Detection and Mapping of dsDNA Breaks using Graphene Nanopore Transistor

Abstract

Single-strand DNA (ssDNA) breaks that are often converted into DNA double-strand (dsDNA) breaks make up a vast majority of lesions a normal human cell undergoes everyday. If the repair mechanism fails, the dsDNA break can cause chromosomal instability leading to tumorigenesis. Additionally, a single break in a critical gene can cause the cell to undergo apoptosis. Existing genome sequencing techniques are not suitable for detecting such changes directly. As an alternative methodology, we propose to employ graphene-Quantum Point Contact nanopore transistor to detect and map defects in the DNA backbone, as miniscule as ssDNA breaks, efficiently using electronic sheet currents obtained across the transistor membrane. For this purpose, we use large-scale comprehensive all-atom molecular dynamics simulation techniques accompanied with electronic transport calculations, data denoising and signal detection. In all our simulations, we observe the molecule sticking in the pore at the nicked site due to strong hydrophobic attraction between the graphene membrane and the damaged-backbone. While the ionic currents calculated for the translocation of 20 base-pair dsDNA strand with a break in the backbone does not show any distinct signature from the nicked-site in the signal, a clear dip is seen in the transverse sheet current signal corresponding to the location of the breakage, thereby enabling us to detect and map these damages, electronically. We validated our methodology by detecting other sequence specific dsDNA breaks along randomly sequenced strands. We strongly believe such a detection mechanism enables the development of versatile semiconductor electronics for early cancer detection caused by structural modification of the genome.