Fluorescence studies on the interaction of ethidium bromide with duplex, triplex and quadruplex DNA structures

Under different conditions, oligonucleotides can form several alternative D NA structures such as duplex, tripler and quadruplex. AU these structures c an interact with ethidium bromide (EB) and make its fluorescence intensity change. The fluorescence spectra and other related parameters provided by s tatic fluorescence techniques showed that the interaction mechanisms betwee n EB and these structures were not always the same. Among them, B type dupl ex and tripler DNA adopt an intercalative mode when binding to the EB, whic h has a relatively high efficiency of energy transfer and the fluorescence of EB cannot he quenched easily. While for the parallel duplex DNA, the int eraction mode is an outside binding in which energy transfer can hardly hap pen and its fluorescence intensity as well as Stern-Volmer constant is almo st the same to the free EB. For the quadruplex, the binding mechanism to EB is more complex. Results from the energy transfer and quenching studies in dicate that the two interaction modes noted above probably coexist at the s ame time.