Fluorescence quenching of parallel-stranded DNA bound ethidium bromide: the effect of 7-deaza-2'-deoxyisoguanosine and 7-halogenated derivatives.

Parallel stranded (ps) duplexes were constructed by incorporating 7-deaza-2'-deoxyisoguanosine (1a) or its 7-halogenated analogs 1b,c in place of 2'-deoxyisoguanosine. UV and Tm analyses prove the high affinity of ethidium bromide (EB) to these modified duplexes. Steady-state fluorescence measurement shows that the fluorescence is quenched when EB is bound to ps duplexes containing compounds 1a-c. The quenching effect depends on the 7-substituent of the nucleobase.