TRIPLE-HELIX FORMATION WITH SHORT OLIGONUCLEOTIDE INTERCALATOR CONJUGATES MATCHING THE HIV-1 U3 LTR END SEQUENCE

In an attempt to target short purine sequences in view of pharmacologi cal application, we have synthesized three new TFO (triple-helix-formi ng oligonucleotide) conjugates in which an intercalating oxazolopyrido carbazole (OPC) chromophore is linked by a pentamethylene linker to a 7-mer oligonucleotide matching the polypurine/polypyrimidine sequence located in the HIV-1 U3 LTR end region. The TFO moiety of conjugates a re 5'CCTTCCC, 5'GGGAAGG, and 5'GGGTTGG. Their ability to bind to doubl e-stranded DNA targets was examined. This binding- is demonstrated by a footprinting technique using DNase I as a cleaving agent. The comple x involved intermolecular pyr-purpyr or pur-purpyr triple helix. Pyrim idine TFO-OPC binds in a pH-dependent manner, whereas the others do no t. The formation of the complex has been investigated at neutral pH an d increasing temperature. We observed that the protection due to the p urine and mixed TFO-OPC was pH independent and remained identical up t o 40-degrees-C. To determine the position of the OPC chromophore, mole cular modeling was undertaken on the purine-conjugate/target complex. It has been suggested that the complex involved the intercalation of t he OPC at the triplex-duplex junction with a small unwinding at the ne xt excluded site.