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

Abstract

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 doubleheaded nucleotides, U W and U Z, featuring a methylene-linked 5aza-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.

Double-headed nucleic acids condense the molecular information of DNA to half the number of nucleotides

“…This drawback was also observed for other 2′-T monomers, 12,13 and work is currently ongoing to design a 2′-T analogue with a better specificity. 16 For the sake of completeness, the modified ON's were also hybridized to their RNA complements, however, as seen before, 10 significant destabilization of 11.0 °C to 13.5 °C were observed compared to the unmodified DNA•RNA hybrids (Fig. S16M+N, ESI †).…”

Double‐Headed Nucleotides with Increased Base‐Pairing Affinity and Specificity

“…Recently, we have focused on C2' functionalized double-headed arabinonucleotides with methylene-linkers (U X , Figure 1A), as they can form WatsonÀ Crick base pairs with both nucleobases and thereby act as condensed dinucleotides in a DNA duplex. [20][21][22][23][24][25][26] Encouragingly, molecular dynamics studies have shown that local adjustments of the backbone counteract the structural alteration induced by the incorporation of a double-headed nucleotide, so that the overall B-type duplex of DNA is retained. [23] Moreover, the thermal duplex stability is not particularly affected (� 4.0 °C) [20][21][22][23][24][25] when dinucleotides are replaced with the corresponding double-headed nucleotides.…”

“…Therefore, new monomers with non-natural nucleobases in the 2'-position were prepared and evaluated for their ability to act as improved analogues (Figure 1B). [23,26] For U T , we probed the spatial position of the thymine WatsonÀ Crick face by using hypoxanthine (U H ), [23] propynyl-linked pseudouracil (U W ) and 5-aza-7-deazaxanthine (U Z ) [26] as alternative nucleobases. However, none of these were found to be superior to the original U T monomer in terms of specificity and affinity.…”