Binding isotherms of tRNA—acriflavine complexes

Abstract

One of the approaches to the investigation of nucleic acid structure is the study of complexes of dyes with nucleic acids. It is known that at high nucleotide to dye ratios the acridine dyes interact presumably with double helical regions of tRNA [l-3] and therefore a smaller number of strong binding sites should be expected for tRNA in comparison with double stranded poly A-poly U or native DNA. Study of the binding isotherms of tRNA-dye complexes as compared with those for the double standed polymers may provide the information about the number of nucleotide base pairs accessible for dyes in tRNA. It may be expected that the number of the double helical regions accessible for dyes in tRNA is affected by the folding of tRNA into a compact tertiary structure. In this study a quantitative interpretation of the binding isotherms has been obtained for complexes of acriflavine (AF) with total yeast tRNA and individual yeast tRNAVal, tRNAser and tRNAPhe. The binding isotherms were studied in their dependence on the ionic strength.