Aptamer selection by high-throughput sequencing and informatic analysis

BioTechniques

Volumn 51, Issue 6, 2011, Pages 413-416

  Hoon, Shawn ^a   Zhou, Bin ^c,d   Janda, Kim D ^c,d   Brenner, Sydney ^a,b   Scolnick, Jonathan ^a,b  

^a AGENCY FOR SCIENCE   (Singapore)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

^c Skaggs Institute for Chemical Biology   (United States)

^d The Worm Institute for Research and Medicine   (United States)

Author keywords

Aptamer; High throughput sequencing; Informatics

Indexed keywords

APTAMER; THROMBIN;

ARTICLE; DNA SEQUENCE; HUMAN; INFORMATION SCIENCE; SEQUENCE ANALYSIS;

APTAMERS, NUCLEOTIDE; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PROTEIN BINDING; SELEX APTAMER TECHNIQUE; THROMBIN;

EID: 83255193503     PISSN: 07366205     EISSN: 19409818     Source Type: Journal    
DOI: 10.2144/000113786     Document Type: Article

References (14)

1. Tuerk, C. and L. Gold. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505-510.
2. Ellington, A.D. and J.W. Szostak. 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346:818-822.
3. Huizenga, D.E. and J.W. Szostak. 1995. A DNA aptamer that binds adenosine and ATP. Biochemistry 34:656-665.
4. Jhaveri, S. and A. Ellington. 2002. In vitro selection of RNA aptamers to a small molecule target. Curr Protoc Nucleic Acid Chem Chapter 9:Unit 9 5.
5. Bock, L.C., L.C. Griffin, J.A. Latham, E.H. Vermaas, and J.J. Toole. 1992. Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 355:564-566.
6. Lupold, S.E., B.J. Hicke, Y. Lin, and D.S. Coffey. 2002. Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer Res. 62:4029-4033.
7. Cho, M., Y. Xiao, J. Nie, and R. Stewart, A.T. Csordas, S.S. Oh, J.A. Thomson, and H.T. Soh. Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proceedings of the National Academy of Sciences 107:15373-15378.
8. Kupakuwana, G.V., J.E. Crill, M.P. McPike, and P.N. Borer. 2011. Acyclic Identification of Aptamers for Human alpha-Thrombin Using Over-Represented Libraries and Deep Sequencing. PLoS One 6(5):e19395.
9. Tasset, D.M., M.F. Kubik, and W. Steiner. 1997. Oligonucleotide inhibitors of human thrombin that bind distinct epitopes. J. Mol. Biol. 272:688-698.
10. Kurtz, S., A. Narechania, J.C. Stein, and D. Ware. 2008. A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 9:517.
11. Edgar, R.C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460-2461.
12. Berezovski, M.V., M.U. Musheev, A.P. Drabovich, J.V. Jitkova, and S.N. Krylov. 2006. Non-SELEX: selection of aptamers without intermediate amplification of candidate oligonucleotides. Nat. Protocols 1:1359-1369.
13. Latham, J.A., R. Johnson, and J.J. Toole. 1994. The application of a modified nucleotide in aptamer selection: novel thrombin aptamers containing 5-(1-pentynyl)-2'-deoxyuridine. Nucleic Acids Res. 22:2817-2822.
14. Gold, L., D. Ayers, J. Bertino, C. Bock, A. Bock, E.N. Brody, J. Carter, A.B. Dalby, et al. 2010. Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS One 5:e15004.