KINKING OF DNA AND RNA HELICES BY BULGED NUCLEOTIDES OBSERVED BY FLUORESCENCE RESONANCE ENERGY-TRANSFER

Fluorescence resonance energy transfer (FRET) has been used to demonst rate the bending of DNA and RNA helices for three series of double-str anded molecules containing bulge loops of unopposed adenosine nucleoti des (A,, n = 0-9). Fluorescein and rhodamine were covalently attached to the 5' termini of the two component strands. Three different method s were applied to measure the FRET efficiencies. The extent of energy transfer within each series increases as the number of bulged nucleoti des varies from 1 to 7, indicating a shortening of the end-to-end dist ance. This is consistent with a bending of DNA and RNA helices that is greater for larger bulges. The FRET efficiency for DNA molecules with As bulges is lower than the efficiency for the corresponding A(7) bul ged molecules, although the Ag molecules exhibit increased electrophor etic retardation. Ranges of bending angles can be estimated from the F RET results.