Tuning urea–phenanthridinium conjugates for DNA/RNA and base pair recognition

A series of novel urea–phenanthridine conjugates was prepared. The variation of linker length connecting two urea–phenanthridinium conjugates regulated their binding mode toward double stranded polynucleotides, consequently controlling selectivity of compounds toward ds-RNA over ds-DNA stabilization as well as selective fluorescence response toward addition of G–C base pair and A–U(T) base pair containing polynucleotides.