1
|
Liu S, Hawkins AR, Schmidt H. Optofluidic devices with integrated solid-state nanopores. Mikrochim Acta 2016; 183:1275-1287. [PMID: 27046940 DOI: 10.1007/s00604-016-1758-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This review (with 90 refs.) covers the state of the art in optofluidic devices with integrated solid-state nanopores for use in detection and sensing. Following an introduction into principles of optofluidics and solid-state nanopore technology, we discuss features of solid-state nanopore based assays using optofluidics. This includes the incorporation of solid-state nanopores into optofluidic platforms based on liquid-core anti-resonant reflecting optical waveguides (ARROWs), methods for their fabrication, aspects of single particle detection and particle manipulation. We then describe the new functionalities provided by solid-state nanopores integrated into optofluidic chips, in particular acting as smart gates for correlated electro-optical detection and discrimination of nanoparticles. This enables the identification of viruses and λ-DNA, particle trajectory simulations, enhancing sensitivity by tuning the shape of nanopores. The review concludes with a summary and an outlook.
Collapse
Affiliation(s)
- Shuo Liu
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Aaron R Hawkins
- ECEn Department, 459 Clyde Building, Brigham Young University, Provo, UT 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| |
Collapse
|
2
|
Rutkowska A, Freedman K, Skalkowska J, Kim MJ, Edel JB, Albrecht T. Electrodeposition and Bipolar Effects in Metallized Nanopores and Their Use in the Detection of Insulin. Anal Chem 2015; 87:2337-44. [DOI: 10.1021/ac504463r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Agnieszka Rutkowska
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
| | - Kevin Freedman
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
- Department
of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Justyna Skalkowska
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
- Department
of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Min Jun Kim
- Department
of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Joshua B. Edel
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
| | - Tim Albrecht
- Department
of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
| |
Collapse
|
3
|
Japrung D, Bahrami A, Nadzeyka A, Peto L, Bauerdick S, Edel JB, Albrecht T. SSB binding to single-stranded DNA probed using solid-state nanopore sensors. J Phys Chem B 2014; 118:11605-12. [PMID: 25222770 DOI: 10.1021/jp506832u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Single-stranded DNA (ssDNA) binding protein plays an important role in the DNA replication process in a wide range of organisms. It binds to ssDNA to prevent premature reannealing and to protect it from degradation. Current understanding of SSB/ssDNA interaction points to a complex mechanism, including SSB motion along the DNA strand. We report on the first characterization of this interaction at the single-molecule level using solid-state nanopore sensors, namely without any labeling or surface immobilization. Our results show that the presence of SSB on the ssDNA can control the speed of nanopore translocation, presumably due to strong interactions between SSB and the nanopore surface. This enables nanopore-based detection of ssDNA fragments as short as 37 nt, which is normally very difficult with solid-state nanopore sensors, due to constraints in noise and bandwidth. Notably, this fragment is considerably shorter than the 65 nt binding motif, typically required for SSB binding at high salt concentrations. The nonspecificity of SSB binding to ssDNA further suggests that this approach could be used for fragment sizing of short ssDNA.
Collapse
Affiliation(s)
- Deanpen Japrung
- Department of Chemistry, Imperial College London , Exhibition Road, South Kensington Campus, London SW7 2AZ, U.K
| | | | | | | | | | | | | |
Collapse
|
4
|
Becton M, Zhang L, Wang X. Molecular Dynamics Study of Programmable Nanoporous Graphene. JOURNAL OF NANOMECHANICS AND MICROMECHANICS 2014. [DOI: 10.1061/(asce)nm.2153-5477.0000094] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Matthew Becton
- College of Engineering, Univ. of Georgia, Athens, GA 30602
| | - Liuyang Zhang
- College of Engineering, Univ. of Georgia, Athens, GA 30602
| | - Xianqiao Wang
- Assistant Professor, College of Engineering, Univ. of Georgia, Athens, GA 30602 (corresponding author)
| |
Collapse
|
5
|
Connelly LS, Meckes B, Larkin J, Gillman AL, Wanunu M, Lal R. Graphene nanopore support system for simultaneous high-resolution AFM imaging and conductance measurements. ACS APPLIED MATERIALS & INTERFACES 2014; 6:5290-6. [PMID: 24581087 PMCID: PMC4232248 DOI: 10.1021/am500639q] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 02/28/2014] [Indexed: 05/24/2023]
Abstract
Accurately defining the nanoporous structure and sensing the ionic flow across nanoscale pores in thin films and membranes has a wide range of applications, including characterization of biological ion channels and receptors, DNA sequencing, molecule separation by nanoparticle films, sensing by block co-polymers films, and catalysis through metal-organic frameworks. Ionic conductance through nanopores is often regulated by their 3D structures, a relationship that can be accurately determined only by their simultaneous measurements. However, defining their structure-function relationships directly by any existing techniques is still not possible. Atomic force microscopy (AFM) can image the structures of these pores at high resolution in an aqueous environment, and electrophysiological techniques can measure ion flow through individual nanoscale pores. Combining these techniques is limited by the lack of nanoscale interfaces. We have designed a graphene-based single-nanopore support (∼5 nm thick with ∼20 nm pore diameter) and have integrated AFM imaging and ionic conductance recording using our newly designed double-chamber recording system to study an overlaid thin film. The functionality of this integrated system is demonstrated by electrical recording (<10 pS conductance) of suspended lipid bilayers spanning a nanopore and simultaneous AFM imaging of the bilayer.
Collapse
Affiliation(s)
- Laura S. Connelly
- Materials Science and Engineering
Program, Department of Bioengineering, and Department of Mechanical and Aerospace Engineering, University of California−San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Brian Meckes
- Materials Science and Engineering
Program, Department of Bioengineering, and Department of Mechanical and Aerospace Engineering, University of California−San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Joseph Larkin
- Department of Physics, Northeastern University, 110 Forsyth Street, Boston, Massachusetts 02115, United States
| | - Alan L. Gillman
- Materials Science and Engineering
Program, Department of Bioengineering, and Department of Mechanical and Aerospace Engineering, University of California−San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, 110 Forsyth Street, Boston, Massachusetts 02115, United States
| | - Ratnesh Lal
- Materials Science and Engineering
Program, Department of Bioengineering, and Department of Mechanical and Aerospace Engineering, University of California−San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| |
Collapse
|
6
|
Crescentini M, Bennati M, Carminati M, Tartagni M. Noise limits of CMOS current interfaces for biosensors: a review. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2014; 8:278-292. [PMID: 24875287 DOI: 10.1109/tbcas.2013.2262998] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Current sensing readout is one of the most frequent techniques used in biosensing due to the charge-transfer phenomena occurring at solid-liquid interfaces. The development of novel nanodevices for biosensing determines new challenges for electronic interface design based on current sensing, especially when compact and efficient arrays need to be organized, such as in recent trends of rapid label-free electronic detection of DNA synthesis. This paper will review the basic noise limitations of current sensing interfaces with particular emphasis on integrated CMOS technology. Starting from the basic theory, the paper presents, investigates and compares charge-sensitive amplifier architectures used in both continuous-time and discrete-time approaches, along with their design trade-offs involving noise floor, sensitivity to stray capacitance and bandwidth. The ultimate goal of this review is providing analog designers with helpful design rules and analytical tools. Also, in order to present a comprehensive overview of the state-of-the-art, the most relevant papers recently appeared in the literature about this topic are discussed and compared.
Collapse
|
7
|
Krasniqi B, Lee JS. RNase A does not translocate the alpha-hemolysin pore. PLoS One 2014; 9:e88004. [PMID: 24505349 PMCID: PMC3913706 DOI: 10.1371/journal.pone.0088004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 01/02/2014] [Indexed: 11/24/2022] Open
Abstract
The application of nanopore sensing utilizing the α-hemolysin pore to probe proteins at single-molecule resolution has expanded rapidly. In some studies protein translocation through the α-hemolysin has been reported. However, there is no direct evidence, as yet, that proteins can translocate the α-hemolysin pore. The biggest challenge to obtaining direct evidence is the lack of a highly sensitive assay to detect very low numbers of protein molecules. Furthermore, if an activity based assay is applied then the proteins translocating by unfolding should refold back to an active confirmation for the assay technique to work. To overcome these challenges we selected a model enzyme, ribonuclease A, that readily refolds to an active conformation even after unfolding it with denaturants. In addition we have developed a highly sensitive reverse transcription polymerase chain reaction based activity assay for ribonuclease A. Initially, ribonuclease A, a protein with a positive net charge and dimensions larger than the smallest diameter of the pore, was subjected to nanopore analysis under different experimental conditions. Surprisingly, although the protein was added to the cis chamber (grounded) and a positive potential was applied, the interaction of ribonuclease A with α-hemolysin pore induced small and large blockade events in the presence and the absence of a reducing and/or denaturing agent. Upon measuring the zeta potential, it was found that the protein undergoes a charge reversal under the experimental conditions used for nanopore sensing. From the investigation of the effect of voltage on the interaction of ribonuclease A with the α-hemolysin pore, it was impossible to conclude if the events observed were translocations. However, upon testing for ribonuclease A activity on the trans chamber it was found that ribonuclease A does not translocate the α-hemolysin pore.
Collapse
Affiliation(s)
- Besnik Krasniqi
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jeremy S. Lee
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
- * E-mail:
| |
Collapse
|
8
|
Brucale M, Schuler B, Samorì B. Single-molecule studies of intrinsically disordered proteins. Chem Rev 2014; 114:3281-317. [PMID: 24432838 DOI: 10.1021/cr400297g] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marco Brucale
- Institute for the Study of Nanostructured Materials (ISMN), Italian National Council of Research (CNR) , Area della Ricerca Roma1, Via Salaria km 29.3 00015 Monterotondo (Rome), Italy
| | | | | |
Collapse
|
9
|
Gibb TR, Ivanov AP, Edel JB, Albrecht T. Single Molecule Ionic Current Sensing in Segmented Flow Microfluidics. Anal Chem 2014; 86:1864-71. [DOI: 10.1021/ac403921m] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Thomas R. Gibb
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7
2AZ, United Kingdom
| | - Aleksandar P. Ivanov
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7
2AZ, United Kingdom
| | - Joshua B. Edel
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7
2AZ, United Kingdom
| | - Tim Albrecht
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7
2AZ, United Kingdom
| |
Collapse
|
10
|
Liu KL, Hsu JP, Tseng S. Capillary osmosis in a charged nanopore connecting two large reservoirs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:9598-9603. [PMID: 23863095 DOI: 10.1021/la401925n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Experimental evidence revealed that the performance of nanopore-based biosensing devices can be improved by applying a salt concentration gradient. To provide a theoretical explanation for this observation and explore the mechanisms involved, we model the capillary osmosis (or diffusioosmosis) in a charged solid-state nanopore connecting two large reservoirs. The effects of nanopore geometry and the reservoir salt concentrations are examined. We show that the capillary osmotic flow is from the high salt concentration reservoir to the low salt concentration one, and its magnitude has a maximum as the reservoir salt concentrations vary. In general, the shorter the nanopore and/or the smaller its radius, the faster the osmotic flow. This flow enhances the current recognition, and the ion concentration polarization across nanopore openings raises the entity capture rate, thereby being capable of improving the performance of electrophoresis-based biosensors. The results gathered provide necessary information for designing nanopore-based biosensor devices.
Collapse
Affiliation(s)
- Kuan-Liang Liu
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan 10617
| | | | | |
Collapse
|
11
|
Japrung D, Dogan J, Freedman KJ, Nadzeyka A, Bauerdick S, Albrecht T, Kim MJ, Jemth P, Edel JB. Single-molecule studies of intrinsically disordered proteins using solid-state nanopores. Anal Chem 2013; 85:2449-56. [PMID: 23327569 DOI: 10.1021/ac3035025] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Partially or fully disordered proteins are instrumental for signal-transduction pathways; however, many mechanistic aspects of these proteins are not well-understood. For example, the number and nature of intermediate states along the binding pathway is still a topic of intense debate. To shed light on the conformational heterogeneity of disordered protein domains and their complexes, we performed single-molecule experiments by translocating disordered proteins through a nanopore embedded within a thin dielectric membrane. This platform allows for single-molecule statistics to be generated without the need of fluorescent labels or other modification groups. These studies were performed on two different intrinsically disordered protein domains, a binding domain from activator of thyroid hormone and retinoid receptors (ACTR) and the nuclear coactivator binding domain of CREB-binding protein (NCBD), along with their bimolecular complex. Our results demonstrate that both ACTR and NCBD populate distinct conformations upon translocation through the nanopore. The folded complex of the two disordered domains, on the other hand, translocated as one conformation. Somewhat surprisingly, we found that NCBD undergoes a charge reversal under high salt concentrations. This was verified by both translocation statistics as well as by measuring the ζ-potential. Electrostatic interactions have been previously suggested to play a key role in the association of intrinsically disordered proteins, and the observed behavior adds further complexity to their binding reactions.
Collapse
Affiliation(s)
- Deanpen Japrung
- Department of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom
| | | | | | | | | | | | | | | | | |
Collapse
|