New permanently charged phenanthridinium–nucleobase conjugates. Interactions with nucleotides and polynucleotides and recognition of ds‐polyAH+

Abstract N‐Methyl‐8‐aminophenathridinium–uracil and –adenine conjugates possessing a nucleobase attached at the phenanthridinium 8‐amino group by a trimethylene spacer were prepared in the form of water‐soluble hydrogensulfate salts. Spectroscopic characteristics of the conjugates reveal the formation of folded conformations in water characterized by intramolecular aromatic stacking between the phenanthridinium unit and the tethered nucleobase. The conjugates form 1:1 complexes in water with either complementary or non‐complementary nucleotides, giving log Ks values between 1 and 2 and showing a lack of any base recognition. Also, the binding studies with single‐stranded polynucleotides showed no preference of conjugates to polynucleotides containing complementary nucleobases. At pH 5, the N‐methylphenanthridinium–adenine conjugate exhibited preferred binding to double‐stranded (ds‐) polyAH+, whereas its protonated analogue bound preferably to polyU. The results reveal that the presence of protonated or permanently charged intercalator units in the conjugates dramatically changes their binding preferences for polynucleotides. Copyright © 2003 John Wiley & Sons, Ltd.