Bicyclo[3.2.1]-DNA, a new DNA analog with a rigid backbone and flexibly linked bases: pairing properties with complementary DNA

Background: The structural and conformational variety in nucleic acid complexes is largely controlled by the sugar-phosphate backbone. In order to modulate specific features such as strength or selectivity of complex formation by designing nucleotide analogs, a deeper understanding of the relationship between mononucleotide structures and the properties of their oligomers is necessary. One approach involves comparing the properties of DNA analogs displaying well defined modifications in their backbone structure with those of natural DNA and RNA. Results: We have designed and synthesized a new DNA analog, 'bicyclo[3.2.1]-DNA', which has a rigid phosphodiester backbone that emulates a B-DNA-type conformation, to which the nucleobases are attached via a flexible open-chain linker. A UV-melting curve analysis shows that bicyclo[3.2.1]-DNA forms stable duplexes with complementary DNA, although generally with lower Tm values than pure DNA duplexes. Duplex formation is strictly constrained to antiparallel complementary sequences, and base-mismatch discrimination is slightly enhanced compared to pure DNA duplexes. In addition, bicyclo[3.2.1]-DNA sequences are resistant to a 3'-exonuclease. Conclusions: The furanose unit present in natural nucleosides is not necessary for a competent and stable phosphodiester-based pairing system, provided that the backbone is conformationally constrained. The information for the preference of antiparallel strand association in B-DNA is not merely a consequence of bases being attached to a specific side of the furanose unit, but is also encoded in the backbone itself. Furthermore, conformational flexibility in the base-pairing region does not lead to a loss of mismatch in base-pair formation.