Structural studies of oligonucleotides with an O4-isopropylated thymine. d(i4TpT), d(Tpi4T), and d(Tpi4TpT)

Abstract

Syntheses are described for d(i4TpT) (1), d(Tpi4T) (2), and d(Tpi4TpT) (3), the O4-isopropylated analogues of d(TpT) (4) and d(TpTpT) (5). The detection of the molecular [M – H]− ions and some [2M – H]− aggregates shows that Fast Atom Bombardment mass spectrometry operating in the negative ion mode is useful for structural analysis of these DNA oligomers. In contrast with the monomer, i4dT, the two O4-isopropyl methyl groups of 1 and 2 are magnetically nonequivalent and give rise to separate 1H and 13C NMR signals. Their chemical shift difference (Δ) decreases gradually with increasing temperature, and can be interpreted as reflecting intramolecular base stacking, in line with circular dichroic data. This chemical shift difference is not seen in the 1H NMR spectra of 3, and is attenuated in the 13C spectra of this trimer. Coupling constant data indicate a shift towards the 3′-endo conformation of the sugar of the i4Tp moiety of 1, a trend observed for the corresponding O4-ethylated moiety of d(e4TpT). 13C–31P and 1H–31P coupling constants indicate that the structural features monitored by these couplings are not significantly altered by O4-isopropylation of the thymine base. Keywords: oligonucleotides, O-alkylation, stereochemistry, NMR, mass spectrometry.