title: Application of OmpF nanochannel forming protein in polynucleotide sequence recognition.
abstract: Recognition of the sequence of human genome sequence is vital to address malfunctions occurring at molecular, cellular and tissue levels and requires a great deal of time, cost and efforts. Thus, various synthetic and natural pores were considered to fabricate high-throughput systems capable to fulfill the task in an efficient manner. Here, voltage gating OmpF nanochannel, whose structure is known at an atomic level, was used to recognize and differentiate between polynucleotide primers through voltage clamp technique. Our results showed that poly(T) occasionally blocked the channel at both polarities, while poly(C) and poly(G) obstructed it only at positive polarity. The channel was blocked at potential differences of as low as 80 mV in the presence of poly(T). The conductance of channel decreased in the presence of poly(C) and poly(G) by 61 and 5% respectively. Analysis of the number of events showed that poly(T) caused more closing events at higher voltages, while poly(G) and poly(C) induced it at lower voltages. Application of the hazard function as a statistical parameter and analysis of event closing times in various voltages demonstrated the most efficient differentiation at 60 mV. The results of practical and theoretical approaches presented here show that OmpF porin channel possesses the structural and dynamic characteristics required to be considered as a biosensor capable for continuous polynucleotide sequencing.
authors.affiliation: Laboratory of Membrane Biophysics and Macromolecules, Institute of Biochemistry and Biophysics, University of Tehran, P.O. Box 13145-1384, Tehran, Iran.
authors.forename: Saeid
authors.initials: S
authors.lastname: Hadi-Alijanvand
authors.forename: Hamid
authors.initials: H
authors.lastname: Mobasheri
authors.forename: Hamid
authors.initials: H
authors.lastname: Hadi-Alijanvand
mesh_terms: D015894:Genome, Human; D006801:Humans; D008958:Models, Molecular; D018408:Patch-Clamp Techniques; D011066:Poly C / Q000737:chemistry; D011068:Poly G / Q000737:chemistry; D011071:Poly T / Q000737:chemistry; D011119:Polynucleotides / Q000737:chemistry*; D018272:Porins / Q000737:chemistry*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: C109237:OmpF protein; D011119:Polynucleotides; D018272:Porins; D011071:Poly T; D011068:Poly G; D011066:Poly C
keywords: artificial membrane; biophysics; ion channel; nucleotide sequencing; voltage clamp