A Tandem Cell for Nanopore-based DNA Sequencing with Exonuclease

TL;DR

This paper proposes a novel tandem nanopore cell with an exonuclease for DNA sequencing, modeled mathematically to ensure high accuracy and order preservation of bases during translocation, enhancing sequencing efficiency.

Contribution

It introduces a new tandem nanopore structure with an exonuclease and electric field profiling, modeled to improve base detection accuracy and sequencing reliability.

Findings

Bases enter DNP in order with probability approaching 1

Bases are detected without loss or regression

Sequencing efficiency depends on base discrimination within DNP

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 [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.