Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel.
Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel.
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DOI：
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发表时间：
2005
影响因子：
11.1
通讯作者：
J. Mathé;A. Aksimentiev;D. Nelson;K. Schulten;A. Meller
中科院分区：
文献类型：
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作者：
J. Mathé;A. Aksimentiev;D. Nelson;K. Schulten;A. Meller
我们表征了大约 1.5 nm α-溶血素孔内捕获的单链 DNA (ssDNA) 分子的电压驱动运动和自由运动，并表明 DNA 通道相互作用强烈依赖于 ssDNA 分子相对于孔的方向。值得注意的是，3'-螺纹DNA的无电压扩散（从反式到顺式方向）比具有相同poly(dA)序列的相应5'-螺纹DNA慢两倍。此外，流过 3' 线 DNA 或 5' DNA 堵塞孔的离子电流相差约 30%。我们系统的全原子分子动力学模拟揭示了不对称行为的微观机制。在限制孔中，ssDNA 伸直，其碱基向 5' 端倾斜，呈现不对称构象。因此，5' 线 DNA 的碱基会经历更大的有效摩擦和强制重新定向，从而有利于离子的共同通过。我们的结果表明，通过窄孔的易位过程比之前认为的更为复杂，并且涉及限制孔内 ssDNA 分子的碱基倾斜和拉伸。
We characterize the voltage-driven motion and the free motion of single-stranded DNA (ssDNA) molecules captured inside the approximately 1.5-nm alpha-hemolysin pore, and show that the DNA-channel interactions depend strongly on the orientation of the ssDNA molecules with respect to the pore. Remarkably, the voltage-free diffusion of the 3'-threaded DNA (in the trans to cis direction) is two times slower than the corresponding 5'-threaded DNA having the same poly(dA) sequence. Moreover, the ion currents flowing through the blocked pore with either a 3'-threaded DNA or 5' DNA differ by approximately 30%. All-atom molecular dynamics simulations of our system reveal a microscopic mechanism for the asymmetric behavior. In a confining pore, the ssDNA straightens and its bases tilt toward the 5' end, assuming an asymmetric conformation. As a result, the bases of a 5'-threaded DNA experience larger effective friction and forced reorientation that favors co-passing of ions. Our results imply that the translocation process through a narrow pore is more complicated than previously believed and involves base tilting and stretching of ssDNA molecules inside the confining pore.