Dlakić M, Harrington R E
Department of Biochemistry/330, University of Nevada, Reno 89557, USA.
Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):3847-52. doi: 10.1073/pnas.93.9.3847.
Recent experiments have exposed significant discrepancies between experimental data and predictive models for DNA structure. These results strongly suggest that DNA structural parameters incorporated in the models are not always sufficient to account for the influence of sequence context and of specific ion effects. In an attempt to evaluate these two effects, we have investigated repetitive DNA sequences with the sequence motif GAGAG.CTCTC located in different helical phasing arrangements with respect to poly(A) tracts and GGGCCC.GGGCCC sequence motifs. Methods used are ligase-mediated cyclization and gel mobility experiments along with DNase I cutting and chemical probe studies. The results provide new evidence for curvature in poly(A) tracts. They also show that the sequence context in which bending and flexible sequence elements are found is an important aspect of sequence-dependent DNA conformation. Although dinucleotide models generally have good predictive power, this work demonstrates that in some instances sequence elements larger than the dinucleotide must be taken into account, and hence it provides a starting point for the appropriate modification and refinement of existing structural models for DNA.
最近的实验揭示了DNA结构的实验数据与预测模型之间存在显著差异。这些结果有力地表明，模型中纳入的DNA结构参数并不总是足以解释序列背景和特定离子效应的影响。为了评估这两种效应，我们研究了具有序列基序GAGAG.CTCTC的重复DNA序列，这些序列相对于聚（A）序列和GGGCCC.GGGCCC序列基序处于不同的螺旋相位排列。所使用的方法包括连接酶介导的环化和凝胶迁移实验，以及DNase I切割和化学探针研究。结果为聚（A）序列中的曲率提供了新证据。它们还表明，发现弯曲和柔性序列元件的序列背景是序列依赖性DNA构象的一个重要方面。尽管二核苷酸模型通常具有良好的预测能力，但这项工作表明，在某些情况下，必须考虑大于二核苷酸的序列元件，因此它为适当修改和完善现有的DNA结构模型提供了一个起点。
