Sequence and structural selectivity of nucleic acid binding ligands

The sequence and structural selectivity of 15 different DNA binding agents was explored using a novel, thermodynamically rigorous, competition dialysi s procedure. In the competition dialysis method, 13 different nucleic acid structures were dialyzed against a common ligand solution. More ligand accu mulated in the dialysis tube containing the structural form with the highes t ligand binding affinity. DNA structural forms included in the assay range d from single-stranded forms, through a variety of duplex forms, to multist randed tripler and tetraplex forms. Left-handed Z-DNA, RNA, and a DNA-RNA h ybrid were also represented. Standard intercalators (ethidium, daunorubicin , and actinomycin D) served as control compounds and were found to show str uctural binding preferences fully consistent with their previously publishe d behavior. Standard groove binding agents (DAPI,dystamycin, and netropsin) showed a strong preference for AT-rich duplex DNA forms, along with appare ntly strong binding to the poly(da)-[poly(dT)](2) tripler. Thermal denatura tion studies revealed the apparent tripler binding to be complex, and perha ps to result from displacement of the third strand. Putative tripler (BePI, coralyne, and berberine) and tetraplex [H2TmPyP, 5,10,15,20-tetrakis [4-(t rimethylammonio)phenyl] -21H,23H-porphine, and N-methyl mesoporphyrin IX] s elective agents showed in many cases less dramatic binding selectivity than anticipated from published reports that compared their binding to only a f ew structural forms. Coralyne was found to bind strongly to single-stranded poly(dA), a novel and previously unreported interaction. Finally, three co mpounds (berenil, chromomycin A, and pyrenemethylamine) whose structural pr eferences are largely unknown were examined. Pyrenemethylamine exhibited an unexpected and unprecedented preference for duplex poly(dAdT).