Synthesis and hybridization properties of the conjugates of oligonucleotides and stabilization agents—II Original Research Article

New pyranone derivatives having tri- or pentamethylenamine linker functions were synthesized. These derivatives were covalently attached through the 5′-phosphoramide linkage to heptanucleotide pd(CCAAACA). Complementary complexes of the octanucleotide pd(TGTTTGGC) and above oligonucleotide conjugates were tested for their thermodynamic response. The Tm data and thermodynamic parameters for complex formation have demonstrated the ability of chromone (γ-pyrone) and coumarin (α-pyrone) derivatives to stabilize strongly 7-mer/8-mer complementary complex, most likely through the stacking interaction of the pyran aromatic system with the neighboring nucleotide bases. The effect of chromone (or coumarin) derivatives on the stability of the oligonucleotide complexes (AAG at 37 °C ranged from −1.0 to −1.7 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 acridineoligonucleotide conjugates served in this study as a reference.