HELIX-STABILIZING COMPOUNDS CC-1065 AND U-71,184 BIND TO RNA-DNA AND DNA-DNA DUPLEXES CONTAINING MODIFIED INTERNUCLEOTIDE LINKAGES AND STABILIZE DUPLEXES AGAINST THERMAL MELTING

CC-1065 and U-71,184 bind and hyperstabilize DNA duplexes, but little is known about their effects on nucleic acid duplexes of different str ucture, A 20 mer DNA sequence (5'-TTACTTCAGTTATGAGACCA) containing a d rug binding sequence (5'-AGTTA) was selected as the target sequence, a nd this was duplexed with complementary antisense sequences containing phosphodiester (PO), phosphorothioate (PS), and methylphosphonate (MP ) bonds, The duplexes containing PO or PS bound 2 CC-1065 molecules pe r duplex, presumably at both the target site and at a lower affinity s ite (5'-AGTAA) on the antisense strand, The duplex containing MP bound only 1 CC-1065, and all duplexes bound only 1 U-71,184, Both CC-1065 and U-71,184 bound to 20 mer duplexes comprised of oligo(dA)-oligo(dT) (2.5 and 2 drugs per duplex, respectively) and poly(rA)-oligo(dT) (1 drug per 20 base pairs), CC-1065 also bound to duplexes between the PO - or PS-based antisense structures and a complementary synthetic 20 me r RNA sequence, with about 1 drug per duplex in each case, CC-1065 inc reased the T-m for the 20 mer DNA duplexes 17 to 29 degrees C, and the corresponding values for U-71,184 ranged from 7 to 19 degrees C, CC-1 065 raised the T-m of oligo(dA)-oligo(dT) and poly(rA)-oligo(dT) 29 de grees C, U-71,184 increased the T-m for oligo(dA)-oligo(dT) 30 degrees C but did not significantly elevate the T-m for the corresponding RNA -DNA duplex, The results show that CC-1065 and U-71,184 are capable of binding and stabilizing a variety of nucleic acid duplexes, These age nts or their analogs may become useful ligands for antisense oligonucl eotide applications.