A Parallel Stranded Linear DNA Duplex Incorporating dG · dC Base Pairs

Publisher Website
Google Scholar
Abstract
DNA oligonucleotides with appropriately designed complementary sequences can form a duplex in which the two strands are paired in a parallel orientation and not in the conventional antiparallel double helix of B-DNA. All parallel stranded (ps) molecules reported to date have consisted exclusively of dA · dT base pairs. We have substituted four dA · dT base pairs of a 25-nt parallel stranded linear duplex (ps-D1 · D2) with dG · dC base pairs. The two strands still adopt a duplex structure with the characteristic spectroscopic properties of the ps conformation but with a reduced thermodynamic stability. Thus, the melting temperature of the ps duplex with four dG · dC base pairs (ps-D5 · D6) is 10-16°C lower and the van't Hoff enthalpy difference ΔvH for the helix-coil transition is reduced by 20% (in NaCl) and 10% (in MgCl2) compared to that of ps-Dl · D2. Based on energy minimizations of a ps-[d(T5GA5) · d(A5CT5)] duplex using force field calculations we propose a model for the conformation of a trans dG · dC base pair in a ps helix.