TY - JOUR T1 - A Tandem Cell for Nanopore-based DNA Sequencing with an Exonuclease Enzyme JF - bioRxiv DO - 10.1101/005934 SP - 005934 AU - G. Sampath Y1 - 2014/01/01 UR - http://biorxiv.org/content/early/2014/06/04/005934.abstract N2 - A tandem electrolytic cell is proposed for DNA sequencing in which an exonuclease enzyme cleaves bases (mononucleotides) from the DNA strand 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. Separate potential differences are applied to the five sections to enable drift-driven translocation of DNA, cleaved bases, and detected bases. A cleaved base cannot regress into cis1 because of the remaining DNA strand in UNP. A profiled electric field across DNP with positive and negative components is suggested for slowing down base translocation through DNP. A Fokker-Planck equation is used to model the system and a piecewise solution presented. Results from the model suggest 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. If this holds in practice then the only determinant of sequencing efficiency would be the level of discrimination among the four (or five, if methylation is included) base types in DNP. A hybrid biological-synthetic implementation is considered. Thus a biological pore (AHL or MspA) may be used for UNP because of the need to covalently attach or genetically fuse the exonuclease to the exit side of UNP. For DNP a multi-layered solid-state pore with interposed graphene sheets is suggested. Other implementation issues and potential extensions are discussed. ER -