Sage Journals: Discover world-class research

Abstract

Nanopore sensors are expected to be one of the most promising next generation sequencing technologies, with label-free, amplification-free and high-throughput features, as well as rapid detections and low cost. Solid-state nanopores have been widely explored due to their diverse fabrication methods and CMOS compatibility. Here, we highlight the fabrication methods of solid-state nanopores, including the direct opening and the tuning methods. In addition, molecular translocation developments, DNA sequencing and protein detections are summarized. Finally, the latest progress relating to solid-state nanopores is discussed, which helps to offer a comprehensive understanding of the current situation for solid-state nanopore sensors.

Keywords

Nanopore Fabrication Molecular Translocation DNA Sequencing Protein Detection

1. Introduction

In recent years, advances in the “Nano-Bio” research field have prompted a great deal of interest in the scientific world. Nanoscale tools serve as ideal interfaces to interrogate biological systems, since the sizes of many nanostructures are comparable to those of typical biomolecules. Among them, nanopore sensors have been highlighted as potential tools to detect individual biomolecules [1 –10]. By mimicking the functions of natural biological ion channels, nanopore sensors can control access and selectively identify for biomolecules at the single molecule level. The principle of nanopore sensing is based on the Coulter counter technique [11, 12]. As shown in Figure 1, an ultra-thin membrane with a nanoscale pore separates two reservoirs filled with electrolyte solutions. Ionic current information is created by electrically driving the individual biomolecule into a nanopore. Furthermore, by analysing the ionic current signature, a molecule's conformation, as well as structural and chemical properties of the biomolecules, can be obtained.

Figure 1.

Nanopore principle scheme: (a) the profile of the device; (b-e) different analytes passing through the pore, which will create characteristic signals

Currently, there are three major types of nanopores: biological nanopores, solid-state nanopores and hybrid nanopores. The biological nanopores are mainly created from natural protein molecules (e.g., channel proteins), which present precisely controlled structures and interfacial chemistry [13, 14]. However, the biological nanopores are limited by a short life time, intrinsic instability and the strict requirement of a specific environment, which are not favoured for a device's long-term operations. Solid-state nanopores are usually fabricated by top-down lithography, which have the advantages of higher stability, precisely tunable size, robust chemical and thermal characteristics, and CMOS compatibility [15 –17]. The detection principles of the nanopores are distinguishing the current fluctuations induced by analytes passing through the nanopores. If analytes are within identical spherical shapes, it is easy for solid state nanopores to distinguish different sizes of the analytes by the recording amplitude of the current fluctuations [18]. However, if the analytes show a little difference in shape and size, the detection results of solid state nanopores are usually unsatisfied [19]. This has been improved by introducing specific interactions between nanopores and analytes by assembling pore-forming synthetic soft materials inside solid-sate nanopores; these are referred to as hybrid nanopores. By combining specific surface chemistry, the drawbacks relating to the solid nanopores can be overcome and the detection limit of nanopore sensors can be improved [20, 21].

This review focuses on solid-state nanopores. We will first introduce the principle of nanopore sensors, and then present fabrications and applications of solid-state nanopores. Furthermore, recent advances, challenges and opportunities of nanopore sensors are discussed as well.

2. Principle

Due to the small size of the sensors, nanopore sensors are capable of detecting small objects (e.g., nanoparticles), even at the individual molecule level [22]. The principles of the detection process and the equivalent circuit are shown in Figure 1. An insulating membrane containing a nanometre pore is sandwiched between two reservoirs filled with electrolytes [14, 23, 24]. Ions are driven through the nanopore to generate an ionic current with the applied voltage. The conductivity of the apparatus remains stationary in a pure electrolyte solution and the current is a constant value with only a few fluctuations, which happens if there are no objects passing through. When analytes are added to one side of the chamber, they can be electrophoretically driven through the pore. A current blockage is created when an object passes through the nanopore. The measurable signal is determined mainly by two factors: steric exclusion and ion polymer properties. Steric exclusion can decrease the effective pore diameter and decrease the current. An ion polymer contains two parts: one is for co-ion repulsion, which will decrease the current, and the other is for counter-ion attraction, which will increase the current. Furthermore, these factors are all affected by the target concentrations. By increasing the concentration of the free analytes, the appearance frequency of the blockage current will increase. It provides a direct measurement of the frequency content, which contains the characteristic timescales of the analyte-nanopore interactions. Therefore, we can analyse the abundant bimolecular properties from the current information, such as their size, charge, length and specificity.

3. Fabrications of Solid-State Nanopores

The solid-state nanopores have gained increasingly attention because of their high stability and potential to be produced on a large scale. A variety of materials have been successfully utilized in fabricating nanopores, such as silicon [25, 26], silicon nitride [27], silicon oxide [28 –30], polymers [31, 32], aluminium oxide [33, 34] and graphene [35 –41]. The general nanopore fabrication process can be divided into the opening and the tuning methods. The opening methods include focused ion beam (FIB) drilling [42 –47], electron beam (e-beam) drilling [16, 30, 36, 39, 41, 48, 49], anodized alumina oxide transferring [50 –53] and the wet etching method [25, 26, 54 –57]. However, in most cases, the pore, with the desired size and shape, cannot be obtained directly. Extra tuning steps are normally required, such as deposition and thermal treatment. By combining all of these techniques, different sizes, shapes and properties of nanopores can be fabricated. Table 1 summarizes the features of these methods.

Table 1.

Nanopore fabrication methods

Method	Material	Description	Feature	Reference
Ion beam (opening, tuning)	SiC, Si₃N₄, SiO₂	1. FIB directly drills the surface to open a pore 2. The ion acceleration sputters the nanoscale pore for shrinkage	1. The pore prefers to be opened at 0°C and closed at room temperature 2. Heavier ions shrink the pores more efficiently than lighter ones 3. Shrinkage happens when the pore diameter is less than the film thickness	[42 –47]
e-beam (opening, tuning)	Si₃N₄, Al₂O₃, graphene SiO₂	1. A focused e-beam directly drills film by water vapours or XeF₂ assisted 2. e-beam irradiates nanoscale pores for shrinkage	1. The pore prefers to open under high e-beam intensity and shrink under low intensity 2. Shrinkage happens when the pore diameter is less than the film thickness	[16, 30, 36, 39, 48, 49]
Wet etching (opening)	SiC, Si	1. Conventional anisotropic wet etching with proper length width ratio	1. Nanopore arrays 2. Larger pore diameter than other methods	[25, 26, 54 –57]
Anodized alumina transferring (opening)	Al₂O₃	2. Plasma etching through a nanoporous template occurs in order to transfer the pore patterns	1. Nanopore arrays 2. Mask can be used multiple times	[50 –53, 61, 62]
Deposition (tuning)	SiC, Si, Si₃N₄, Al₂O₃	1. Chemical vapour or mental deposits on a nanoscale pore enable tuning of the diameter	1. LBL-dominated shrinking process 2. Fine-tuning the size and surface properties	[16, 27, 30, 31, 35, 70, 71]
Thermal treatment (tuning)	Si, SiO₂	1. Direct heating due to a high temperature (1,000–1,250 °C) causes shrinkage	1. Linear shrinkage rate 2. Unfavourable surface charge and electrical noise will not be introduced	[72, 73]

3.1 Direct opening methods

FIB involves a direct drilling method, which can create nanopores in specific areas relating to different types of membranes [47, 48, 58]. It was reported as the first technique for fabricating a single nanopore in 2001 by Li et al. [47]. The drilling process is shown in Figure 2(a). Li et al. used an Ar+ ion beam to drill a nanohole in a free-standing silicon nitride (Si₃N₄) membrane with a cavity on its opposite surface. A feedback detector was attached below the ion beam machine to indicate the stop point when the ions penetrated the membrane. By controlling the exposure time of the ion beam, the size of the nanopore can be well controlled. In addition, some critical parameters during the FIB process are also important in order to adjust the pore size, which will be discussed in 3.2.

Figure 2.

Schematic illustration of the nanopore fabrication process: (a) FIB, (b) e-beam, (c) anodized alumina transferring and (d) wet chemical etching methods

An intense e-beam is involved in another common method to fabricate nanopores [16, 30, 36, 39, 48, 49]. The first reported example using an e-beam to drill nanopores was Storm et al. [59]. An e-beam can fabricate nanopores in the range of 2–200 nm by manipulating the beam parameters, such as current, intensity and dwell time. However, the diameter of the nanopore is limited to the thickness of the membrane. In order to prepare nanopores with high precision in feature size, auxiliary gases are introduced. Yemini et al. first reported etching Si₃N₄ using XeF₂, which eventually resulted in 17–200 nm nanopores in the Si₃N₄ membrane [49]. The drilling process is shown in Figure 2(b). Furthermore, Kim et al. found that the intensity of e-beam determines the formations of the nanopores: (a) nanopore expansion is caused by atom sputtering at higher intensities, while (b) surface-tension-driven nanopore contraction occurs at lower intensities [60].

Anodized alumina oxide transferring can be used to fabricate nanopores as well; see Figure 2(c). This method utilizes plasma etching through a nanoporous template to transfer the pore patterns onto the underneath substrates [50 –53]. A typical nano-alumina template can be created by electrochemical anodization of aluminium film, which is rather easy compared with FIB or e-beam fabrications, while the templates can be used multiple times [61, 62]. Another advantage of this masked method is that the nanopore array can be efficiently fabricated.

Besides directly nanodrilling, wet chemical etching, which follows the standard micro-scale lithography process, has been demonstrated to be an alternative nanopore fabrication technique. The advantages of this method are simple and cost-effective, as well as offering multifunctional characters [25, 26, 54 –57]. Figure 2(d) shows a typical wet etching process. First, a standard micrometre pattern is fabricated by the standard lithography process, then an inverted pyramid structure with a sharp tip on the bottom is created using anisotropic wet etching. Finally, nanopores are formed by etching the back on the other side of the substrate using alkaline solutions (e.g., KOH). Given the different etching rates in each of the crystal faces, anisotropic wet etching can fabricate nanopores with conical or pyramidal geometries, in contrast to the cylindrical inner structures drilled by FIB or e-beam. Nanopore arrays can be efficiently fabricated by wet etching as well [63, 64].

3.2 Tuning methods

In order to obtain the desired dimensions of the nanopores, a tuning process to further enlarge or shrink the nanopores is usually required following direct drilling. In FIB tuning, temperature plays an important role in pore opening and shrinking. According to the experiments of Li et al. [47], when an Ar ion beam is sputtered on the edge of the nanopore at room temperature, the pore prefers to be closed, since a very thin (∼5 nm) stressed viscous surface layer is created by the ion beam energy. However, when the temperature is reduced to 0 °C, the nanopore prefers to be opened [59, 65, 66]. Besides the temperature, the type of ions has an effect on the shrinkage of the pore. The shrinkage happens when the diameter of the pore is smaller than the thickness of the membrane [47, 48, 58]. Heavier ions (He, Ne, Ar, Kr and Xe) can shrink the pores more efficiently than lighter ones [67, 68]. By fine tuning these factors, nanopores with desired diameters can be fabricated.

The e-beam can tune the nanopores as well. When the membrane is exposed to a higher intensity of e-beam, the size of nanopore tends to be expanded through atom sputtering. On the other hand, a lower e-beam intensity will lead to nanopore shrinkage [60]. In addition, similar to the FIB, nanopore shrinkage also happens when the diameter of the pore is smaller than half of its thickness [49, 69].

Deposition of nanoscale thin films on nanopores is another effective method to decrease the pore diameter. Atomic layer deposition is one of the most popular deposition methods. Deposition of thin polymer films through a layer-by-layer (LBL) assembly approach has been reported to shrink nanopores; this approach also has great advantages in terms of low cost and the ability to tune the surface chemistry of the nanopores [16, 27, 30, 31, 35, 70, 71].

Direct annealing can shrink the nanopore as well [72, 73]. In contrast to FIB and e-beam shrinkage, thermal treatment can change the morphology of the nanopores. For a silicon dioxide (SiO₂) membrane, it was found that, at the appropriate temperature (1,125 °C), the average shrinking rate of the pore is ∼22 nm per minute. Meanwhile, at a lower temperature (<1,000 °C), the diameter of the pore shows little or even no change. When the nanopore is exposed to a higher temperature (>1,250 °C), the SiO₂ membrane may be broken, while the shrinkage rate is too fast to be controlled. Another advantage of thermal shrinkage is that it will not increase the noise of the electrical signal of the nanopore sensors, since no additional surface charge is added.

4. Applications

Due to the simple operating principle of nanopore sensing and the technology available for nanopore fabrications, increasing developments regarding nanopore sensors have occurred. Solid-state nanopore devices have been successfully applied, from an initial method as a simple detector to a powerful technique to study complex molecular interactions, as well as mimicking the functions of natural systems. In this section, we will discuss the applications of nanopores as sensing platforms, including molecular translocation, DNA sequencing and protein detections.

4.1 Molecular translocation

Biomolecular translocation is an important process in the life sciences. In the biological system, migration of large biomolecules through pores (1∼10 nm) is a common physical behaviour and usually plays key biological roles. Typical examples include DNA transduction between cells, phages causing viral infections, RNA translation and protein secretion.

Kasianowicz et al. first reported their studies into DNA translocation using nanopore devices [69]. As shown in Figure 3(a), they were able to measure the length of the polynucleotide according to the durations of the transient current. After a large amount of experiments, for a given polymer size, they found that the durations of the transient current showed a linear relationship with the polymer length. Since then, the measurement of the length of different biopolymers using nanopore devices has been carried out by many other groups [74 –78]. However, it was also found that the linear relationship between the molecule length and the durations of transient current cannot be applied to every case. It only works well when the scale of nanopores is well matched to the polymer size. A possible reason for this is that the length of the molecule not only dominates polymer effective friction with the wall, the shape of the pore and the state of the polymer also affect the time taken by the polymer to pass through the pore. Storm et al. reported their experiments on electrophoretically deriving DNA molecules, ranging from 6,500 to 97,000 base pairs through a 10 nm pore [79]. They proposed that both hydrodynamic dragging and electrically driving contribute to the force on polymers. When the pore is much larger than the polymer, the linear relationship between the signals and polymer size is not correct. Instead, the exponential relationship can be applied [80]. In this case, the forces on the polynucleotide are complicated, which may include the applied driving voltage, pore-polymer interactions, viscous forces and the force from non-targeted polymers. All of these factors will affect the durations of the polymer translocations. Furthermore, it was found that the directionality of polynucleotide molecules passing through the nanopore is very important for translocation analysis [81, 82]. Polynucleotides have global orientation, with one end at 5′ and the other end at 3′. Experiment showed that the ionic blockade current is different when DNA passes through the nanopore from different directions [83]. If it is threaded from 5′, the bases of a five-threaded DNA experience larger effective frictions, resulting in a higher blockage current and better signal resolution [81, 82].

Figure 3.

Typical applications of nanopore sensors: a nanopore device for (a) polymer length measurement, (b) DNA sequencing tool and (c) single protein detections [84]

4.2 DNA sequencing

To date, the most attractive application for nanopore sensing is DNA sequencing; indeed, it is expected to result in the third generation of DNA sequencing technology. Compared with previous methods, such as Sanger, Illumina and Ion Torrent sequencing, nanopore devices show great advantages in terms of label-free, amplification-free, high-throughput DNA sequencing without the requirement of cutting long DNA chains into segments. The implementation of nanopore devices in DNA sequencing should represent substantial progress, along with a higher speed and a lower price.

Li et al. reported the first DNA sequencing experiment using solid-state nanopores [85]. As shown in Figure 3(b), a bias is applied between the two chambers and the polynucleotides are pushed into the nanopore due to being negatively charged. When DNA molecules pass through the nanopore, the ionic conductance changes due to the relatively smaller charge carried by DNA molecules. Meanwhile, salt concentration influences the current as well. Changes in the current depend on the conductance difference between salt concentration and DNA molecules [29, 86]. The base structures of DNA are different. Purine bases (A and G) are larger than pyrimidine bases (C and T), which will result in stronger interactions with the nanopore surface. Thus, the purine bases show a stronger blockade current than pyrimidine bases. Besides, each base has different charges, interaction potentials and orientations relating to the dipole moments against the nanopore surface. Due to the different properties of these bases, each base can be discriminated by analysing the spikes of the ionic current (spike durations, blockade fractions or voltage fluctuations in the longitudinal direction of the pore).

The sensing rate of DNA sequencing, when using nanopores, is limited due to the fast translocation rate of DNA molecules. This problem could be solved by controlling the electrolyte temperature, salt concentration, solution viscosity and the bias voltage across the nanopores. Fologea et al. reduced the molecule translocation speed by an order of magnitude, which largely facilitated the base discrimination ability at such a low translocation speed [87]. Meanwhile, numerous studies have focused on DNA sequencing using nanopore arrays, which will largely increase the throughput of sequencing [88 –90].

4.3 Protein detections

Proteins are significant to life. They transform into different multidimensional structures to execute an amazing variety of functions [91]. Using nanopores is also leading to rapid strides in protein detections (Figure 3c). It offers a distinct advantage when protein size, shape or charge state can be identified at the scale of a single molecule. Besides, protein folding or unfolding states can be analysed as well, which is important in order to understand the stability and conformation properties of proteins. Purnell [92] demonstrated that, by adding the chemical denaturing agent to the protein solutions, the signal of the protein translocation shows different blockades, which are responding to the folded and unfolded states of the proteins, respectively. Furthermore, the dynamic nature of the proteins can be detected in real time by nanopores, which is crucial in order to understand protein structures and functions [93]. It has been reported that the conversion from normal proteins to misfolded ones is the pathogenesis of many diseases, such as prion proteins [94 –96]. Nanopore-based protein detections can distinguish the conformation difference from the current properties [97]. Based on these results, a nanopore detection system is a rather promising tool in the realm of portable healthcare devices.

5. Recent Advances and Challenges

5.1 Recent advances

Nanopore sensors, which offer a fantastic technique for detecting molecules at the single molecule level, have been developed for more than 15 years. Many promising applications have been explored in the process, including genome sequencing and medical diagnostics. In recent years, due to the development of two-dimensional (2D) materials, many studies have used these new types of materials to fabricate nanopore devices (figure 4a), such as graphene [35 –41], mica [98] and MoS₂ [99]. Compared with conventional solid materials, 2D materials are thinner and more flexible, as well as demonstrating higher sensitivity [100]. Meanwhile, the effects of the geometric nanopores on an ionic current have been studied. The electric field inside the pore will be different when the pore has a different geometry [101 –104].

Figure 4.

Recent advances in nanopore devices: (a) graphene nanopore device [105] and (b-c) surface modifications of nanopores

The surface modifications of nanopore have been developed to reduce the non-specific adsorptions, pore clogging and electrical noises [106 –111] (Figure 4(b-c)). Chemical [27, 70, 112, 113], physical [30] and biological modifications [81, 114] have been applied to realize diverse functions of solidstate nanopores [115 –117]. In previous report, the physical modification of nanopores is usually neglected as a surface modification technique. As mentioned in Section 2, different ions caused shrinkage and thermal treatments on nanopores showed a great improvement in device performance, indicating the ability to fine-tune the surface properties with angstrom precisions. Besides, after the physical modifications, the surface charge is neutralized, which is preferable for DNA captures, and the 1/f noise can be reduced. All of these modifications improve the DNA sequencing resolutions [118]. The chemical surface modifications (such as through silane or thiol chemistry) are applied to functionalize the nanopores to different chemical reactive groups, which can be used to further attach other biomolecule probes. Thus, the chemical selectivity of nanopore sensors increases. The receptors' modified nanopores will reduce the translocation rate [119]. Lipid coating has been applied to nanopore sensing to achieve better controlled surface properties and fine-tune pore diameters in subnanometre resolutions. When specific ligands are incorporated into the lipid bilayer, the specific molecule interactions will reduce the translocation rate of the DNA sufficiently to time-resolve translocation events of individual bases; in turn, all four of the ionic current blockage levels can be easily distinguished from the current [84, 120].

In addition to the development of the nanopore itself, there has been significant progress in relation to detection systems for nanopores in recent years. Traditional nanopore detection is based on ionic current blockage [9, 121 –123]. Alternative read-out methods, which are based on force, optical detections and electronic transverse current, have been explored to further promote nanopore sensing [87, 124, 125]. Nanopore force spectroscopy, as a new detection method, exerts the localized bond-rupture force to the native electrical charge of biomolecules. Furthermore, one can detect the biomolecules' responses and their mechanical properties [126]. Liu et al. used an optofluidic chip with an integrated nanopore [127]. By controlling the single nanoparticles in relation to an optical excitation region, the results regarding the discrimination of fluorescent-labelled influenza viruses within a mixture of equally sized fluorescent nanoparticles showed 100% fidelity. Lagerqvist et al., who first introduced electronic transverse current detections, embedded electrodes in the walls of a nanopore, which performed orders of magnitude faster than conventional methods [87]. Until now, the transverse current and optical signals are the most promising read-out methods, while the identity of the nucleo-bases based on optoelectronic differences are more reliable.

5.2 Challenges

Many advantages have been offered by the nanopore sensing method, including fast detection rate, label- and amplification-free detections, less sample consumed and low cost. However, there are still problems to be solved. Solid-state nanopores present the properties of chemical and thermal characteristics, which are precisely size-tuned and reliable, as well as the possibility for them to be integrated with electrical and optical systems. That said, the sensitivity of solid-state nanopores needs to be improved to discriminate molecules with similar sizes but different biological characteristics. New types of nanopore materials, advanced processing techniques and better surface modification schemes have been applied to overcome the drawbacks of nanopores. More experiments are still required, along with new concepts to realize higher specific detections. For example, the electronic properties of probe-DNA interactions still need to be optimized to control DNA translocation, orientation and base contrast [111, 128].

Another challenge for nanopore detections is the translocation rate of analytes. Some experimental data indicate that it is difficult to identify different bases if the DNA translocation rate is too fast [111]. However, if we can properly control the passing rate, high signal-to-noise ratios (SNRs) and spatial resolution can be attained. Thus, the sensitivity of the nanopore would be greatly improved. Besides, not only for DNA and protein detections, counting single molecules or nanoparticles, which are homogeneously mixed in the solution, is still challenging. It is difficult to control the analyte capture and detection efficiency, predominantly due to the limited of the diffusions. It is helpful if some extra electrokinetic forces are added, such as electrophoresis and dielectrophoresis. The analytes can be controlled in order to pass through the nanopore without delaying or clogging [129 –131]. However, the applied electric field will induce heat in the solutions, which will influence the SNR during the detections. The solid-state nanopore itself reveals two dominant noise sources. The capacitance of the silicon support chip causes a high-frequency noise (dielectric noise), while 1/f α characteristics cause a low-frequency current fluctuation (flicker noise). Besides, the measurement system also influences the SNR of nanopores. During the detections, both the signal bandwidth and the noise of the current are very important factors; however, if we want to obtain more information content at a high signal bandwidth, the noise of current recording also strongly increases. Further optimization is still required to reduce the unwanted effects [132, 133]. Novel device architecture and developing more sophisticated read-out methods are desirable to increase the SNR. Efforts to fabricate nanopore sensors, which contain nanogap-based tunnelling detectors and electronic transverse signals, and optical read-out methods are currently underway [134].

6. Conclusion

Nanopore-based sensing is structured with an ionic conductance of nanoscale pores when analytes are driven through by an extra applied electric field. Solid-state nanopores represent the most promising sensor devices for single molecule detections, due to their relatively easy fabrications and high stability, prompting a great deal of interest in this scientific research field. Besides, nanopore sequencing technology is believed to be one of the next generation DNA sequencing techniques. It will provide a huge reduction in sequencing costs and may well achieve the USD 1,000 per mammalian genome. The principles, fabrications, applications and challenges of solid-state nanopore devices are reviewed here. However, most applications are still at their initial proof of principle stage. It can be expected that continuous research to improve the performance of nanopore sensing technology will appear in the near future.

Footnotes

7. Acknowledgements

The authors gratefully acknowledge the financial support they have received, particularly from Tianjin Applied Basic Research and Advanced Technology (14JCYBJC41500) and the 111 Project (B07014).

References

Kasianowicz

Robertson

Chan

Reiner

Stanford

. Nanoscopic porous sensors. Annual review of analytical chemistry. 2008;1:737–66.

Lemay

. Nanopore-based biosensors: the interface between ionics and electronics. ACS nano. 2009;3(4):775–9.

Venkatesan

Bashir

. Nanopore sensors for nucleic acid analysis. Nature nanotechnology. 2011;6(10):615–24.

Ying

Zhang

Gao

Long

. Nanopore-based sequencing and detection of nucleic acids. Angewandte chemie. 2013;52(50):13154–61.

Dekker

. Solid-state nanopores. Nature nanotechnology. 2007;2(4):209–15.

Branton

Deamer

Marziali

Bayley

Benner

Butler

. The potential and challenges of nanopore sequencing. Nature biotechnology. 2008;26(10):1146–53.

Palyulin

Ala-Nissila

Metzler

. Polymer translocation: the first two decades and the recent diversification. Soft matter. 2014;10(45):9016–37.

Steinbock

Radenovic

. The emergence of nanopores in next-generation sequencing. Nanotechnology. 2015;26(7):074003.

Zwolak

Di Ventra

. Colloquium: physical approaches to DNA sequencing and detection. Reviews of Modern Physics. 2008;80(1):141.

10.

Fyta

. Threading DNA through nanopores for biosensing applications. Journal of physics: condensed Matter. 2015;27(27):273101.

11.

Bull

Schneiderman

Brecher

. Platelet counts with the Coulter counter. American journal of clinical pathology. 1965;44(6):678.

12.

Koch

Evans

Brunnschweiler

. Design and fabrication of a micromachined Coulter counter. Journal of micromechanics and microengineering. 1999;9(2):159.

13.

Buchsbaum

Mitchell

Martin

Wiggin

Marziali

Coveney

. Disentangling steric and electrostatic factors in nanoscale transport through confined space. Nano letters. 2013;13(8): 3890–6.

14.

Shim

. Single molecule sensing by nanopores and nanopore devices. The analyst. 2010;135(3):441–51.

15.

Kim

McNally

Murata

Meller

. Characteristics of solid-state nanometre pores fabricated using a transmission electron microscope. Nanotechnology. 2007;18(20):205302.

16.

Kox

Chen

Maes

Lagae

Borghs

. Shrinking solid-state nanopores using electron-beam-induced deposition. Nanotechnology. 2009;20(11): 115302.

17.

Pedone

Langecker

Munzer

Wei

Nagel

Rant

. Fabrication and electrical characterization of a pore-cavity-pore device. Journal of physics: condensed matter: an Institute of Physics journal. 2010;22(45):454115.

18.

Lan

W-J

Holden

Zhang

White

. Nanoparticle transport in conical-shaped nanopores. Analytical chemistry. 2011;83(10):3840–7.

19.

Gouaux

MacKinnon

. Principles of selective ion transport in channels and pumps. Science. 2005;310(5753):1461–5.

20.

Hall

Scott

Rotem

Mehta

Bayley

Dekker

. Hybrid pore formation by directed insertion of alpha-haemolysin into solid-state nanopores. Nature nanotechnology. 2010;5(12): 874–7.

21.

Heng

Aksimentiev

Marks

Grinkova

Sligar

. The electromechanics of DNA in a synthetic nanopore. Biophysical journal. 2006;90(3):1098–106.

22.

Branton

Deamer

Marziali

Bayley

Benner

Butler

. The potential and challenges of nanopore sequencing. Nature biotechnology. 2008;26(10):1146–53.

23.

Jubery

Prabhu

Kim

Dutta

. Modeling and simulation of nanoparticle separation through a solid-state nanopore. Electrophoresis. 2012;33(2): 325–33.

24.

Kowalczyk

Dekker

. Measurement of the docking time of a DNA molecule onto a solid-state nanopore. Nano letters. 2012;12(8):4159–63.

25.

Lee

C-L

Tsujino

Kanda

Ikeda

Matsumura

. Pore formation in silicon by wet etching using micrometre-sized metal particles as catalysts. Journal of materials chemistry. 2008;18(9):1015–20.

26.

Park

Peng

Ling

. Fabrication of nanopores in silicon chips using feedback chemical etching. Small. 2007;3(1):116–9.

27.

Chen

Mitsui

Farmer

Golovchenko

Gordon

Branton

. Atomic layer deposition to fine-tune the surface properties and diameters of fabricated nanopores. Nano letters. 2004;4(7): 1333–7.

28.

Storm

Chen

Zandbergen

Dekker

. Translocation of double-strand DNA through a silicon oxide nanopore. Physical review E. 2005;71(5):051903.

29.

Chang

Kosari

Andreadakis

Alam

Vasmatzis

Bashir

. DNA-mediated fluctuations in ionic current through silicon oxide nanopore channels. Nano letters. 2004;4(8):1551–6.

30.

Danelon

Santschi

Brugger

Vogel

. Fabrication and functionalization of nanochannels by electron-beam-induced silicon oxide deposition. Langmuir: the ACS journal of surfaces and colloids. 2006;22(25):10711–5.

31.

Peng

Tseng

Darling

Elam

. Nanoscopic patterned materials with tunable dimensions via atomic layer deposition on block copolymers. Advanced materials 2010;22(45):5129–33.

32.

Mara

Siwy

Trautmann

Wan

Kamme

. An asymmetric polymer nanopore for single molecule detection. Nano letters. 2004;4(3):497–501.

33.

Lee

Nielsch

Gösele

. Self-ordering behavior of nanoporous anodic aluminium oxide (AAO) in malonic acid anodization. Nanotechnology. 2007;18(47):475713.

34.

Gaede

Luckett

Polozov

Gawrisch

. Multinuclear NMR studies of single lipid bilayers supported in cylindrical aluminium oxide nanopores. Langmuir: the ACS journal of surfaces and colloids. 2004;20(18):7711–9.

35.

Andreozzi

Lamagna

Seguini

Fanciulli

Schamm-Chardon

Castro

. The fabrication of tunable nanoporous oxide surfaces by block copolymer lithography and atomic layer deposition. Nanotechnology. 2011;22(33):335303.

36.

Fischbein

Drndić

. Electron beam nanosculpting of suspended graphene sheets. Applied physics letters. 2008;93(11):113107.

37.

Tsutsui

Ryuzaki

Yokota

Taniguchi

Kawai

. Graphene/hexagonal boron nitride/graphene nanopore for electrical detection of single molecules. NPG Asia materials. 2014;6(6):e104.

38.

Merchant

Healy

Wanunu

Ray

Peterman

Bartel

. DNA translocation through graphene nanopores. Nano letters. 2010;10(8): 2915–21.

39.

Meyer

Eder

Kurasch

Skakalova

Kotakoski

Park

. Accurate measurement of electron beam induced displacement cross sections for single-layer graphene. Physical review letters. 2012;108(19).

40.

Russo

Golovchenko

. Atom-by-atom nucleation and growth of graphene nanopores. Proceedings of the National Academy of Sciences of the United States of America. 2012;109(16):5953–7.

41.

Puster

Rodríguez-Manzo

Balan

Drndic

. Toward sensitive graphene nanoribbon–nanopore devices by preventing electron beam-induced damage. ACS nano. 2013;7(12):11283–9.

42.

Biance

Gierak

Bourhis

Madouri

Lafosse

Patriarche

. Focused ion beam sculpted membranes for nanoscience tooling. Microelectronic engineering. 2006;83(4–9):1474–7.

43.

Lillo

Losic

. Ion-beam pore opening of porous anodic alumina: The formation of single nanopore and nanopore arrays. Materials letters. 2009;63(3–4): 457–60.

44.

Zhou

Yang

. Focused Ion-Beam Based Nanohole Modeling, Simulation, Fabrication, and Application. Journal of manufacturing science and engineering. 2010;132(1):011005.

45.

Gierak

Madouri

Biance

Bourhis

Patriarche

Ulysse

. Sub-5nm FIB direct patterning of nanodevices. Microelectronic engineering. 2007;84(5–8):779–83.

46.

Schiedt

Auvray

Bacri

Oukhaled

Madouri

Bourhis

. Direct FIB fabrication and integration of “single nanopore devices” for the manipulation of macromolecules. Microelectronic engineering. 2010;87(5–8):1300–3.

47.

Stein

McMullan

Branton

Aziz

Golovchenko

. Ion-beam sculpting at nanometre length scales. Nature. 2001;412(6843):166–9.

48.

Aref

Bezryadin

. Fabrication of symmetric sub-5 nm nanopores using focused ion and electron beams. Nanotechnology. 2006;17(13):3264.

49.

Yemini

Hadad

Liebes

Goldner

Ashkenasy

. The controlled fabrication of nanopores by focused electron-beam-induced etching. Nanotechnology. 2009;20(24):245302.

50.

Harrell

Martin

. Conical nanopore membranes: preparation and transport properties. Analytical chemistry. 2004;76(7): 2025–30.

51.

Liang

Chik

Yin

. Two-dimensional lateral superlattices of nanostructures: nonlithographic formation by anodic membrane template. Journal of applied physics. 2002;91(4):2544–6.

52.

Menon

Ram

Patibandla

Aurongzeb

Holtz

Yun

. Plasma etching transfer of a nanoporous pattern on a generic substrate. Journal of the Electrochemical Society. 2004;151(7):C492–C4.

53.

Rico

Du Bois

Witvrouw

Van Hoof

Celis

J-P

. Fabrication of porous membranes for MEMS packaging by one-step anodization in sulfuric acid. Journal of the Electrochemical Society. 2007;154(9):K74–K8.

54.

Deng

Chen

Yin

Liu

. Fabrication of silicon nanopore arrays using a combination of dry and wet etching. Journal of vacuum science and technology B: microelectronics and nanometer Structures. 2012;30(6):061804.

55.

Deng

Chen

Liu

. Fabrication of inverted-pyramid silicon nanopore arrays with three-step wet etching. ECS journal of solid state science and technology. 2013;2(11):P419–P22.

56.

Kelly

Philipsen

HGG

. Anisotropy in the wetetching of semiconductors. Current opinion in solid state and materials science. 2005;9(1–2):84–90.

57.

Taniguchi

Tsutsui

Yokota

Kawai

. Fabrication of the gating nanopore device. Applied physics letters. 2009;95(12):123701.

58.

George

Tang

Chen

Hutchinson

Golovchenko

. Nanopore fabrication in amorphous Si: viscous flow model and comparison to experiment. Journal of applied physics. 2010;108(1):014310.

59.

Storm

Chen

Ling

Zandbergen

Dekker

. Fabrication of solid-state nanopores with single-nanometre precision. Nature materials. 2003;2(8): 537–40.

60.

Kim

Wanunu

Bell

Meller

. Rapid fabrication of uniformly sized nanopores and nanopore arrays for parallel DNA analysis. Advanced materials. 2006;18(23):3149–53.

61.

Lee

Gösele

Nielsch

. Fast fabrication of long-range ordered porous alumina membranes by hard anodization. Nature materials. 2006;5(9):741–7.

62.

Lee

Schwirn

Steinhart

Pippel

Scholz

Gösele

. Structural engineering of nanoporous anodic aluminium oxide by pulse anodization of aluminium. Nature nanotechnology. 2008;3(4): 234–9.

63.

Lanyon

De Marzi

Watson

Quinn

Gleeson

Redmond

. Fabrication of nanopore array electrodes by focused ion beam milling. Analytical chemistry. 2007;79(8):3048–55.

64.

Deng

Chen

Liu

. Fabrication of inverted-pyramid silicon nanopore arrays with three-step wet etching. ECS journal of solid state science and technology. 2013;2(11):P419–P22.

65.

Schiedt

Auvray

Bacri

Oukhaled

Madouri

Bourhis

. Direct FIB fabrication and integration of “single nanopore devices” for the manipulation of macromolecules. Microelectronic engineering. 2010;87(5):1300–3.

66.

Van den Hout

Hall

Zandbergen

Dekker

. Controlling nanopore size, shape and stability. Nanotechnology. 2010;21(11):115304.

67.

Cai

Ledden

Krueger

Golovchenko

. Nanopore sculpting with noble gas ions. Journal of applied physics. 2006;100(2):024914.

68.

Radhanpura

Hargreaves

Lewis

Sirbu

Tiginyanu

. Heavy noble gas (Kr, Xe) irradiated (111) InP nanoporous honeycomb membranes with enhanced ultrafast all-optical terahertz emission. Applied physics letters. 2010;97(18):181921.

69.

Chang

Iqbal

Stach

King

Zaluzec

Bashir

. Fabrication and characterization of solid-state nanopores using a field emission scanning electron microscope. Applied physics letters. 2006;88(10):103109.

70.

Ikoma

Yahaya

Kuriyama

Sakita

Nishino

Motooka

. Semiconductor nanopores formed by chemical vapor deposition of heteroepitaxial SiC films on SOI(100) substrates. Journal of vacuum science and technology B: microelectronics and nanometer structures. 2011;29(6):062001.

71.

Leskelä

Kemell

Kukli

Pore

Santala

Ritala

. Exploitation of atomic layer deposition for nanostructured materials. Materials science and engineering: C. 2007;27(5–8):1504–8.

72.

Asghar

Ilyas

Billo

Iqbal

. Shrinking of solid-state nanopores by direct thermal heating. Nanoscale research letters. 2011;6(1):1–6.

73.

Nasir

Ali

Ensinger

. Thermally controlled permeation of ionic molecules through synthetic nanopores functionalized with amine-terminated polymer brushes. Nanotechnology. 2012;23(22): 225502.

74.

Bernaschi

Melchionna

Succi

Fyta

Kaxiras

. Quantized current blockade and hydrodynamic correlations in biopolymer translocation through nanopores: evidence from multiscale simulations. Nano letters. 2008;8(4):1115–9.

75.

Fyta

Melchionna

Succi

Kaxiras

. Hydrodynamic correlations in the translocation of a biopolymer through a nanopore: theory and multiscale simulations. Physical review E. 2008;78(3):036704.

76.

Luo

Ala-Nissila

Ying

S-C

Metzler

. Driven polymer translocation through nanopores: Slow-vs.-fast dynamics. Europhysics letters. 2009;88(6): 68006.

77.

Meller

. Dynamics of polynucleotide transport through nanometre-scale pores. Journal of physics: condensed matter. 2003;15(17):R581.

78.

Movileanu

. Squeezing a single polypeptide through a nanopore. Soft matter. 2008;4(5):925–31.

79.

Storm

Chen

Zandbergen

Joanny

J-F

Dekker

. Fast DNA translocation through a solid-state nanopore. Nano letters. 2005;5(7):1193–7.

80.

Biance

A-L

Gierak

Bourhis

Madouri

Lafosse

Patriarche

. Focused ion beam sculpted membranes for nanoscience tooling. Microelectronic engineering. 2006;83(4):1474–7.

81.

Purnell

Schmidt

. Discrimination of single base substitutions in a DNA strand immobilized in a biological nanopore. ACS nano. 2009;3(9):2533–8.

82.

Malmstadt

Nash

Purnell

Schmidt

. Automated formation of lipid-bilayer membranes in a microfluidic device. Nano letters. 2006;6(9): 1961–5.

83.

Mathé

Aksimentiev

Nelson

Schulten

Meller

. Orientation discrimination of single-stranded DNA inside the α-hemolysin membrane channel. Proceedings of the National Academy of Sciences of the United States of America. 2005;102(35):12377–82.

84.

Yusko

Johnson

Majd

Prangkio

Rollings

. Controlling protein translocation through nanopores with bio-inspired fluid walls. Nature nanotechnology. 2011;6(4):253–60.

85.

Gershow

Stein

Brandin

Golovchenko

. DNA molecules and configurations in a solid-state nanopore microscope. Nature materials. 2003;2(9):611–5.

86.

Smeets

Keyser

Krapf

M-Y

Dekker

. Salt dependence of ion transport and DNA translocation through solid-state nanopores. Nano letters. 2006;6(1):89–95.

87.

Fologea

Uplinger

Thomas

McNabb

. Slowing DNA translocation in a solid-state nanopore. Nano letters. 2005;5(9):1734–7.

88.

Kim

Wanunu

Bell

Meller

. Rapid fabrication of uniformly sized nanopores and nanopore arrays for parallel DNA analysis. Advanced materials. 2006;18(23):3149.

89.

Osaki

Suzuki

Le Pioufle

Takeuchi

. Multichannel simultaneous measurements of single-molecule translocation in α-hemolysin nanopore array. Analytical chemistry. 2009;81(24): 9866–70.

90.

Chen

Jiang

Dunphy

Adams

Hodges

Liu

. DNA translocation through an array of kinked nanopores. Nature materials. 2010;9(8): 667–75.

91.

Henzler-Wildman

Kern

. Dynamic personalities of proteins. Nature. 2007;450(7172):964–72.

92.

Purnell

Mehta

Schmidt

. Nucleotide identification and orientation discrimination of DNA homopolymers immobilized in a protein nanopore. Nano letters. 2008;8(9):3029–34.

93.

Kowalczyk

Hall

Dekker

. Detection of local protein structures along DNA using solidstate nanopores. Nano letters. 2009;10(1):324–8.

94.

Madampage

Tavassoly

Christensen

Kumari

Lee

. Nanopore analysis: an emerging technique for studying the folding and misfolding of proteins. Prion. 2012;6(2):116–23.

95.

Dobson

. Protein misfolding, evolution and disease. Trends in biochemical sciences. 1999;24(9): 329–32.

96.

Lyubchenko

. Early stages for Parkinson's development: α-synuclein misfolding and aggregation. Journal of neuroimmune pharmacology. 2009;4(1):10–6.

97.

Merstorf

Cressiot

Pastoriza-Gallego

Oukhaled

Betton

J-M

Auvray

. Wild type, mutant protein unfolding and phase transition detected by single-nanopore recording. ACS chemical biology. 2012;7(4):652–8.

98.

Gao

Guo

Geng

Hou

Shuai

Jiang

. Layer-by-layer removal of insulating few-layer mica flakes for asymmetric ultra-thin nanopore fabrication. Nano research. 2012;5(2):99–108.

99.

Farimani

Min

Aluru

. DNA base detection using a single-layer MoS2. ACS nano. 2014;8(8): 7914–22.

100.

Garaj

Hubbard

Reina

Kong

Branton

Golovchenko

. Graphene as a subnanometre transelectrode membrane. Nature. 2010;467(7312):190–3.

101.

Qian

Joo

Cheney

Hou

. Effect of linear surface-charge non-uniformities on the electrokinetic ionic-current rectification in conical nanopores. Journal of colloid and interface science. 2009;329(2):376–83.

102.

Meller

Nivon

Brandin

Golovchenko

Branton

. Rapid nanopore discrimination between single polynucleotide molecules. Proceedings of the National Academy of Sciences of the United States of America. 2000;97(3):1079–84.

103.

Ramírez

Apel

Cervera

Mafé

. Pore structure and function of synthetic nanopores with fixed charges: tip shape and rectification properties. Nanotechnology. 2008;19(31):315707.

104.

Firnkes

Pedone

Knezevic

Döblinger

Rant

. Electrically facilitated translocations of proteins through silicon nitride nanopores: conjoint and competitive action of diffusion, electrophoresis, and electroosmosis. Nano letters. 2010;10(6):2162–7.

105.

Aksimentiev

Brunner

Cohen

Comer

Cruz-Chu

Hardy

. Computer modeling in biotechnology. Nanostructure design: Springer; 2008. pp. 181–234.

106.

Anderson

Muthukumar

Meller

. pH tuning of DNA translocation time through organically functionalized nanopores. ACS nano. 2012;7(2):1408–14.

107.

Clarke

H-C

Jayasinghe

Patel

Reid

Bayley

. Continuous base identification for single-molecule nanopore DNA sequencing. Nature nanotechnology. 2009;4(4):265–70.

108.

Freudiger

Min

Saar

Holtom

. Label-free biomedical imaging with high sensitivity by stimulated Raman scattering microscopy. Science. 2008;322(5909):1857–61.

109.

Chang

Ebong

Bhadviya

Mazumder

. Nanoscale memristor device as synapse in neuromorphic systems. Nano letters. 2010;10(4): 1297–301.

110.

Huang

Chang

Zhang

Liang

. Identifying single bases in a DNA oligomer with electron tunnelling. Nature nanotechnology. 2010;5(12):868–73.

111.

Tsutsui

Taniguchi

Yokota

Kawai

. Identifying single nucleotides by tunnelling current. Nature nanotechnology. 2010;5(4):286–90.

112.

Gyurcsányi

. Chemically-modified nanopores for sensing. Trends in analytical chemistry. 2008;27(7):627–39.

113.

Wanunu

Meller

. Chemically modified solidstate nanopores. Nano letters. 2007;7(6):1580–5.

114.

Nawy

. Nanobiotechnology: Nanopores sense protein modifications. Nature methods. 2014;11(3): 226–7.

115.

Meunier

Krstić

. Enhancement of the transverse conductance in DNA nucleotides. Journal of chemical physics. 2008;128(4):041103.

116.

Lin

Zhang

Lindsay

. Identification of DNA basepairing via tunnel-current decay. Nano letters. 2007;7(12):3854–8.

117.

Nilsson

Lee

Ratto

Létant

. Localized functionalization of single nanopores. Advanced materials. 2006;18(4):427–31.

118.

Wei

Pedone

Zürner

Döblinger

Rant

. Fabrication of metallized nanopores in silicon nitride membranes for single-molecule sensing. Small. 2010;6(13):1406–14.

119.

Wei

Gatterdam

Wieneke

Tampé

Rant

. Stochastic sensing of proteins with receptor-modified solid-state nanopores. Nature nanotechnology. 2012;7(4):257–63.

120.

Hernández-Ainsa

Muus

Bell

Steinbock

Thacker

Keyser

. Lipid-coated nanocapillaries for DNA sensing. The analyst. 2013;138(1):104–6.

121.

Zwolak

Di Ventra

. Electronic signature of DNA nucleotides via transverse transport. Nano letters. 2005;5(3):421–4.

122.

Lagerqvist

Zwolak

Di Ventra

. Fast DNA sequencing via transverse electronic transport. Nano letters. 2006;6(4):779–82.

123.

Kasianowicz

Brandin

Branton

Deamer

. Characterization of individual polynucleotide molecules using a membrane channel. Proceedings of the National Academy of Sciences of the United States of America. 1996;93(24):13770–3.

124.

Jonsson

Dekker

. Plasmonic nanopore for electrical profiling of optical intensity landscapes. Nano letters. 2013;13(3):1029–33.

125.

Soni

Meller

. Progress toward ultrafast DNA sequencing using solid-state nanopores. Clinical chemistry. 2007;53(11):1996–2001.

126.

Dudko

Mathé

Meller

. Nanopore force spectroscopy tools for analyzing single biomolecular complexes. Methods in enzymology. 2010;475:565–89.

127.

Liu

Zhao

Parks

Deamer

Hawkins

Schmidt

. Correlated electrical and optical analysis of single nanoparticles and biomolecules on a nanopore-gated optofluidic chip. Nano letters. 2014;14(8):4816–20.

128.

Pech

Brunet

Durou

Huang

Mochalin

Gogotsi

. Ultrahigh-power micrometre-sized supercapacitors based on onion-like carbon. Nature nanotechnology. 2010;5(9):651–4.

129.

Guo

Cao

Xia

Nie

Xue

. Energy harvesting with single-ion-selective nanopores: a concentration-gradient-driven nanofluidic power source. Advanced functional materials. 2010;20(8):1339–44.

130.

Qian

. Electrokinetic particle translocation through a nanopore. Physical chemistry chemical physics. 2011;13(9):4060–71.

131.

Freedman

Otto

Ivanov

Barik

Edel

. Nanopore sensing at ultra-low concentrations using single-molecule dielectrophoretic trapping. Nature communications. 2016;7.

132.

Coasne

Gubbins

Pellenq

RJ-M

. Temperature effect on adsorption/desorption isotherms for a simple fluid confined within various nanopores. Adsorption. 2005;11(1):289–94.

133.

Dzubiella

Hansen

J-P

. Electric-field-controlled water and ion permeation of a hydrophobic nanopore. Journal of chemical physics. 2005;122(23): 234706.

134.

Lanza

Gao

Yin

Zhang

Liu

Tong

. Nanogap based graphene coated AFM tips with high spatial resolution, conductivity and durability. Nanoscale. 2013;5(22):10816–23.

Fabrications,Applications and Challenges of Solid-State Nanopores: A Mini Review

Abstract

Keywords

1. Introduction

2. Principle

3. Fabrications of Solid-State Nanopores

3.1 Direct opening methods

3.2 Tuning methods

4. Applications

4.1 Molecular translocation

4.2 DNA sequencing

4.3 Protein detections

5. Recent Advances and Challenges

5.1 Recent advances

5.2 Challenges

6. Conclusion

Footnotes

7. Acknowledgements

References