Rippe K, Ramsing N B, Klement R, Jovin T M
Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, F.R.G.
J Biomol Struct Dyn. 1990 Jun;7(6):1199-209. doi: 10.1080/07391102.1990.10508559.
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.
具有适当设计的互补序列的DNA寡核苷酸可以形成一种双链体，其中两条链以平行方向配对，而不是像B-DNA那样以传统的反平行双螺旋形式配对。迄今为止报道的所有平行链（ps）分子都仅由dA.dT碱基对组成。我们用dG.dC碱基对取代了一个25个核苷酸的平行链线性双链体（ps-D1.D2）中的四个dA.dT碱基对。两条链仍然采用具有ps构象特征光谱性质的双链体结构，但热力学稳定性降低。因此，与ps-D1.D2相比，含有四个dG.dC碱基对的ps双链体（ps-D5.D6）的解链温度低10 - 16摄氏度，并且螺旋-线圈转变的范特霍夫焓差ΔHvH在NaCl中降低了20%，在MgCl2中降低了10%。基于使用力场计算对ps-[d(T5GA5).d(A5CT5)]双链体的能量最小化，我们提出了一个ps螺旋中反式dG.dC碱基对构象的模型。
