A Tandem Cell for Nanopore-based DNA Sequencing with Exonuclease

BioRxiv : the Preprint Server for Biology
Gopalan Sampath

Abstract

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 [ cis 1, upstream nanopore (UNP), trans 1 = cis 2, downstream nanopore (DNP), trans 2]. The exonuclease is attached to the exit side of UNP in trans 1/ cis 2. A cleaved base cannot regress into cis 1 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 trans 2. Sequencing efficiency with a tandem cell would then be determined solely by the level of discrimination among the base types inside DNP.

Related Concepts

DNA
Down Syndrome
Exonuclease
Flavin Mononucleotide
DNA, Double-Stranded
Downstream
Structure
Sequence Determinations, DNA
Analysis
Nucleic Acid Sequencing

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