Synthesis of the Polycation Thymidyl DNG, Its Fidelity in Binding Polyanionic DNA/RNA, and the Stability and Nature of the Hybrid Complexes

Putative drugs consisting of oligonucleotide analogs capable of combining with RNA or DNA, thereby arresting cellular processes at the translational or transcriptional level, are known as antisense and antigene agents. The backbones of viable antisense/antigene agents do not incorporate phosphodiester linkages because of the susceptibility of this linkage to degradation by cellular nucleases. To be effective, such agents must bind with fidelity to target nucleic acids via Watson-Crick and Hoogsteen base pairing. Since antisense/antigene agents must compete with specific oligonucleotides and proteins for RNA/DNA targets, it is desirable that these agents bind with high affinity to compatible RNA/DNA sequences. The stability of double- and triple-stranded RNA and DNA would increase if the electrostatic repulsion among the polyanionic single strands could be alleviated. This is seen in the enhanced binding of the neutrally charged peptide nucleic acids (PNA) to ssDNA. One might suspect, therefore, that a strand complementary to DNA and connected together by positively charged linkages would act as a particularly effective antisense/antigene agent since the repulsive electrostatic effects in dsDNA would be replaced by attractive electrostatic interactions. On the other hand, the electrostatic bonding between polycationic and polyanionic structures might be quite nonspecific and independent of complementary base pairing. We report herein the synthesis of the pentameric thymidyl deoxyribonucleic guanidine (DNG) 1 in which the phosphodiester linkages of DNA [-O(PO sub(2) super(-))O-] are replaced by guanidinium linkages [-NHC(=NH sub(2) super(+))NH-]. Preliminary results indicate that this DNG model compound exhibits complementary base pair recognition toward both RNA and DNA, and the double- and triple-helical structures composed of DNG with RNA or DNA demonstrate unprecedented stability. One should note that DNG is expected to be stable in vivo due to the absence of phosphodiester linkages.