Use of the 295- to 300-nanometer circular dichroism through of ribonucleic acid to study helix winding: effect of acridine orange.

Acridine orange decreases the amplitude of the 295-nm circular dichroism (CD) trough of ribosomal ribonucleic acid (rRNA) where the trough has been related to coil character. Since acridine orange is known from earlier work to intercalate between base pairs of nucleic acids, causing an unwinding of the coil, and our studies show a decrease in the 295-nm CD trough, it appears that CD measurements may be used to observe relative unwinding of rRNA. Under similar solution conditions, melting temperatures with acridine orange indicate no significant change in the stabilization of rRNA structure by acridine orange. Hypochromicity studies show no increase in the percent base pairing in rRNA when 0.1 M tris(hydroxymethyl)aminomethane (pH 7.6) with 1.35 M KCl is used. These results indicate that CD changes in the amplitude of the 295-nm trough of rRNA are related to helix winding in rRNA.