Sequence-Specific Ultrasonic Cleavage of DNA
Sequence-Specific Ultrasonic Cleavage of DNA
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DOI：
10.1016/j.bpj.2010.10.052
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发表时间：
2011-01-05
影响因子：
3.4
通讯作者：
Nechipurenko, Yury D.
中科院分区：
文献类型：
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作者：
Grokhovsky, Sergei L.;Il'icheva, Irina A.;Nechipurenko, Yury D.
我们用聚丙烯酰胺凝胶电泳法分析了一大组DNA限制性片段的切割模式，从而研究了DNA的超声切割现象。发现单个磷酸二酯键的断裂强度取决于核苷酸序列和键相对于片段末端的位置。用多元统计分析方法测定了16个二核苷酸和256个四核苷酸的中心磷酸二酯键断裂的相对强度。我们观察到脱氧胞苷后磷酸二酯键的相对裂解强度(裂解速率)的平均值显著增加，在二核苷酸：D(CpG)&Gt；d(CPA)&Gt；d(CPt)&Gt；d(CPC)的顺序中减小。各对互补二核苷酸的裂解率有显著差异。四核苷酸中侧翼核苷酸对所有16种中心二核苷酸的裂解率的影响也具有统计学意义。二核苷酸序列相关的超声裂解速率与报道的5‘-脱氧核糖构象运动强度的数据一致。作为局部构象动态的一种衡量标准，卵裂率可能有助于描述基因组的功能区域。
We investigated the phenomenon of ultrasonic cleavage of DNA by analyzing a large set of cleavage patterns of DNA restriction fragments using polyacrylamide gel electrophoresis. The cleavage intensity of individual phosphodiester bonds was found to depend on the nucleotide sequence and the position of the bond with respect to the ends of the fragment. The relative intensities of cleavage of the central phosphodiester bond in 16 dinucleotides and 256 tetranucleotides were determined by multivariate statistical analysis. We observed a remarkable enhancement of the mean values of the relative intensities of cleavage (cleavage rates) in phosphodiester bonds following deoxycytidine, which diminished in the row of dinucleotides: d(CpG) > d(CpA) > d(CpT) >> d(CpC). The cleavage rates for all pairs of complementary dinucleotides were significantly different from each other. The effect of flanking nucleotides in tetranucleotides on cleavage rates of all 16 types of central dinucleotides was also statistically significant. The sequence-dependent ultrasonic cleavage rates of dinucleotides are consistent with reported data on the intensity of the conformational motion of their 5'-deoxyribose. As a measure of local conformational dynamics, cleavage rates may be useful for characterizing functional regions of the genome.