Internal vs fishhook hairpin DNA: unzipping locations and mechanisms in the α-hemolysin nanopore.
Internal vs fishhook hairpin DNA: unzipping locations and mechanisms in the α-hemolysin nanopore.
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DOI：
10.1021/jp5101413
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发表时间：
2014-11-13
期刊：
影响因子：
--
通讯作者：
Burrows CJ
中科院分区：
文献类型：
--
作者：
Ding Y;Fleming AM;White HS;Burrows CJ
对发夹DNA与α-溶血素（α-HL）纳米孔的相互作用的研究已经确定了发夹解链动力学、热力学和序列依赖性DNA/蛋白质相互作用。这些结果中缺少一项系统性研究，比较了鱼钩（单尾）与内部（双尾）发夹通过30-mer单链尾从α-HL的顺式到反式侧的构象驱动时的解链过程。在目前的研究中，鱼钩发夹显示长的解拉链时间与一个深阻塞电流水平。相比之下，内部发夹表现出相对快速的解压缩和特征脉冲状电流模式。进一步探讨了这些差异与茎长度和序列背景。此外，研究了一系列具有不对称尾部的内部发夹，确定了长于12个核苷酸的第二个尾部导致内部发夹解链行为，而6个核苷酸的尾部长度表现得像鱼钩发夹。有趣的是，这些研究能够解决固定在纳米孔中等待解压缩的发夹DNA与易位解压缩的DNA之间的106%的电流差异，后者显示出更深的电流阻断水平。固定和易位DNA的不同电流的这种证明以前没有描述过。这些结果被解释为鱼钩发夹在前庭内解链，而内部发夹在前庭外解链。最后，我们利用这些知识研究了α-HL前庭外长双链DNA（>50个碱基对）的解压缩。从这些研究中得出的结论预计将是有益的，在未来的应用纳米孔分析的核酸。
Studies on the interaction of hairpin DNA with the α-hemolysin (α-HL) nanopore have determined hairpin unzipping kinetics, thermodynamics, and sequence-dependent DNA/protein interactions. Missing from these results is a systematic study comparing the unzipping process for fishhook (one-tail) vs internal (two-tail) hairpins when they are electrophoretically driven from the cis to the trans side of α-HL via a 30-mer single-stranded tail. In the current studies, fishhook hairpins showed long unzipping times with one deep blockage current level. In contrast, the internal hairpins demonstrated relatively fast unzipping and a characteristic pulse-like current pattern. These differences were further explored with respect to stem length and sequence context. Further, a series of internal hairpins with asymmetric tails were studied, for which it was determined that a second tail longer than 12 nucleotides results in internal hairpin unzipping behavior, while tail lengths of 6 nucleotides behaved like fishhook hairpins. Interestingly, these studies were able to resolve a current difference of ∼6% between hairpin DNA immobilized in the nanopore waiting to unzip vs the translocating unzipped DNA, with the latter showing a deeper current blockage level. This demonstration of different currents for immobilized and translocating DNA has not been described previously. These results were interpreted as fishhook hairpins unzipping inside the vestibule, while the internal hairpins unzip outside the vestibule of α-HL. Lastly, we used this knowledge to study the unzipping of a long double-stranded DNA (>50 base pairs) outside the vestibule of α-HL. The conclusions drawn from these studies are anticipated to be beneficial in future application of nanopore analysis of nucleic acids.
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影响因子：
--
作者：
Maglia, Giovanni;Heron, Andrew J.;Stoddart, David;Japrung, Deanpen;Bayley, Hagan
通讯作者：
Bayley, Hagan
DOI：
10.1073/pnas.0502947102
发表时间：
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影响因子：
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46.9
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DOI：
10.1073/pnas.93.24.13770
发表时间：
1996-11-26
影响因子：
11.1
作者：
Kasianowicz, JJ;Brandin, E;Deamer, DW
通讯作者：
Deamer, DW
DOI：
10.1073/pnas.1415944111
发表时间：
2014-10-07
影响因子：
11.1
作者：
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通讯作者：
Burrows, Cynthia J.