Dlakic M, Harrington R E
Department of Biochemistry 330, University of Nevada at Reno, Reno, NV 89557-0014, USA.
Nucleic Acids Res. 1998 Sep 15;26(18):4274-9. doi: 10.1093/nar/26.18.4274.
A novel, multiple DNA phasing analysis is described in which three sequence motifs associated with bent DNA are clustered together in oligomers of identical base composition, but with different phasing relationships of these motifs to each other. Synthetic oligonucleotides containing different combinations of AAAAA(A), GGGCCC and GAGAG sequence motifs were ligated and analyzed by gel mobility and cyclization experiments to determine their global curvature. These assays were used to obtain relative bending contributions of the analyzed sequence motifs. The experimental results also provide a rigorous test of predictive models for DNA bending. We report, using molecular modeling, that none of the most widely used dinucleotide (nearest neighbor) models can accurately describe the conformational properties of these DNA sequences and that more complex models, at least at the trinucleotide level, are required.
本文描述了一种新颖的多重DNA相位分析方法，其中与弯曲DNA相关的三个序列基序在碱基组成相同但这些基序彼此具有不同相位关系的寡聚物中聚集在一起。通过凝胶迁移和环化实验连接并分析含有AAAAA(A)、GGGCCC和GAGAG序列基序不同组合的合成寡核苷酸，以确定它们的整体曲率。这些测定用于获得所分析序列基序的相对弯曲贡献。实验结果还为DNA弯曲的预测模型提供了严格的检验。我们通过分子建模报告，最广泛使用的二核苷酸（最近邻）模型均无法准确描述这些DNA序列的构象特性，并且需要更复杂的模型，至少在三核苷酸水平上。
