Skip to main content
SpringerLink
Log in

RNA–RNA SELEX

  • Protocol
  • First Online:
Book cover RNA-RNA Interactions

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1240))

Abstract

Systematic evolution of ligands by exponential enrichment (SELEX) protocol is a valuable technique to identify RNA aptamers interacting with RNA structural motifs. RNA aptamers are mainly resolved with affinity column chromatography and electrophoretic mobility shift assay (EMSA). Here, we describe the separation of the RNA aptamers binding to an RNA stem-loop target with affinity chromatography using the column attached the target RNA and nondenaturing polyacrylamide gel electrophoresis to obtain a single predominant RNA aptamer family.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Schmidt FJ, Cho B, Nicholas HB Jr (1996) RNA libraries and RNA recognition. Ann N Y Acad Sci 782:526–533

    Article  CAS  PubMed  Google Scholar 

  2. Cho B, Taylor DC, Nicholas HB Jr, Schmidt FJ (1997) Interacting RNA species identified by combinatorial selection. Bioorgan Med Chem 5:1107–1113

    Article  CAS  Google Scholar 

  3. Ko J, Lee Y, Park I, Cho B (2001) Identification of a structural motif of 23S rRNA interacting with 5S rRNA. FEBS Lett 508:300–304

    Article  CAS  PubMed  Google Scholar 

  4. Shin E-S, Hong SK, Cho B (2008) Identification of structural motifs of RNA aptamers interacting with the stem-loop sequence at the gag-pol junction of HIV-1 RNA. Bull Korean Chem Soc 29:2227–2230

    Article  CAS  Google Scholar 

  5. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature (London) 346:818–822

    Article  CAS  Google Scholar 

  6. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510

    Article  CAS  PubMed  Google Scholar 

  7. Ellington AD, Szostak JW (1992) In vitro selection of single-stranded DNA molecules that fold into specific ligand-binding structures. Nature 355:850–852

    Article  CAS  PubMed  Google Scholar 

  8. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, p B11

    Google Scholar 

  9. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp B13–B14

    Google Scholar 

  10. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 6.46–6.48

    Google Scholar 

  11. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, p 9

    Google Scholar 

  12. Gesteland RF, Atkins JF (1993) The RNA world: in vitro selection of functional rna sequences. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 511–533

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Applied Chemistry, Cheongju University, 298 Daeseongro, Cheongju Chungbuk, 360-764, S. Korea

    B. Cho

Authors
  1. B. Cho
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to B. Cho .

Editor information

Editors and Affiliations

  1. Department of Biochemistry, University of Missouri, Columbia, Missouri, USA

    Frank J. Schmidt

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this protocol

Cite this protocol

Cho, B. (2015). RNA–RNA SELEX. In: Schmidt, F. (eds) RNA-RNA Interactions. Methods in Molecular Biology, vol 1240. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1896-6_3

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-1896-6_3

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1895-9

  • Online ISBN: 978-1-4939-1896-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation