Dlakic M, Park K, Griffith J D, Harvey S C, Harrington R E
Department of Biochemistry 330, University of Nevada at Reno, Reno, Nevada 89557, USA.
J Biol Chem. 1996 Jul 26;271(30):17911-9. doi: 10.1074/jbc.271.30.17911.
Contemporary predictive models for sequence-dependent DNA structure provide a good estimation of overall DNA curvature in most cases. However, the two current models differ fundamentally in their view of the origin of DNA curvature. An earlier model that associates DNA bending primarily, although not exclusively, with stretches of adenines (A-tracts) is based on results of comparative gel retardation, cyclization kinetics, hydroxyl radical cutting, and other solution measurements. It represents an intersection of wedge and junction models. More recently, a non-A-tract bending model has been proposed, built on structural results from x-ray crystallography and molecular modeling. In this view, A-tracts are proposed to be straight and rigid, whereas mixed sequence DNA is bent. Because a key premise of the non-A-tract bending model is the crystallographic observation that A-tracts are straight, we have examined the effect in solution of 2-methyl-2,4-pentanediol (MPD), an organic solvent used in crystal preparation for crystallographic DNA structure determinations. Using cyclization analysis, DNase I cutting, chemical probing, and electron microscopy on DNA oligomers with and without A-tracts, we show that the presence of MPD in solution dramatically affects A-tracts and that the effect is specific to these sequence elements. Combined with the previous observation that MPD affects gel mobility of curved sequences with A-tracts, our findings support the bent A-tract model and call for caution in the interpretation of crystallographic results on DNA structure as these are presently obtained.
当代用于预测序列依赖性DNA结构的模型在大多数情况下能够很好地估计DNA的整体曲率。然而，目前的两种模型在对DNA曲率起源的看法上存在根本差异。较早的一种模型主要（但并非唯一）将DNA弯曲与腺嘌呤序列（A序列）联系起来，该模型基于比较凝胶阻滞、环化动力学、羟基自由基切割及其他溶液测量结果。它代表了楔形模型和连接模型的交叉。最近，基于X射线晶体学和分子建模的结构结果，提出了一种非A序列弯曲模型。按照这种观点，A序列被认为是直的且刚性的，而混合序列的DNA是弯曲的。由于非A序列弯曲模型的一个关键前提是晶体学观察到A序列是直的，我们研究了2-甲基-2,4-戊二醇（MPD）在溶液中的作用，MPD是一种用于晶体学DNA结构测定的晶体制备中的有机溶剂。通过对含有和不含有A序列的DNA寡聚物进行环化分析、DNase I切割、化学探针检测和电子显微镜观察，我们发现溶液中MPD的存在会显著影响A序列，且这种影响对这些序列元件具有特异性。结合之前观察到MPD会影响含有A序列的弯曲序列的凝胶迁移率，我们的研究结果支持弯曲A序列模型，并呼吁在解释目前所获得的关于DNA结构的晶体学结果时要谨慎。
