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 severalfields of application within biotechnology and inthe pharmaceutical industry. We have previously introduced nucleotideswith an additional functional nucleobase linked to C2 ' of arabinonucleo-tides (BX). These double-headed nucleotidesfit neatly into DNAmiddotDNAduplexes, where they can replace the corresponding natural dinucleotidesand thus condense the molecular information. Here, we introduce a 2 '-deoxy version of theBXdesign with inversion of the C2 ' stereochemistry(dSBX) with the aim of obtaining improved RNA recognition. Specifically,dSBXanalogues with cytosine or isocytosine attached to C2 ' of 2 '-deoxyuridine (dSUCanddSUiC) were synthesized and evaluated induplexes. Whereas thedSBXdesign did not outperform theBXdesign 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 thedSUCcytosine toform stable mis-matching base pairs with opposite cytosines identified as hemiprotonated CmiddotC+pairs. Furthermore, specific base-pairing with guanine was only observed for the isocytosine-bearingdSUiCmonomer. Very stable duplexes were obtained withdSUC/iCmonomers in each strand indicating that fully modified double-headed nucleic acid sequences could be based on the dSBXdesign

Automated summary

By modifying nucleotides, synthetic nucleic acids have been applied in various fields of biotechnology and the pharmaceutical industry. This study introduces a 2'-deoxy version of the BX design (dSBX) with the purpose of improving RNA recognition. The dSBX design was found to engage in reverse Watson-Crick pairing using its 2'-base and form stable base pairs with specific nucleobases.