A Tandem Cell for Nanopore-based DNA Sequencing with Exonuclease

BioRxiv : the Preprint Server for Biology
Gopalan Sampath


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

Down Syndrome
Flavin Mononucleotide
DNA, Double-Stranded
Sequence Determinations, DNA
Nucleic Acid Sequencing

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.