DNA in nanochannels: theory and applications.

IF 7.2 2区 生物学 Q1 BIOPHYSICS
Karolin Frykholm, Vilhelm Müller, Sriram Kk, Kevin D Dorfman, Fredrik Westerlund
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引用次数: 4

Abstract

Nanofluidic structures have over the last two decades emerged as a powerful platform for detailed analysis of DNA on the kilobase pair length scale. When DNA is confined to a nanochannel, the combination of excluded volume and DNA stiffness leads to the DNA being stretched to near its full contour length. Importantly, this stretching takes place at equilibrium, without any chemical modifications to the DNA. As a result, any DNA can be analyzed, such as DNA extracted from cells or circular DNA, and it is straight-forward to study reactions on the ends of linear DNA. In this comprehensive review, we first give a thorough description of the current understanding of the polymer physics of DNA and how that leads to stretching in nanochannels. We then describe how the versatility of nanofabrication can be used to design devices specifically tailored for the problem at hand, either by controlling the degree of confinement or enabling facile exchange of reagents to measure DNA-protein reaction kinetics. The remainder of the review focuses on two important applications of confining DNA in nanochannels. The first is optical DNA mapping, which provides the genomic sequence of intact DNA molecules in excess of 100 kilobase pairs in size, with kilobase pair resolution, through labeling strategies that are suitable for fluorescence microscopy. In this section, we highlight solutions to the technical aspects of genomic mapping, including the use of enzyme-based labeling and affinity-based labeling to produce the genomic maps, rather than recent applications in human genetics. The second is DNA-protein interactions, and several recent examples of such studies on DNA compaction, filamentous protein complexes, and reactions with DNA ends are presented. Taken together, these two applications demonstrate the power of DNA confinement and nanofluidics in genomics, molecular biology, and biophysics.

纳米通道中的DNA:理论与应用。
在过去的二十年里,纳米流体结构已经成为一个强大的平台,可以在千碱基对长度尺度上对DNA进行详细分析。当DNA被限制在纳米通道中时,排除的体积和DNA刚度的结合导致DNA被拉伸到接近其完整的轮廓长度。重要的是,这种拉伸是在平衡状态下进行的,没有对DNA进行任何化学修饰。因此,可以分析任何DNA,例如从细胞中提取的DNA或圆形DNA,并且可以直接研究线性DNA末端的反应。在这篇全面的综述中,我们首先对目前对DNA聚合物物理的理解以及这如何导致纳米通道中的拉伸进行了全面的描述。然后,我们描述了如何使用纳米制造的多功能性来设计专门针对手头问题的设备,通过控制限制程度或使试剂易于交换来测量dna -蛋白质反应动力学。其余的综述集中在两个重要的应用限制DNA在纳米通道。第一种是光学DNA作图,通过适合于荧光显微镜的标记策略,提供超过100千碱基对大小的完整DNA分子的基因组序列,具有千碱基对分辨率。在本节中,我们将重点介绍基因组图谱技术方面的解决方案,包括使用基于酶的标记和基于亲和的标记来生成基因组图谱,而不是最近在人类遗传学中的应用。第二个是DNA-蛋白质相互作用,并介绍了最近关于DNA压实、丝状蛋白质复合物和DNA末端反应的几个研究实例。总之,这两个应用展示了DNA约束和纳米流体在基因组学、分子生物学和生物物理学中的力量。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Quarterly Reviews of Biophysics
Quarterly Reviews of Biophysics 生物-生物物理
CiteScore
12.90
自引率
1.60%
发文量
16
期刊介绍: Quarterly Reviews of Biophysics covers the field of experimental and computational biophysics. Experimental biophysics span across different physics-based measurements such as optical microscopy, super-resolution imaging, electron microscopy, X-ray and neutron diffraction, spectroscopy, calorimetry, thermodynamics and their integrated uses. Computational biophysics includes theory, simulations, bioinformatics and system analysis. These biophysical methodologies are used to discover the structure, function and physiology of biological systems in varying complexities from cells, organelles, membranes, protein-nucleic acid complexes, molecular machines to molecules. The majority of reviews published are invited from authors who have made significant contributions to the field, who give critical, readable and sometimes controversial accounts of recent progress and problems in their specialty. The journal has long-standing, worldwide reputation, demonstrated by its high ranking in the ISI Science Citation Index, as a forum for general and specialized communication between biophysicists working in different areas. Thematic issues are occasionally published.
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