Differences in the red fluorescence of acridine orange bound to single-stranded RNA and DNA.

Abstract

AbstractFluorescence of acridine orange bound to RNA or DNA in the single‐stranded form including single‐stranded synthetic polyribo‐ or polydeoxyribonucleotides was measured in the expectation that some distinct structural characteristic between single‐stranded RNA and DNA might be reflected by a specific fluorescent behaviour of bound dyes. It was found that the complex of the dye with single‐stranded RNA emits a weaker red fluorescence around 650 nm than the complex with single‐stranded DNA at low phosphate‐to‐dye ratios. The fact could be explained neither by a direct interaction of bound dyes with the 2′‐hydroxyl group of ribose in RNA nor by the difference in the G‐C content of the nucleic acids. On the basis of the character of dye molecules emitting the red fluorescence, it was suggested that the bases in single‐stranded RNA might be buried in some hydrophobic environment that would make the dyes less likely to interact with them, compared with the bases in single‐stranded DNA. It was further inferred that some conformational rigidity of single‐stranded RNA may partially be responsible for the weaker red fluorescence.