Novel DNA analogues with 2-, 3- and 4-pyridylphosphonate internucleotide bonds: synthesis and hybridization properties

Abstract

Oligothymidylates modified with stereodefined 2-pyridyl-, 3-pyridyl- and 4-pyridylphosphonate moieties at one or two juxtaposed internucleotide positions were prepared, and their avidity towards complementary single stranded DNA and RNA, as well as toward double stranded DNA were evaluated by UV melting temperature and CD studies. It was found that the sense of chirality at the phosphorus centre and the position of the nitrogen atom in the pyridyl ring of a pyridylphosphonate moiety are important factors governing stability of double- and triple-stranded complexes formed by these oligonucleotides. DNA/DNA and DNA/RNA duplexes containing oligothymidylate strands with R_P-pyridylphosphonate units differed only slightly from unmodified reference complexes. In contrast to this, the S_P-pyridylphosphonate derivatives exhibited lower binding affinity than both their R_P-counterparts and the unmodified reference oligonucleotide T₂₀. Triplexes of oligo(thymidyl pyridylphosphonate)s with hairpin oligomer d(A₂₁C₄T₂₁) were found mostly to be thermodynamically slightly more stable in pH 7.4 and less stable in pH 5.0 than non-modified complexes. As expected, oligonucleotides with pyridylphosphonate internucleotide bonds were recognised by 3′- and 5′-exonucleases but the chimeric oligonucleotide chains were not cleaved at the modification sites.