DNA sequencing with nanopores from an ab initio perspective

Abstract

Advances in materials research means that we find ourselves at the verge of constructing nano-scale devices capable of electrically addressing individual molecules in order to identify or utilize their electrical or electromechanical properties. An important application in life sciences would be electromechanical translocation of a DNA molecule through a nanopore, between nano-scale electrodes, allowing to electrically read out the base sequence (genome). This approach promises to drastically lower the cost per genome, allowing for extensive application in medical diagnostics. Owing to the involved extremely small dimensions which require nanometer-resolution in the fabrication, atomistic modeling plays a crucial role in testing hypothetical device architectures for their performance in nucleobase distinction. First-principles simulations are ideally suited to explore the interactions involved in such scenarios and lay the foundation for electronic transport calculations. This role of computations is even more important here, since it is experimentally not possible to observe directly the kinetics occurring during translocation of a DNA molecule through a nanopore. Here, we provide a brief review of the state of the field, focusing on ab initio studies of nanopore-based DNA sequencing, in particular on the promising recent development regarding graphene nanopores and nanogaps. © 2012 Springer Science+Business Media, LLC.