基于纳米孔的DNA核酸外切酶测序的串联池
A Tandem Cell for Nanopore-based DNA Sequencing with Exonuclease
摘要：
提出了一种用于DNA测序的串联单元，其中核酸外切酶从DNA链切割碱基（单核苷酸）以用于在纳米孔内进行鉴定。它有两个纳米孔和三个隔室，结构为[顺式1，上游纳米孔（UNP），反式1 =顺式2，下游纳米孔（DNP），反式2]。核酸外切酶以反式1/顺式2连接到UNP的出口侧。由于UNP中剩余的DNA链，切割的碱基不能退化为顺式1。在DNP上具有正分量和负分量的异形电场减缓了通过DNP的碱基移位。提出的结构建模与福克-普朗克方程和分段的解决方案。从模型的结果表明，概率接近1碱基进入DNP在其自然顺序，检测到没有任何损失，并没有回归到DNP后，进入trans 2。串联细胞的测序效率将仅由DNP内碱基类型之间的区分水平决定。
英文摘要：
A tandem cell is proposed for DNA sequencing in which an exonuclease enzyme cleaves bases (mononucleotides) from a strand of DNA for identification inside a nanopore. It has two nanopores and three compartments with the structure [cis1, upstream nanopore (UNP), trans1=cis2, downstream nanopore (DNP), trans2]. The exonuclease is attached to the exit side of UNP in trans1/cis2. A cleaved base cannot regress into cis1 because of the remaining DNA strand in UNP. A profiled electric field over DNP with positive and negative components slows down base translocation through DNP. The proposed structure is modeled with a Fokker-Planck equation and a piecewise solution presented. Results from the model indicate that with probability approaching 1 bases enter DNP in their natural order, are detected without any loss, and do not regress into DNP after progressing into trans2. Sequencing efficiency with a tandem cell would then be determined solely by the level of discrimination among the base types inside DNP.
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