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

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

doi:10.1016/j.bmc.2008.08.066

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

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

Chemistry

Research output: Contribution to journal › Article › peer-review

21 Scopus citations

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 language	English (US)
Pages (from-to)	8914-8921
Number of pages	8
Journal	Bioorganic and Medicinal Chemistry
Volume	16
Issue number	19
DOIs	https://doi.org/10.1016/j.bmc.2008.08.066
State	Published - Oct 1 2008

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

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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.",

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AU - Beal, Peter A.

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AB - 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.

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KW - High-throughput screening

KW - RNA recognition

KW - Threading intercalation

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

Abstract

Keywords

ASJC Scopus subject areas

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