Screening helix-threading peptides for RNA binding using a thiazole orange displacement assay

Malathy Krishnamurthy, Nicole T. Schirle, Peter A. Beal

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

The fluorescent intercalator displacement assay using thiazole orange has been adapted to the study of RNA-binding helix-threading peptides (HTPs). This assay is highly sensitive with HTP-binding RNAs and provides binding affinity data in good agreement with quantitative ribonuclease footprinting without the need for radiolabeling or gel electrophoresis. The FID assay was used to define structure activity relationships for a small library of helix-threading peptides. Results of these studies indicate their RNA binding is dependent on peptide sequence, α-amino acid stereochemistry, and cyclization (vs linear peptides), but independent of macrocyclic ring size for the penta-, tetra- and tri-peptides analyzed.

Original languageEnglish (US)
Pages (from-to)8914-8921
Number of pages8
JournalBioorganic and Medicinal Chemistry
Volume16
Issue number19
DOIs
StatePublished - Oct 1 2008

Fingerprint

Assays
Screening
RNA
Peptides
Intercalating Agents
Rubiaceae
Stereochemistry
Cyclization
Structure-Activity Relationship
Ribonucleases
thiazole orange
Electrophoresis
Amino Acid Sequence
Gels
Amino Acids

Keywords

  • Cyclic peptides
  • High-throughput screening
  • RNA recognition
  • Threading intercalation

ASJC Scopus subject areas

  • Pharmaceutical Science
  • Drug Discovery
  • Organic Chemistry
  • Molecular Medicine
  • Molecular Biology
  • Clinical Biochemistry
  • Biochemistry

Cite this

Screening helix-threading peptides for RNA binding using a thiazole orange displacement assay. / Krishnamurthy, Malathy; Schirle, Nicole T.; Beal, Peter A.

In: Bioorganic and Medicinal Chemistry, Vol. 16, No. 19, 01.10.2008, p. 8914-8921.

Research output: Contribution to journalArticle

Krishnamurthy, Malathy ; Schirle, Nicole T. ; Beal, Peter A. / Screening helix-threading peptides for RNA binding using a thiazole orange displacement assay. In: Bioorganic and Medicinal Chemistry. 2008 ; Vol. 16, No. 19. pp. 8914-8921.
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