinity GTP aptamers from partially structured RNA libraries,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 18, pp. 11616–11621, 2002. View at Publisher · View at Google Scholar · View at Scopus
  19. X. Luo, M. Mckeague, S. Pitre et al., “Computational approaches toward the design of pools for the in vitro selection of complex aptamers,” RNA, vol. 16, no. 11, pp. 2252–2262, 2010. View at Publisher · View at Google Scholar · View at Scopus
  20. K. M. Ruff, T. M. Snyder, and D. R. Liu, “Enhanced functional potential of nucleic acid aptamer libraries patterned to increase secondary structure,” Journal of the American Chemical Society, vol. 132, no. 27, pp. 9453–9464, 2010. View at Publisher · View at Google Scholar · View at Scopus
  21. L. C. Bock, L. C. Griffin, J. A. Latham, E. H. Vermaas, and J. J. Toole, “Selection of single-stranded DNA molecules that bind and inhibit human thrombin,” Nature, vol. 355, no. 6360, pp. 564–566, 1992. View at Publisher · View at Google Scholar · View at Scopus
  22. D. M. Tasset, M. F. Kubik, and W. Steiner, “Oligonucleotide inhibitors of human thrombin that bind distinct epitopes,” Journal of Molecular Biology, vol. 272, no. 5, pp. 688–698, 1997. View at Publisher · View at Google Scholar · View at Scopus
  23. J. A. Bittker, B. V. Le, and D. R. Liu, “Nucleic acid evolution and minimization by nonhomologous random recombination,” Nature Biotechnology, vol. 20, no. 10, pp. 1024–1029, 2002. View at Publisher · View at Google Scholar · View at Scopus
  24. R. F. Macaya, P. Schultze, F. W. Smith, J. A. Roe, and J. Feigon, “Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 90, no. 8, pp. 3745–3749, 1993. View at Publisher · View at Google Scholar · View at Scopus
  25. D. J. Patel, A. K. Suri, F. Jiang et al., “Structure, recognition and adaptive binding in RNA aptamer complexes,” Journal of Molecular Biology, vol. 272, no. 5, pp. 645–664, 1997. View at Publisher · View at Google Scholar · View at Scopus
  26. G. Zheng, A. M. Torres, and W. S. Price, “Solvent suppression using phase-modulated binomial-like sequences and applications to diffusion measurements,” Journal of Magnetic Resonance, vol. 194, no. 1, pp. 108–114, 2008. View at Publisher · View at Google Scholar · View at Scopus
  27. K. Wuthrich, NMR of Proteins and Nucleic Acids, John Wiley & Sons, New York, NY, USA, 1986.
  28. G. V. Kupakuwana, J. E. Crill III, M. P. McPike, and P. N. Borer, “Acyclic identification of aptamers for human alpha-thrombin using over-represented libraries and deep sequencing,” PLoS ONE, vol. 6, no. 5, Article ID e19395, 2011. View at Publisher · View at Google Scholar · View at Scopus
  29. J. A. Hagen, S. N. Kim, B. Bayraktaroglu et al., “Biofunctionalized zinc oxide field effect transistors for selective sensing of riboflavin with current modulation,” Sensors, vol. 11, no. 7, pp. 6645–6655, 2011. View at Publisher · View at Google Scholar · View at Scopus
  30. J. A. Martin, J. L. Chávez, Y. Chushak, R. R. Chapleau, J. Hagen, and N. Kelley-Loughnane, “Tunable stringency aptamer selection and gold nanoparticle assay for detection of cortisol,” Analytical and Bioanalytical Chemistry, vol. 406, no. 19, pp. 4637–4647, 2014. View at Publisher · View at Google Scholar · View at Scopus