title: Detection of short single-strand DNA homopolymers with ultrathin Si3N4 nanopores.
abstract: A series of nanopores with diameters ranging from 2.5 to 63 nm are fabricated on a reduced Si3N4 membrane by focused ion beam and high energy electron beam. Through measuring the blocked ionic currents for DNA strands threading linearly through those solid-state nanopores, it is found that the blockade ionic current is proportional to the square of the hydrodynamic diameter of the DNA strand. With the nanopore diameter reduced to be comparable with that of DNA strands, the hydrodynamic diameter of the DNA becomes smaller, which is attributed to the size confinement effects. The duration time for the linear DNA translocation events increases monotonically with the nanopore length. By comparing the spatial configurations of DNA strands through nanopores with different diameters, it is found that the nanopore with large diameter has enough space to allow the DNA strand to translocate through with complex conformation. With the decrease of the nanopore diameter, the folded part of the DNA is prone to be straightened by the nanopore, which leads to the increase in the occurrence frequency of the linear DNA translocation events. Reducing the diameter of the nanopore to 2.5 nm allows the detection and discrimination of three nucleotide "G" and three nucleotide "T" homopolymer DNA strands based on differences in their physical dimensions.
authors.affiliation: Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Ma
authors.affiliation: Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China.
authors.forename: Yinghua
authors.initials: Y
authors.lastname: Qiu
authors.affiliation: Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China.
authors.forename: Zhishan
authors.initials: Z
authors.lastname: Yuan
authors.affiliation: Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China.
authors.forename: Yin
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China.
authors.forename: Jingjie
authors.initials: J
authors.lastname: Sha
authors.affiliation: Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Liu
authors.affiliation: China Education Council Key Laboratory of MEMS, Southeast University, Nanjing 210096, China.
authors.forename: Litao
authors.initials: L
authors.lastname: Sun
authors.affiliation: Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China.
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Ni
authors.affiliation: Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Yi
authors.affiliation: Department of Mechanical Engineering, Vanderbilt University, Nashville, Tennessee 37235-1592, USA.
authors.forename: Deyu
authors.initials: D
authors.lastname: Li
authors.affiliation: Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China.
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Chen
mesh_terms: D004277:DNA, Single-Stranded / Q000737:chemistry; D004560:Electricity; D004583:Electrons; D057446:Hydrodynamics; D007477:Ions / Q000737:chemistry; D008567:Membranes, Artificial; D018625:Microscopy, Atomic Force; D046529:Microscopy, Electron, Transmission; D008957:Models, Genetic; D008958:Models, Molecular; D058608:Nanopores / Q000648:ultrastructure; D036103:Nanotechnology / Q000379:methods; D011108:Polymers / Q000737:chemistry; D017422:Sequence Analysis, DNA / Q000379:methods; D017655:Silicon Compounds / Q000737:chemistry; D012965:Sodium Chloride / Q000737:chemistry; D013997:Time Factors
chemical_list: D004277:DNA, Single-Stranded; D007477:Ions; D008567:Membranes, Artificial; D011108:Polymers; D017655:Silicon Compounds; D012965:Sodium Chloride; C032734:silicon nitride