Double-Headed Nucleotides with Non-Native Nucleobases: Synthesis and Duplex Studies

Double-headed nucleotides are DNA building blocks that store, in principle, twice as much information as native nucleotides due to the incorporation of an additional functional nucleobase. Herein, we present the development of two new double-headed nucleotides, U-W and U-Z(,) featuring a methylene-linked 5-aza-7-deazaxanthine (Z) and a propynyl-linked pseudouracil (W), respectively, attached to the 2 '-position of arabinouridine. These analogs are evaluated in DNA duplexes for their ability to act as dinucleotides, and the base-pairing specificities of the 2 '-nucleobases are compared to previous analogues. Although an improved discrimination was observed in the context of a cytosine mismatch using U-Z, neither of the two new analogs gave rise to increased overall base-pairing fidelity possibly due to the formation of stable wobble pairs. Furthermore, we present an improved synthetic strategy for the preparation of the corresponding diaminopurine analog (U-D), in which the key fluoro-to-amino substitution is achieved post-synthetically to avoid the use of doubly protected diaminopurines and complicated deprotections.

Automated summary

Double-headed nucleotides theoretically store twice as much information as native nucleotides, but the two newly developed analogs still need improvement in enhancing base-pairing specificity. Additionally, an improved synthetic strategy is proposed to avoid using doubly protected diaminopurines and complicated deprotections.