title: Slowing single-stranded DNA translocation through a solid-state nanopore by decreasing the nanopore diameter.
abstract: To slow the translocation of single-stranded DNA (ssDNA) through a solid-state nanopore, a nanopore was narrowed, and the effect of the narrowing on the DNA translocation speed was investigated. In order to accurately measure the speed, long (5.3 kb) ssDNA (namely, ss-poly(dA)) with uniform length (±0.4 kb) was synthesized. The diameters of nanopores fabricated by a transmission electron microscope were controlled by atomic-layer deposition. Reducing the nanopore diameter from 4.5 to 2.3 nm slowed down the translocation of ssDNA by more than 16 times (to 0.18 μs base(-1)) when 300 mV was applied across the nanopore. It is speculated that the interaction between the nanopore and the ssDNA dominates the translocation speed. Unexpectedly, the translocation speed of ssDNA through the 4.5 nm nanopore is more than two orders of magnitude higher than that of double-stranded DNA (dsDNA) through a nanopore of almost the same size. The cause of such a faster translocation of ssDNA can be explained by the weaker drag force inside the nanopore. Moreover, the measured translocation speeds of ssDNA and dsDNA agree well with those calculated by molecular-dynamics (MD) simulation. The MD simulation predicted that reducing the nanopore diameter to almost the same as that of ssDNA (i.e. 1.4 nm) decreases the translocation speed (to 1.4 μs base(-1)). Narrowing the nanopore is thus an effective approach for accomplishing nanopore DNA sequencing.
authors: Central Research Laboratory, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan.
authors: Rena
authors: R
authors: Akahori
authors: Takanobu
authors: T
authors: Haga
authors: Toshiyuki
authors: T
authors: Hatano
authors: Itaru
authors: I
authors: Yanagi
authors: Takeshi
authors: T
authors: Ohura
authors: Hirotaka
authors: H
authors: Hamamura
authors: Tomio
authors: T
authors: Iwasaki
authors: Takahide
authors: T
authors: Yokoi
authors: Takashi
authors: T
authors: Anazawa
mesh_terms: D004277:DNA, Single-Stranded / Q000032:analysis* / Q000138:chemical synthesis; D006801:Humans; D056004:Molecular Dynamics Simulation; D009038:Motion; D058608:Nanopores; D017422:Sequence Analysis, DNA / Q000295:instrumentation* / Q000379:methods
chemical_list: D004277:DNA, Single-Stranded