Furanose ring conformations in a 1′-alkynyl C-nucleoside and the dinucleotide

A large-scale synthesis was carried out for alkynyl C-nucleotide oligomers in order to clarify the structural details of the artificial DNA. A liquid-phase synthesis by means of phosphoramidite methodology enabled us to handle ∼0.1 g of the DNA oligomers possessing a pseudouracil derivative (T*) as a non-natural nucleobase. ¹H NMR measurements in aqueous media were carried out for the oligomers, succeeded in the accurate assignments of the protons accompanying with determination of the coupling constants (J values). These J values revealed that average conformation of the alkynylribose rings in the DNA was substantially biased toward the S-type conformers ( ²T ₁/E ₁/ ^OT ₁). X-ray crystal analysis of the non-natural nucleoside also supported the S-type conformation ( ²E/ ²T ₁) as seen in natural B-DNA.