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 (2T1/E1/OT1). X-ray crystal analysis of the non-natural nucleoside also supported the S-type conformation (2E/2T1) as seen in natural B-DNA.