Structural analysis of hyperperiodic DNA from Caenorhabditis elegans.
Structural analysis of hyperperiodic DNA from Caenorhabditis elegans.
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DOI：
10.1093/nar/gkl397
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发表时间：
2006
影响因子：
14.9
通讯作者：
Dekker, Nynke H.
中科院分区：
文献类型：
--
作者：
Moreno-Herrero, Fernando;Seidel, Ralf;Johnson, Steven M.;Fire, Andrew;Dekker, Nynke H.
一些生物信息学研究已经在秀丽线虫基因组的某些区域发现了一种意想不到但非常普遍的∼10bp的AA/TT二核苷酸周期(超周期)。尽管相关线虫DNA片段与来自其他来源(如锥虫线粒体)的弯曲DNA具有某些序列特征，但线虫序列表现出更广泛和明确的超周期。鉴于线虫的一些关键基因中存在超周期结构，超周期DNA的物理特性引起了人们的极大兴趣。在这项工作中，我们用高分辨率原子力显微镜(AFM)和凝胶电泳法证明了线虫的几个超周期DNA片段显示出结构异常。我们对AFM图像的定量分析表明，与长度相近的非周期DNA相比，超周期DNA采用了更小的均方端到端距离，因此具有更紧密的线圈结构。虽然分子仍然能够采用弯曲和直(棒状)构型，这表明它们的灵活性仍然保持不变，但对DNA轮廓长度的局部曲率的检查表明，均方端到端距离的减小可以归因于超周期DNA中存在长尺度本征弯曲。在非周期DNA中没有检测到这种弯曲。对在微球菌核酸酶消化后存活下来的较短的核小体长度的DNA进行的类似研究表明，短片段中的序列超周期同样可以诱导强烈的内在弯曲。因此，线虫基因组的区域似乎显示出DNA序列和异常机械特性之间的显著关联。
Several bioinformatics studies have identified an unexpected but remarkably prevalent ∼10 bp periodicity of AA/TT dinucleotides (hyperperiodicity) in certain regions of the Caenorhabditis elegans genome. Although the relevant C.elegans DNA segments share certain sequence characteristics with bent DNAs from other sources (e.g. trypanosome mitochondria), the nematode sequences exhibit a much more extensive and defined hyperperiodicity. Given the presence of hyperperiodic structures in a number of critical C.elegans genes, the physical characteristics of hyperperiodic DNA are of considerable interest. In this work, we demonstrate that several hyperperiodic DNA segments from C.elegans exhibit structural anomalies using high-resolution atomic force microscopy (AFM) and gel electrophoresis. Our quantitative analysis of AFM images reveals that hyperperiodic DNA adopts a significantly smaller mean square end-to-end distance, hence a more compact coil structure, compared with non-periodic DNA of similar length. While molecules remain capable of adopting both bent and straight (rod-like) configurations, indicating that their flexibility is still retained, examination of the local curvatures along the DNA contour length reveals that the decreased mean square end-to-end distance can be attributed to the presence of long-scale intrinsic bending in hyperperiodic DNA. Such bending is not detected in non-periodic DNA. Similar studies of shorter, nucleosome-length DNAs that survived micrococcal nuclease digestion show that sequence hyperperiodicity in short segments can likewise induce strong intrinsic bending. It appears, therefore, that regions of the C.elegans genome display a significant correlation between DNA sequence and unusual mechanical properties.
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使用混合模型改善了核小体DNA序列的比对。
影响因子：
14.9
作者：
Wang, JPZ;Widom, J
通讯作者：
Widom, J
影响因子：
5.6
作者：
Lowary, PT;Widom, J
通讯作者：
Widom, J
影响因子：
64.8
作者：
NELSON, HCM;FINCH, JT;KLUG, A
通讯作者：
KLUG, A
DOI：
10.1073/pnas.77.7.3816
发表时间：
1980-01-01
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES
影响因子：
--
作者：
TRIFONOV, EN;SUSSMAN, JL
通讯作者：
SUSSMAN, JL
影响因子：
5.6
作者：
Rivetti, C;Walker, C;Bustamante, C
通讯作者：
Bustamante, C