Synthesis and hybridization properties of the conjugates of oligonucleotides and stabilization agents. Part 3

New compds. having tri- or penta-methylenamine linker functions were synthesized.  These derivs. were covalently attached through the 5'-phosphoramide linkage to heptanucleotide pd(CCAAACA).  Complementary complexes of the octa-nucleotide pd(TGTTTGGC) and above oligonucleotide conjugates were tested for their thermodn. response.  The Tm data and thermodn. parameters for complex formation confirmed the ability of chromone (γ-pyrone) derivs. to stabilize strongly the 7-mer/8-mer complementary complex.  Moreover, benzochromone (naphthopyrane) and, surprisingly, tetrahydropyrimidinethanone derivs. showed the capacity of stabilizing this 7-mer/8-mer complementary complex.  The effect of all these compds. on the stability of the oligonucleotide complexes (ΔΔG at 37 °C ranged from -1.2 to -2.0 kcal/mol) was shown to be comparable to the effect of one nucleotide base pair and similar to the effect (ΔΔG at 37 °C ranged from -1.5 to -2.0 kcal/mol) found for acridine-oligonucleotide conjugates, which served as a ref. in this study.