Screening helix-threading peptides for RNA binding using a thiazole orange displacement assay.
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, alpha-amino acid stereochemistry, and cyclization (vs linear peptides), but independent of macrocyclic ring size for the penta-, tetra- and tri-peptides analyzed.
Krishnamurthy
Malathy
M
Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
Schirle
Nicole T
NT
Beal
Peter A
PA
D052160:Benzothiazoles / Q000737:chemistry*; D001665:Binding Sites; D001681:Biological Assay / Q000379:methods*; D003500:Cyclization; D004586:Electrophoresis / Q000379:methods; D005456:Fluorescent Dyes / Q000737:chemistry*; D007364:Intercalating Agents / Q000737:chemistry*; D007553:Isotope Labeling; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D017433:Protein Structure, Secondary; D011804:Quinolines / Q000737:chemistry*; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D013329:Structure-Activity Relationship
D052160:Benzothiazoles; D005456:Fluorescent Dyes; D007364:Intercalating Agents; D010455:Peptides; D011804:Quinolines; C051000:thiazole orange; D012313:RNA
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