Guckian Kevin M, Schweitzer Barbara A, Ren Rex X-F, Sheils Charles J, Tahmassebi Deborah C, Kool Eric T
Contribution from the Department of Chemistry, University of Rochester, Rochester, New York 14627.
J Am Chem Soc. 2000 Feb 10;122(10):2213-2222. doi: 10.1021/ja9934854.
We report the use of thermodynamic measurements in a self-complementary DNA duplex (5'-dXCGCGCG)(2), where X is an unpaired natural or nonnatural deoxynucleoside, to study the forces that stabilize aqueous aromatic stacking in the context of DNA. Thermal denaturation experiments show that the core duplex (lacking X) is formed with a free energy (37 °C) of -8.1 kcal·mol(-1) in a pH 7.0 buffer containing 1 M Na(+). We studied the effects of adding single dangling nucleosides (X) where the aromatic "base" is adenine, guanine, thymine, cytosine, pyrrole, benzene, 4-methylindole, 5-nitroindole, trimethylbenzene, difluorotoluene, naphthalene, phenanthrene, and pyrene. Adding these dangling residues is found to stabilize the duplex by an additional -0.8 to -3.4 kcal·mol(-1). At 5 μM DNA concentration, T(m) values range from 41.7 °C (core sequence) to 64.1 °C (with dangling pyrene residues). For the four natural bases, the order of stacking ability is A > G ≥ T = C. The nonpolar analogues stack more strongly in general than the more polar natural bases. The stacking geometry was confirmed in two cases (X = adenine and pyrene) by 2-D NOESY experiments. Also studied is the effect of ethanol cosolvent on the stacking of natural bases and pyrene. Stacking abilities were compared to calculated values for hydrophobicity, dipole moment, polarizability, and surface area. In general, hydrophobic effects are found to be larger than other effects stabilizing stacking (electrostatic effects, dispersion forces); however, the natural DNA bases are found to be less dependent on hydrophobic effects than are the more nonpolar compounds. The results also point out strategies for the design nucleoside analogues that stack considerably more strongly than the natural bases; such compounds may be useful in stabilizing designed DNA structures and complexes.
我们报道了在一种自我互补的DNA双链体（5'-dXCGCGCG）₂中利用热力学测量，其中X是一个未配对的天然或非天然脱氧核苷，以研究在DNA环境中稳定水性芳香堆积的作用力。热变性实验表明，在含有1 M Na⁺的pH 7.0缓冲液中，核心双链体（不含X）形成时的自由能（37℃）为 -8.1 kcal·mol⁻¹。我们研究了添加单个悬垂核苷（X）的影响，其中芳香“碱基”为腺嘌呤、鸟嘌呤、胸腺嘧啶、胞嘧啶、吡咯、苯、4-甲基吲哚、5-硝基吲哚、三甲苯、二氟甲苯、萘、菲和芘。发现添加这些悬垂残基可使双链体额外稳定 -0.8至 -3.4 kcal·mol⁻¹。在5 μM的DNA浓度下，熔解温度（Tm）值范围从41.7℃（核心序列）到64.1℃（带有悬垂芘残基）。对于四种天然碱基，堆积能力的顺序为A > G ≥ T = C。一般来说，非极性类似物比极性更强的天然碱基堆积得更强烈。通过二维NOESY实验在两种情况下（X =腺嘌呤和芘）证实了堆积几何结构。还研究了乙醇共溶剂对天然碱基和芘堆积的影响。将堆积能力与疏水性、偶极矩、极化率和表面积的计算值进行了比较。一般来说，发现疏水作用比其他稳定堆积的作用（静电作用、色散力）更大；然而，发现天然DNA碱基比更非极性的化合物对疏水作用的依赖性更小。结果还指出了设计核苷类似物的策略，这些类似物的堆积比天然碱基强得多；此类化合物可能有助于稳定设计的DNA结构和复合物。
