Detection of urea-induced internal denaturation of dsDNA using solid-state nanopores
Detection of urea-induced internal denaturation of dsDNA using solid-state nanopores
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DOI：
10.1088/0953-8984/22/45/454111
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发表时间：
2010-11-17
影响因子：
2.7
通讯作者：
Meller, Amit
中科院分区：
文献类型：
--
作者：
Singer, Alon;Kuhn, Heiko;Meller, Amit
检测和测量dsDNA热波动的能力对于理解转录和复制调控的潜在机制具有极其重要的意义。我们在这里描述了固态纳米孔检测由于化学增强的热波动而导致的DNA结构的亚纳米变化的能力。在这项研究中，我们研究了具有3-5 nm固态纳米孔的dsDNA分子的平均有效直径随尿素浓度和DNA的AT含量的微妙变化。我们的研究表明，在8.7M尿素下，DNA分子的平均有效直径增加了约0.6 nm。与DNA局部变性的机制一致，我们观察到这些效应与尿素浓度呈S型依赖关系。我们发现，如果动力学主要由粘性效应控制，尿素中的移位时间明显慢于预期。此外，我们发现，纳米孔的灵敏度足以在统计上区分长度几乎相同的DNA分子，只是在序列上不同，当放置在3.5M尿素中时，AT含量不同。我们的结果表明，纳米孔可以检测到细微的结构变化，因此是检测生物分子环境差异的有价值的工具。
The ability to detect and measure dsDNA thermal fluctuations is of immense importance in understanding the underlying mechanisms responsible for transcription and replication regulation. We describe here the ability of solid-state nanopores to detect sub-nanometer changes in DNA structure as a result of chemically enhanced thermal fluctuations. In this study, we investigate the subtle changes in the mean effective diameter of a dsDNA molecule with 3-5 nm solid-state nanopores as a function of urea concentration and the DNA's AT content. Our studies reveal an increase in the mean effective diameter of a DNA molecule of approximately 0.6 nm at 8.7 M urea. In agreement with the mechanism of DNA local denaturation, we observe a sigmoid dependence of these effects on urea concentration. We find that the translocation times in urea are markedly slower than would be expected if the dynamics were governed primarily by viscous effects. Furthermore, we find that the sensitivity of the nanopore is sufficient to statistically differentiate between DNA molecules of nearly identical lengths differing only in sequence and AT content when placed in 3.5 M urea. Our results demonstrate that nanopores can detect subtle structural changes and are thus a valuable tool for detecting differences in biomolecules' environment.