C. Epple et C. Leumann, BICYCLO[3.2.1]-DNA, A NEW DNA ANALOG WITH A RIGID BACKBONE AND FLEXIBLY LINKED BASES - PAIRING PROPERTIES WITH COMPLEMENTARY-DNA, Chemistry & biology, 5(4), 1998, pp. 209-216
Background: The structural and conformational variety in nucleic acid
complexes is largely controlled by the sugar-phosphate backbone. In or
der to modulate specific features such as strength or selectivity of c
omplex formation by designing nucleotide analogs, a deeper understandi
ng of the relationship between mononucleotide structures and the prope
rties of their oligomers is necessary. One approach involves comparing
the properties of DNA analogs displaying well defined modifications i
n their backbone structure with those of natural DNA and RNA. Results:
We have designed and synthesized a new DNA analog, 'bicyclo[3.2.1]-DN
A', which has a rigid phosphodiester backbone that emulates a B-DNA-ty
pe 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 generall
y with lower Tm values than pure DNA duplexes. Duplex formation is str
ictly constrained to antiparallel complementary sequences, and base-mi
smatch discrimination is slightly enhanced compared to pure DNA duplex
es. In addition, bicyclo[3.2.1]-DNA sequences are resistant to a 3'-ex
onuclease. Conclusions: The furanose unit present in natural nucleosid
es is not necessary for a competent and stable phosphodiester-based pa
iring system, provided that the backbone is conformationally constrain
ed. The information for the preference of antiparallel strand associat
ion 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 backbon
e itself. Furthermore, conformational flexibility in the base-pairing
region does not lead to a loss of mismatch in base-pair formation.