title: A parallel stranded linear DNA duplex incorporating dG.dC base pairs.
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 degrees C lower and the van't Hoff enthalpy difference delta HvH for the helix-coil transition is reduced by 20% (in NaCl) and 10% (in MgCl2) compared to that of ps-D1.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.
authors.affiliation: Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, F.R.G.
authors.forename: K
authors.initials: K
authors.lastname: Rippe
authors.forename: N B
authors.initials: NB
authors.lastname: Ramsing
authors.forename: R
authors.initials: R
authors.lastname: Klement
authors.forename: T M
authors.initials: TM
authors.lastname: Jovin
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003596:Cytosine; D004247:DNA / Q000032:analysis / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D006147:Guanine; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides; D013056:Spectrophotometry, Ultraviolet
chemical_list: D009838:Oligodeoxyribonucleotides; D006147:Guanine; D003596:Cytosine; D004247:DNA