Dolinnaya N G, Braswell E H, Fossella J A, Klump H, Fresco J R
Department of Molecular Biology, Princeton University, New Jersey 08544-1014.
Biochemistry. 1993 Sep 28;32(38):10263-70. doi: 10.1021/bi00089a049.
Previously (Dolinnaya & Fresco, 1992), on the basis of an analysis of UV absorption and CD properties as a function of temperature and pH, the secondary structure of the deoxyoligonucleotide d(A(+)-G)10 was hypothesized to be helical and intramolecular in origin, being stabilized not by stacked bases or hydrogen-bonded base pairs but instead by ionic bonds between positively charged adenine residues and distal negatively charged phosphates. Several other properties are now shown to be consistent with this unusual type of structure. The molecular weight determined for d(A(+)-G)10 by sedimentation equilibrium is that of the single strand, and consistent with this, there is no molecular weight change on helix disruption. Formation of the d(A(+)-G)10 helix is accompanied by cooperative uptake of nine protons, corresponding to nine adenine residues that can form ionic bonds with all the available distal phosphates, i.e., the n+1 or the n+2 phosphates. The thermodynamic parameters of this helical structure obtained from both van't Hoff analysis of the melting of the structure and calorimetric measurements are in keeping with the ionic properties of the proposed structure. So are the dependence of its stability on pH and ionic strength, and also on oligomer length when compared with the behavior of d(A(+)-G)6. The possible role of this type of secondary structure in protein recognition of the single-stranded homopurine element of H-DNA is evaluated.
此前（多利纳亚和弗雷斯科，1992年），基于对紫外吸收和圆二色性（CD）性质随温度和pH值变化的分析，脱氧寡核苷酸d(A(+)-G)10的二级结构被推测为螺旋状且起源于分子内，其稳定并非通过堆积碱基或氢键碱基对，而是通过带正电荷的腺嘌呤残基与远端带负电荷的磷酸基团之间的离子键。现在已证明其他几个性质与这种不寻常的结构类型相符。通过沉降平衡测定的d(A(+)-G)10的分子量为单链分子量，与此一致的是，螺旋破坏时分子量没有变化。d(A(+)-G)10螺旋的形成伴随着九个质子的协同摄取，这对应于九个能与所有可用远端磷酸基团（即n + 1或n + 2磷酸基团）形成离子键的腺嘌呤残基。从该结构熔解的范特霍夫分析和量热测量获得的这种螺旋结构的热力学参数与所提出结构的离子性质相符。其稳定性对pH值和离子强度的依赖性，以及与d(A(+)-G)6行为相比对寡聚物长度的依赖性也是如此。评估了这种二级结构类型在蛋白质识别H-DNA单链同型嘌呤元件中的可能作用。
