Double-Headed 2′-Deoxynucleotides That Hybridize to DNA and RNA Targets via Normal and Reverse Watson–Crick Base Pairs

Through the use of modified nucleotides, synthetic nucleic acids have found several fields of application within biotechnology and in the pharmaceutical industry. We have previously introduced nucleotides with an additional functional nucleobase linked to C2′ of arabinonucleotides (B_X). These double-headed nucleotides fit neatly into DNA·DNA duplexes, where they can replace the corresponding natural dinucleotides and thus condense the molecular information. Here, we introduce a 2′-deoxy version of the B_X design with inversion of the C2′ stereochemistry (^dSB_X) with the aim of obtaining improved RNA recognition. Specifically, ^dSB_X analogues with cytosine or isocytosine attached to C2′ of 2′-deoxyuridine (^dSU_C and ^dSU_iC) were synthesized and evaluated in duplexes. Whereas the ^dSB_X design did not outperform the B_X design in terms of mimicking dinucleotides in nucleic acid duplexes, it was able to engage in reverse Watson–Crick pairing using its 2′-base. This was evident from the ability of the ^dSU_C cytosine to form stable mis-matching base pairs with opposite cytosines identified as hemiprotonated C·C⁺ pairs. Furthermore, specific base-pairing with guanine was only observed for the isocytosine-bearing ^dSU_iC monomer. Very stable duplexes were obtained with ^dSU_C/iC monomers in each strand indicating that fully modified double-headed nucleic acid sequences could be based on the ^dSB_X design.