Conformational flexibility of ribosomal decoding-site RNA monitored by fluorescent pteridine base analogues

Conformational transitions in ribosomal decoding-site RNA have previously been monitored by replacement of flexible adenine bases with fluorescent 2-aminopurine (2AP). Here, we have studied pteridine base analogues 3-methylisoxanthopterin (3MI) and 6-methylisoxanthopterin (6MI) as fluorescent labels for the investigation of conformational changes in the decoding site that are triggered by ligand binding. The higher quantum yield of 3MI and 6MI along with their relatively red-shifted excitation and emission wavelengths renders the pteridines interesting alternatives to 2AP for the establishment of ligand-binding assays for RNA based on fluorescence labelling.