1
|
Alam I, Boonkoom T, Pitakjakpipop H, Boonbanjong P, Loha K, Saeyang T, Vanichtanankul J, Japrung D. Single-Molecule Analysis of SARS-CoV-2 Double-Stranded Polynucleotides Using Solid-State Nanopore with AI-Assisted Detection and Classification: Implications for Understanding Disease Severity. ACS APPLIED BIO MATERIALS 2024; 7:1017-1027. [PMID: 38194666 DOI: 10.1021/acsabm.3c00998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
This study utilized solid-state nanopores, combined with artificial intelligence (AI), to analyze the double-stranded polynucleotides encoding angiotensin-converting enzyme 2, receptor-binding domain, and N protein, important parts of SARS-CoV-2 infection. By examining ionic current signals during DNA translocation, we revealed the dynamic interactions and structural characteristics of these nucleotide sequences and also quantified their abundance. Nanopores of sizes 3 and 10 nm were efficiently fabricated and characterized, ensuring an optimal experimental approach. Our results showed a clear relationship between DNA capture rates and concentration, proving our method's effectiveness. Notably, longer DNA sequences had higher capture rates, suggesting their importance for potential disease marker analysis. The 3 nm nanopore demonstrated superior performance in our DNA analysis. Using dwell time measurements and excluded currents, we were able to distinguish the longer DNA fragments, paving the way for a DNA length-based analysis. Overall, our research underscores the potential of nanopore technology, enhanced with AI, in analyzing COVID-19-related DNA and its implications for understanding disease severity. This provides insight into innovative diagnostic and treatment strategies.
Collapse
Affiliation(s)
- Ibrar Alam
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Thitikorn Boonkoom
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Harit Pitakjakpipop
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Poramin Boonbanjong
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Kawin Loha
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Thanaya Saeyang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Deanpen Japrung
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| |
Collapse
|
2
|
Afrasiabian N, Wei M, Denniston C. Enhanced Pulley Effect for Translocation: The Interplay of Electrostatic and Hydrodynamic Forces. Biomacromolecules 2023; 24:4103-4112. [PMID: 37417981 PMCID: PMC10498446 DOI: 10.1021/acs.biomac.3c00473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/19/2023] [Indexed: 07/08/2023]
Abstract
Solid-state nanopore sensors remain a promising solution to the rising global demand for genome sequencing. These single-molecule sensing technologies require single-file translocation for high resolution and accurate detection. In a previous publication, we discovered a hairpin unraveling mechanism, namely, the pulley effect, in a pressure-driven translocation system. In this paper, we further investigate the pulley effect in the presence of pressure-driven fluid flow and an opposing force provided by an electrostatic field as an approach to increase single-file capture probability. A hydrodynamic flow is used to move the polymer forward, and two oppositely charged electrostatic square loops are used to create an opposing force. By optimizing the balance between forces, we show that the single-file capture can be amplified from about 50% to almost 95%. The force location, force strength, and flow rate are used as the optimizing variables.
Collapse
Affiliation(s)
- Navid Afrasiabian
- Department of Physics and
Astronomy, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Matthew Wei
- Department of Physics and
Astronomy, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Colin Denniston
- Department of Physics and
Astronomy, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| |
Collapse
|
3
|
Chen P, Sun Z, Wang J, Liu X, Bai Y, Chen J, Liu A, Qiao F, Chen Y, Yuan C, Sha J, Zhang J, Xu LQ, Li J. Portable nanopore-sequencing technology: Trends in development and applications. Front Microbiol 2023; 14:1043967. [PMID: 36819021 PMCID: PMC9929578 DOI: 10.3389/fmicb.2023.1043967] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023] Open
Abstract
Sequencing technology is the most commonly used technology in molecular biology research and an essential pillar for the development and applications of molecular biology. Since 1977, when the first generation of sequencing technology opened the door to interpreting the genetic code, sequencing technology has been developing for three generations. It has applications in all aspects of life and scientific research, such as disease diagnosis, drug target discovery, pathological research, species protection, and SARS-CoV-2 detection. However, the first- and second-generation sequencing technology relied on fluorescence detection systems and DNA polymerization enzyme systems, which increased the cost of sequencing technology and limited its scope of applications. The third-generation sequencing technology performs PCR-free and single-molecule sequencing, but it still depends on the fluorescence detection device. To break through these limitations, researchers have made arduous efforts to develop a new advanced portable sequencing technology represented by nanopore sequencing. Nanopore technology has the advantages of small size and convenient portability, independent of biochemical reagents, and direct reading using physical methods. This paper reviews the research and development process of nanopore sequencing technology (NST) from the laboratory to commercially viable tools; discusses the main types of nanopore sequencing technologies and their various applications in solving a wide range of real-world problems. In addition, the paper collates the analysis tools necessary for performing different processing tasks in nanopore sequencing. Finally, we highlight the challenges of NST and its future research and application directions.
Collapse
Affiliation(s)
- Pin Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Zepeng Sun
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Jiawei Wang
- School of Computer Science and Technology, Southeast University, Nanjing, China
| | - Xinlong Liu
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Yun Bai
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Jiang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Anna Liu
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Feng Qiao
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China
| | - Yang Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Chenyan Yuan
- Clinical Laboratory, Southeast University Zhongda Hospital, Nanjing, China
| | - Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing, China
| | - Jinghui Zhang
- School of Computer Science and Technology, Southeast University, Nanjing, China
| | - Li-Qun Xu
- China Mobile (Chengdu) Industrial Research Institute, Chengdu, China,*Correspondence: Li-Qun Xu, ✉
| | - Jian Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China,Jian Li, ✉
| |
Collapse
|
4
|
Zhang L, Burns N, Ji Z, Sun S, Deutscher SL, Carson WE, Guo P. Nipple fluid for breast cancer diagnosis using the nanopore of Phi29 DNA-packaging motor. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2023; 48:102642. [PMID: 36581256 PMCID: PMC10035634 DOI: 10.1016/j.nano.2022.102642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/14/2022] [Accepted: 12/02/2022] [Indexed: 12/27/2022]
Abstract
Detection of cancer in its early stage is a challenging task for oncologists. Inflammatory breast cancer has symptoms that are similar to mastitis and can be mistaken for microbial infection. Currently, the differential diagnosis between mastitis and Inflammatory breast cancer via nipple aspirate fluid (NAF) is difficult. Here, we report a label-free and amplification-free detection platform using an engineered nanopore of the phi29 DNA-packaging motor with biomarker Galectin3 (GAL3), Thomsen-Friedenreich (TF) binding peptide as the probe fused at its C-terminus. The binding of the biomarker in NAF samples from breast cancer patients to the probe results in the connector's conformational change with a current blockage of 32 %. Utilization of dwell time, blockage ratio, and peak signature enable us to detect basal levels of biomarkers from patient NAF samples at the single-molecule level. This platform will allow for breast cancers to be resolved at an early stage with accuracy and thoroughness.
Collapse
Affiliation(s)
- Long Zhang
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Zhouxiang Ji
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Steven Sun
- OSU Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Susan L Deutscher
- Department of Biochemistry, University of Missouri, Harry S. Truman Memorial VA Hospital, Columbia, MO 65211, USA.
| | - William E Carson
- OSU Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
5
|
Bhullar AS, Zhang L, Burns N, Cheng X, Guo P. Voltage controlled shutter regulates channel size and motion direction of protein aperture as durable nano-electric rectifier-----An opinion in biomimetic nanoaperture. Biomaterials 2022; 291:121863. [PMID: 36356474 PMCID: PMC9766157 DOI: 10.1016/j.biomaterials.2022.121863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/30/2022] [Accepted: 10/15/2022] [Indexed: 11/09/2022]
Abstract
In optical devices such as camera or microscope, an aperture is used to regulate light intensity for imaging. Here we report the discovery and construction of a durable bio-aperture at nanometerscale that can regulate current at the pico-ampere scale. The nano-aperture is made of 12 identical protein subunits that form a 3.6-nm channel with a shutter and "one-way traffic" property. This shutter responds to electrical potential differences across the aperture and can be turned off for double stranded DNA translocation. This voltage enables directional control, and three-step regulation for opening and closing. The nano-aperture was constructed in vitro and purified into homogeneity. The aperture was stable at pH2-12, and a temperature of -85C-60C. When an electrical potential was held, three reproducible discrete steps of current flowing through the channel were recorded. Each step reduced 32% of the channel dimension evident by the reduction of the measured current flowing through the aperture. The current change is due to the change of the resistance of aperture size. The transition between these three distinct steps and the direction of the current was controlled via the polarity of the voltage applied across the aperture. When the C-terminal of the aperture was fused to an antigen, the antibody and antigen interaction resulted in a 32% reduction of the channel size. This phenomenon was used for disease diagnosis since the incubation of the antigen-nano-aperture with a specific cancer antibody resulted in a change of 32% of current. The purified truncated cone-shape aperture automatically self-assembled efficiently into a sheet of the tetragonal array via head-to-tail self-interaction. The nano-aperture discovery with a controllable shutter, discrete-step current regulation, formation of tetragonal sheet, and one-way current traffic provides a nanoscale electrical circuit rectifier for nanodevices and disease diagnosis.
Collapse
Affiliation(s)
- Abhjeet S Bhullar
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; And Comprehensive Cancer Center. The Ohio State University, Columbus, OH, 43210, USA; Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Long Zhang
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; And Comprehensive Cancer Center. The Ohio State University, Columbus, OH, 43210, USA
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; And Comprehensive Cancer Center. The Ohio State University, Columbus, OH, 43210, USA
| | - Xiaolin Cheng
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA; College of Pharmacy, Translational Data Analytics Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; And Comprehensive Cancer Center. The Ohio State University, Columbus, OH, 43210, USA; Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA; College of Pharmacy, Translational Data Analytics Institute, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
6
|
Denuga S, Whelan DE, O'Neill SP, Johnson RP. Capture and analysis of double‐stranded DNA with the α‐hemolysin nanopore: Fundamentals and applications. ELECTROCHEMICAL SCIENCE ADVANCES 2022. [DOI: 10.1002/elsa.202200001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
| | | | | | - Robert P. Johnson
- School of Chemistry University College Dublin Ireland
- UCD‐Centre for Food Safety University College Dublin Dublin Ireland
| |
Collapse
|
7
|
Li X, Song G, Dou L, Yan S, Zhang M, Yuan W, Lai S, Jiang X, Li K, Sun K, Zhao C, Geng J. The structure and unzipping behavior of dumbbell and hairpin DNA revealed by real-time nanopore sensing. NANOSCALE 2021; 13:11827-11835. [PMID: 34152351 DOI: 10.1039/d0nr08729g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Hairpin structures play an essential role in DNA replication, transcription, and recombination. Single-molecule studies enable the real-time measurement and observation of the energetics and dynamics of hairpin structures, including folding and DNA-protein interactions. Nanopore sensing is emerging as a powerful tool for DNA sensing and sequencing, and previous research into hairpins using an α-hemolysin (α-HL) nanopore suggested that hairpin DNA enters from its stem side. In this work, the translocation and interaction of hairpin and dumbbell DNA samples with varying stems, loops, and toeholds were investigated systematically using a Mycobacterium smegmatis porin A (MspA) nanopore. It was found that these DNA constructs could translocate through the pore under a bias voltage above +80 mV, and blockage events with two conductance states could be observed. The events of the lower blockage were correlated with the loop size of the hairpin or dumbbell DNA (7 nt to 25 nt), which could be attributed to non-specific collisions with the pore, whereas the dwell time of events with the higher blockage were correlated with the stem length, thus indicating effective translocation. Furthermore, dumbbell DNA with and without a stem opening generated different dwell times when driven through the MspA nanopore. Finally, a new strategy based on the dwell time difference was developed to detect single nucleotide polymorphisms (SNPs). These results demonstrated that the unzipping behaviors and DNA-protein interactions of hairpin and dumbbell DNA could be revealed using nanopore technology, and this could be further developed to create sensors for the secondary structures of nucleic acids.
Collapse
Affiliation(s)
- Xinqiong Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Li M, Yin F, Song L, Mao X, Li F, Fan C, Zuo X, Xia Q. Nucleic Acid Tests for Clinical Translation. Chem Rev 2021; 121:10469-10558. [PMID: 34254782 DOI: 10.1021/acs.chemrev.1c00241] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.
Collapse
Affiliation(s)
- Min Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fangfei Yin
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Song
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Xia
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| |
Collapse
|
9
|
Translation of the long-term fundamental studies on viral DNA packaging motors into nanotechnology and nanomedicine. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1103-1129. [DOI: 10.1007/s11427-020-1752-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023]
|
10
|
DNA Nanotechnology for Building Sensors, Nanopores and Ion-Channels. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:331-370. [PMID: 31713205 DOI: 10.1007/978-981-13-9791-2_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA nanotechnology has revolutionised the capabilities to shape and control three-dimensional structures at the nanometre scale. Designer sensors, nanopores and ion-channels built from DNA have great potential for both cross-disciplinary research and applications. Here, we introduce the concept of structural DNA nanotechnology, including DNA origami, and give an overview of the work flow from design to assembly, characterisation and application of DNA-based functional systems. Chemical functionalisation of DNA has opened up pathways to transform static DNA structures into dynamic nanomechanical sensors. We further introduce nanopore sensing as a powerful label-free single-molecule technique and discuss how it can benefit from DNA nanotechnology. Especially exciting is the possibility to create membrane-inserted DNA nanochannels that mimic their protein-based natural counterparts in form and function. In this chapter we review the status quo of DNA sensors, nanopores and ion channels, highlighting opportunities and challenges for their future development.
Collapse
|
11
|
Guo P, Driver D, Zhao Z, Zheng Z, Chan C, Cheng X. Controlling the Revolving and Rotating Motion Direction of Asymmetric Hexameric Nanomotor by Arginine Finger and Channel Chirality. ACS NANO 2019; 13:6207-6223. [PMID: 31067030 PMCID: PMC6595433 DOI: 10.1021/acsnano.8b08849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Nanomotors in nanotechnology are as important as engines in daily life. Many ATPases are nanoscale biomotors classified into three categories based on the motion mechanisms in transporting substrates: linear, rotating, and the recently discovered revolving motion. Most biomotors adopt a multisubunit ring-shaped structure that hydrolyzes ATP to generate force. How these biomotors control the motion direction and regulate the sequential action of their multiple subunits is intriguing. Many ATPases are hexameric with each monomer containing a conserved arginine finger. This review focuses on recent findings on how the arginine finger controls motion direction and coordinates adjacent subunit interactions in both revolving and rotating biomotors. Mechanisms of intersubunit interactions and sequential movements of individual subunits are evidenced by the asymmetrical appearance of one dimer and four monomers in high-resolution structural complexes. The arginine finger is situated at the interface of two subunits and extends into the ATP binding pocket of the downstream subunit. An arginine finger mutation results in deficiency in ATP binding/hydrolysis, substrate binding, and transport, highlighting the importance of the arginine finger in regulating energy transduction and motor function. Additionally, the roles of channel chirality and channel size are discussed as related to controlling one-way trafficking and differentiating the revolving and rotating mechanisms. Finally, the review concludes by discussing the conformational changes and entropy conversion triggered by ATP binding/hydrolysis, offering a view different from the traditional concept of ATP-mediated mechanochemical energy coupling. The elucidation of the motion mechanism and direction control in ATPases could facilitate nanomotor fabrication in nanotechnology.
Collapse
Affiliation(s)
- Peixuan Guo
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
- E-mail:
| | - Dana Driver
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Zhengyi Zhao
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Zhen Zheng
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Chun Chan
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| | - Xiaolin Cheng
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy
and College of Medicine, Dorothy M. Davis Heart and Lung Research
Institute, Comprehensive Cancer Center and College of Pharmacy, Biophysics
Graduate Program, Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United
States
| |
Collapse
|
12
|
Tan CS, Fleming AM, Ren H, Burrows CJ, White HS. γ-Hemolysin Nanopore Is Sensitive to Guanine-to-Inosine Substitutions in Double-Stranded DNA at the Single-Molecule Level. J Am Chem Soc 2018; 140:14224-14234. [PMID: 30269492 DOI: 10.1021/jacs.8b08153] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biological nanopores provide a unique single-molecule sensing platform to detect target molecules based on their specific electrical signatures. The γ-hemolysin (γ-HL) protein produced by Staphylococcus aureus is able to assemble into an octamer nanopore with a ∼2.3 nm diameter β-barrel. Herein, we demonstrate the first application of γ-HL nanopore for DNA structural analysis. To optimize conditions for ion-channel recording, the properties of the γ-HL pore (e.g., conductance, voltage-dependent gating, and ion-selectivity) were characterized at different pH, temperature, and electrolyte concentrations. The optimal condition for DNA analysis using γ-HL corresponds to 3 M KCl, pH 5, and T = 20 °C. The γ-HL protein nanopore is able to translocate dsDNA at about ∼20 bp/ms, and the unique current-signature of captured dsDNA can directly distinguish guanine-to-inosine substitutions at the single-molecule level with ∼99% accuracy. The slow dsDNA threading and translocation processes indicate this wild-type γ-HL channel has potential to detect other base modifications in dsDNA.
Collapse
Affiliation(s)
- Cherie S Tan
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Hang Ren
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Henry S White
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| |
Collapse
|
13
|
Ren YA, Gao H, Ouyang X. Advances in DNA Origami Nanopores: Fabrication, Characterization and Applications. CHINESE J CHEM 2018. [DOI: 10.1002/cjoc.201800173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yong-An Ren
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Key Laboratory of Modern Separation Science in Shaanxi Province, College of Chemistry & Material Science; Northwest University; Xi'an Shaanxi 710127 China
| | - Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Key Laboratory of Modern Separation Science in Shaanxi Province, College of Chemistry & Material Science; Northwest University; Xi'an Shaanxi 710127 China
| | - Xiangyuan Ouyang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China, Key Laboratory of Modern Separation Science in Shaanxi Province, College of Chemistry & Material Science; Northwest University; Xi'an Shaanxi 710127 China
| |
Collapse
|
14
|
Tu B, Bai S, Lu B, Fang Q. Conic shapes have higher sensitivity than cylindrical ones in nanopore DNA sequencing. Sci Rep 2018; 8:9097. [PMID: 29904117 PMCID: PMC6002541 DOI: 10.1038/s41598-018-27517-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 05/31/2018] [Indexed: 11/09/2022] Open
Abstract
Nanopores have emerged as helpful research tools for single molecule detection. Through continuum modeling, we investigated the effects of membrane thickness, nanopore size, and pore shape on current signal characteristics of DNA. The simulation results showed that, when reducing the pore diameter, the amplitudes of current signals of DNA increase. Moreover, we found that, compared to cylindrically shaped nanopores, conical-shaped nanopores produce greater signal amplitudes from biomolecules translocation. Finally, we demonstrated that continuum model simulations for the discrimination of DNA and RNA yield current characteristics approximately consistent with experimental measurements and that A-T and G-C base pairs can be distinguished using thin conical solid-state nanopores. Our study not only suggests that computational approaches in this work can be used to guide the designs of nanopore for single molecule detection, but it also provides several possible ways to improve the current amplitudes of nanopores for better resolution.
Collapse
Affiliation(s)
- Bin Tu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, beijing, 100190, China
| | - Shiyang Bai
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, beijing, 100190, China
| | - Benzhuo Lu
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Qiaojun Fang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, beijing, 100190, China. .,Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Sino-Danish Center for Education and Research, Beijing, 101408, China.
| |
Collapse
|
15
|
Haque F, Zhang H, Wang S, Chang CL, Savran C, Guo P. Methods for Single-Molecule Sensing and Detection Using Bacteriophage Phi29 DNA Packaging Motor. Methods Mol Biol 2018; 1805:423-450. [PMID: 29971730 DOI: 10.1007/978-1-4939-8556-2_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Bacteriophage phi29 DNA packaging motor consists of a dodecameric portal channel protein complex termed connector that allows transportation of genomic dsDNA and a hexameric packaging RNA (pRNA) ring to gear the motor. The elegant design of the portal protein has facilitated its applications for real-time single-molecule detection of biopolymers and chemicals with high sensitivity and selectivity. The robust self-assembly property of the pRNA has enabled biophysical studies of the motor complex to determine the stoichiometry and structure/folding of the pRNA at single-molecule level. This chapter focuses on biophysical and analytical methods for studying the phi29 motor components at the single-molecule level, such as single channel conductance assays of membrane-embedded connectors; single molecule photobleaching (SMPB) assay for determining the stoichiometry of phi29 motor components; fluorescence resonance energy transfer (FRET) assay for determining the structure and folding of pRNA; atomic force microscopy (AFM) for imaging pRNA nanoparticles of various size, shape, and stoichiometry; and bright-field microscopy with magnetomechanical system for direct visualization of viral DNA packaging process. The phi29 system with explicit engineering capability has incredible potentials for diverse applications in nanotechnology and nanomedicine including, but not limited to, DNA sequencing, drug delivery to diseased cells, environmental surveillance, and early disease diagnosis.
Collapse
Affiliation(s)
- Farzin Haque
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA.,Department of Physiology and Cell Biology, Dorothy M Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.,Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Hui Zhang
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA.,Department of Physiology and Cell Biology, Dorothy M Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.,Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Shaoying Wang
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA.,Department of Physiology and Cell Biology, Dorothy M Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.,Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Chun-Li Chang
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA.,School of Mechanical Engineering, Purdue University, West Lafayette, IN, USA.,Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Cagri Savran
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA.,School of Mechanical Engineering, Purdue University, West Lafayette, IN, USA.,Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA. .,Department of Physiology and Cell Biology, Dorothy M Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA. .,Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA. .,Markey Cancer Center, University of Kentucky, Lexington, KY, USA. .,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA. .,Sylvan G. Frank Endowed Chair in Pharmaceutics and Drug Delivery, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
16
|
Khan MS, Dosoky NS, Mustafa G, Patel D, Berdiev B, Williams JD. Electrophysiology of Epithelial Sodium Channel (ENaC) Embedded in Supported Lipid Bilayer Using a Single Nanopore Chip. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:13680-13688. [PMID: 29131643 DOI: 10.1021/acs.langmuir.7b02404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Nanopore-based technologies are highly adaptable supports for developing label-free sensor chips to characterize lipid bilayers, membrane proteins, and nucleotides. We utilized a single nanopore chip to study the electrophysiology of the epithelial Na+ channel (ENaC) incorporated in supported lipid membrane (SLM). An isolated nanopore was developed inside the silicon cavity followed by fusing large unilamellar vesicles (LUVs) of DPPS (1,2-dipalmitoyl-sn-glycero-3-phosphoserine) and DPPE (1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine) to produce a solvent-free SLM with giga-ohm (GΩ) sealed impedance. The presence and thickness of SLM on the nanopore chip were confirmed using atomic force spectroscopy. The functionality of SLM with and without ENaC was verified in terms of electrical impedance and capacitance by sweeping the frequency from 0.01 Hz to 100 kHz using electrochemical impedance spectroscopy. The nanopore chip exhibits long-term stability for the lipid bilayer before (144 h) and after (16 h) incorporation of ENaC. Amiloride, an inhibitor of ENaC, was utilized at different concentrations to test the integrity of fused ENaC in the lipid bilayer supported on a single nanopore chip. The developed model presents excellent electrical properties and improved mechanical stability of SLM, making this technology a reliable platform to study ion channel electrophysiology.
Collapse
Affiliation(s)
- Muhammad Shuja Khan
- Electrical and Computer Engineering Department, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
| | - Noura Sayed Dosoky
- Biotechnology Science and Engineering Program, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
| | - Ghulam Mustafa
- Department of Nuclear Medicine, The State University of New York at Buffalo , Buffalo, New York 14214, United States
| | - Darayas Patel
- Department of Mathematics and Computer Science, Oakwood University , Huntsville, Alabama 35896, United States
| | - Bakhrom Berdiev
- Department of Biomedical Sciences, Nazarbayev University School of Medicine , Astana 010000, Kazakhstan
| | - John Dalton Williams
- Electrical and Computer Engineering Department, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
| |
Collapse
|
17
|
Caraglio M, Orlandini E, Whittington SG. Driven Translocation of Linked Ring Polymers through a Pore. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b02023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Caraglio
- Dipartimento di Fisica e Astronomia, Sezione CNISM, and Università di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - E. Orlandini
- Dipartimento di Fisica e Astronomia, Sezione INFN, and Università di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - S. G. Whittington
- Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 3H6
| |
Collapse
|
18
|
Jing P, Burris B, Zhang R. Forces from the Portal Govern the Late-Stage DNA Transport in a Viral DNA Packaging Nanomotor. Biophys J 2017; 111:162-77. [PMID: 27410744 DOI: 10.1016/j.bpj.2016.05.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/08/2016] [Accepted: 05/10/2016] [Indexed: 01/09/2023] Open
Abstract
In the Phi29 bacteriophage, the DNA packaging nanomotor packs its double-stranded DNA genome into the virus capsid. At the late stage of DNA packaging, the negatively charged genome is increasingly compacted at a higher density in the capsid with a higher internal pressure. During the process, two Donnan effects, osmotic pressure and Donnan equilibrium potentials, are significantly amplified, which, in turn, affect the channel activity of the portal protein, GP10, embedded in the semipermeable capsid shell. In the research, planar lipid bilayer experiments were used to study the channel activities of the viral protein. The Donnan effect on the conformational changes of the viral protein was discovered, indicating GP10 may not be a static channel at the late stage of DNA packaging. Due to the conformational changes, GP10 may generate electrostatic forces that govern the DNA transport. For the section of the genome DNA that remains outside of the connector channel, a strong repulsive force from the viral protein would be generated against the DNA entry; however, for the section of the genome DNA within the channel, the portal protein would become a Brownian motor, which adopts the flash Brownian ratchet mechanism to pump the DNA against the increasingly built-up internal pressure (up to 20 atm) in the capsid. Therefore, the DNA transport in the nanoscale viral channel at the late stage of DNA packaging could be a consequence of Brownian movement of the genomic DNA, which would be rectified and harnessed by the forces from the interior wall of the viral channel under the influence of the Donnan effect.
Collapse
Affiliation(s)
- Peng Jing
- Department of Chemistry, College of Arts and Sciences, Indiana University-Purdue University Fort Wayne, Fort Wayne, Indiana.
| | - Benjamin Burris
- Department of Chemistry, College of Arts and Sciences, Indiana University-Purdue University Fort Wayne, Fort Wayne, Indiana
| | - Rong Zhang
- Division of Endocrinology, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
19
|
Wang S, Zhou Z, Zhao Z, Zhang H, Haque F, Guo P. Channel of viral DNA packaging motor for real time kinetic analysis of peptide oxidation states. Biomaterials 2017; 126:10-17. [PMID: 28237908 PMCID: PMC5421631 DOI: 10.1016/j.biomaterials.2017.01.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/22/2016] [Accepted: 01/27/2017] [Indexed: 10/20/2022]
Abstract
Nanopore technology has become a powerful tool in single molecule sensing, and protein nanopores appear to be more advantageous than synthetic counterparts with regards to channel amenability, structure homogeneity, and production reproducibility. However, the diameter of most of the well-studied protein nanopores is too small to allow the passage of protein or peptides that are typically in multiple nanometers scale. The portal channel from bacteriophage SPP1 has a large channel size that allows the translocation of peptides with higher ordered structures. Utilizing single channel conductance assay and optical single molecule imaging, we observed translocation of peptides and quantitatively analyzed the dynamics of peptide oligomeric states in real-time at single molecule level. The oxidative and the reduced states of peptides were clearly differentiated based on their characteristic electronic signatures. A similar Gibbs free energy (ΔG0) was obtained when different concentrations of substrates were applied, suggesting that the use of SPP1 nanopore for real-time quantification of peptide oligomeric states is feasible. With the intrinsic nature of size and conjugation amenability, the SPP1 nanopore has the potential for development into a tool for the quantification of peptide and protein structures in real time.
Collapse
Affiliation(s)
- Shaoying Wang
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA; College of Pharmacy, Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Zhi Zhou
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Zhengyi Zhao
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA; College of Pharmacy, Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Hui Zhang
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Farzin Haque
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Peixuan Guo
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA.
| |
Collapse
|
20
|
Affiliation(s)
- Wenqing Shi
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Alicia K. Friedman
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lane A. Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
21
|
Khisamutdinov EF, Jasinski DL, Li H, Zhang K, Chiu W, Guo P. Fabrication of RNA 3D Nanoprisms for Loading and Protection of Small RNAs and Model Drugs. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:10079-10087. [PMID: 27758001 PMCID: PMC5224701 DOI: 10.1002/adma.201603180] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/30/2016] [Indexed: 05/22/2023]
Abstract
Constructing containers with defined shape and size to load and protect therapeutics and subsequently control their release in the human body has long been a dream. The fabrication of 3D RNA prisms, characterized by atomic force microscopy, cryo-electron microscopy, dynamic light scattering, and polyacrylamide gel electrophoresis, is reported for the loading and protection of small molecules, proteins, small RNA molecules, and their controlled release.
Collapse
Affiliation(s)
- Emil F. Khisamutdinov
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | - Daniel L. Jasinski
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
- College of Pharmacy, Department of Physiology & Cell Biology, College of Medicine, and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Hui Li
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
- College of Pharmacy, Department of Physiology & Cell Biology, College of Medicine, and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Kaiming Zhang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
- College of Pharmacy, Department of Physiology & Cell Biology, College of Medicine, and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
22
|
Ji Z, Wang S, Zhao Z, Zhou Z, Haque F, Guo P. Fingerprinting of Peptides with a Large Channel of Bacteriophage Phi29 DNA Packaging Motor. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:4572-8. [PMID: 27435806 PMCID: PMC5166430 DOI: 10.1002/smll.201601157] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/16/2016] [Indexed: 05/27/2023]
Abstract
Nanopore technology has become a highly sensitive and powerful tool for single molecule sensing of chemicals and biopolymers. Protein pores have the advantages of size amenability, channel homogeneity, and fabrication reproducibility. But most well-studied protein pores for sensing are too small for passage of peptide analytes that are typically a few nanometers in dimension. The funnel-shaped channel of bacteriophage phi29 DNA packaging motor has previously been inserted into a lipid membrane to serve as a larger pore with a narrowest N-terminal constriction of 3.6 nm and a wider C-terminal end of 6 nm. Here, the utility of phi29 motor channel for fingerprinting of various peptides using single molecule electrophysiological assays is reported. The translocation of peptides is proved unequivocally by single molecule fluorescence imaging. Current blockage percentage and distinctive current signatures are used to distinguish peptides with high confidence. Each peptide generated one or two distinct current blockage peaks, serving as typical fingerprint for each peptide. The oligomeric states of peptides can also be studied in real time at single molecule level. The results demonstrate the potential for further development of phi29 motor channel for detection of disease-associated peptide biomarkers.
Collapse
|
23
|
Zhou Z, Ji Z, Wang S, Haque F, Guo P. Oriented single directional insertion of nanochannel of bacteriophage SPP1 DNA packaging motor into lipid bilayer via polar hydrophobicity. Biomaterials 2016; 105:222-227. [PMID: 27529454 DOI: 10.1016/j.biomaterials.2016.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 07/21/2016] [Accepted: 08/01/2016] [Indexed: 12/23/2022]
Abstract
Insertion of biological nanopore into artificial membrane is of fundamental importance in nanotechnology. Many applications require control and knowledge of channel orientation. In this work, the insertion orientation of the bacteriophage SPP1 and phi29 DNA packaging motors into lipid membranes was investigated. Single molecule electrophysiological assays and Ni-NTA-nanogold binding assays revealed that both SPP1 and phi29 motor channels exhibited a one-way traffic property for TAT peptide translocation from N- to C-termini of the protein channels. SPP1 motor channels preferentially inserts into liposomes with their C-terminal wider region facing inward. Changing the hydrophobicity of the N- or C-termini of phi29 connector alters the insertion orientation, suggesting that the hydrophobicity and hydrophilicity of the termini of the protein channel governs the orientation of the insertion into lipid membrane. It is proposed that the specificity in motor channel orientation is a result of the hydrophilic/hydrophobic interaction at the air/water interface when the protein channels are incorporating into liposome membranes.
Collapse
Affiliation(s)
- Zhi Zhou
- College of Pharmacy, College of Medicine/Dept. Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Zhouxiang Ji
- College of Pharmacy, College of Medicine/Dept. Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Shaoying Wang
- College of Pharmacy, College of Medicine/Dept. Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Farzin Haque
- College of Pharmacy, College of Medicine/Dept. Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- College of Pharmacy, College of Medicine/Dept. Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
24
|
Cao C, Ying YL, Hu ZL, Liao DF, Tian H, Long YT. Discrimination of oligonucleotides of different lengths with a wild-type aerolysin nanopore. NATURE NANOTECHNOLOGY 2016; 11:713-8. [PMID: 27111839 DOI: 10.1038/nnano.2016.66] [Citation(s) in RCA: 279] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 03/21/2016] [Indexed: 05/22/2023]
Abstract
Protein nanopores offer an inexpensive, label-free method of analysing single oligonucleotides. The sensitivity of the approach is largely determined by the characteristics of the pore-forming protein employed, and typically relies on nanopores that have been chemically modified or incorporate molecular motors. Effective, high-resolution discrimination of oligonucleotides using wild-type biological nanopores remains difficult to achieve. Here, we show that a wild-type aerolysin nanopore can resolve individual short oligonucleotides that are 2 to 10 bases long. The sensing capabilities are attributed to the geometry of aerolysin and the electrostatic interactions between the nanopore and the oligonucleotides. We also show that the wild-type aerolysin nanopores can distinguish individual oligonucleotides from mixtures and can monitor the stepwise cleavage of oligonucleotides by exonuclease I.
Collapse
Affiliation(s)
- Chan Cao
- Key Laboratory for Advanced Materials &Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials &Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Zheng-Li Hu
- Key Laboratory for Advanced Materials &Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Dong-Fang Liao
- Key Laboratory for Advanced Materials &Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - He Tian
- Key Laboratory for Advanced Materials &Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials &Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| |
Collapse
|
25
|
Lavezzo E, Barzon L, Toppo S, Palù G. Third generation sequencing technologies applied to diagnostic microbiology: benefits and challenges in applications and data analysis. Expert Rev Mol Diagn 2016; 16:1011-23. [PMID: 27453996 DOI: 10.1080/14737159.2016.1217158] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION The diagnosis of infectious diseases is among the most successful areas of application of new generation sequencing technologies. The field has seen the development of numerous experimental and analytical approaches for the detection and the fine description of pathogenic and non-pathogenic microorganisms. AREAS COVERED Without claiming to be exhaustive with respect to all applications and methods developed over the years, this review focuses on the advantages and the issues brought by the new technologies, with an eye in particular to third generation sequencing methods. Both experimental procedures and algorithmic strategies are presented, following the most relevant publications which have led to progress in our ability of detecting infectious agents. Expert commentary: The technical advance brought by third generation sequencing platforms has the potential to significantly expand the range of diagnostic tools that will be available to clinicians. Nonetheless, the implementation of these technologies in clinical practice is still far from being actionable and will temporally follow the path undertaken by second generation methods, which still require the setup of standardized pipelines in both wet and dry laboratory procedures.
Collapse
Affiliation(s)
- Enrico Lavezzo
- a Department of Molecular Medicine , University of Padova , Padova , Italy
| | - Luisa Barzon
- a Department of Molecular Medicine , University of Padova , Padova , Italy
| | - Stefano Toppo
- a Department of Molecular Medicine , University of Padova , Padova , Italy
| | - Giorgio Palù
- a Department of Molecular Medicine , University of Padova , Padova , Italy
| |
Collapse
|
26
|
Fabrication of Solid State Nanopore in Thin Silicon Membrane Using Low Cost Multistep Chemical Etching. MATERIALS 2015; 8:7389-7400. [PMID: 28793644 PMCID: PMC5458877 DOI: 10.3390/ma8115390] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/21/2015] [Accepted: 10/27/2015] [Indexed: 01/29/2023]
Abstract
Nanopore-based analysis is currently an area of great interest in many disciplines with the potential for exceptionally versatile applications in medicine. This work presents a novel step towards fabrication of a single solid-state nanopore (SSSN) in a thin silicon membrane. Silicon nanopores are realized using multistep processes on both sides of n-type silicon-on-insulator (SOI) <100> wafer with resistivity 1-4 Ω·cm. An electrochemical HF etch with low current density (0.47 mA/cm²) is employed to produce SSSN. Blue LED is considered to emit light in a narrow band region which facilitates the etching procedure in a unilateral direction. This helps in production of straight nanopores in n-type Si. Additionally, a variety of pore diameters are demonstrated using different HF concentrations. Atomic force microscopy is used to demonstrate the surface morphology of the fabricated pores in non-contact mode. Pore edges exhibit a pronounced rounded shape and can offer high stability to fluidic artificial lipid bilayer to study membrane proteins. Electrochemically-fabricated SSSN has excellent smoothness and potential applications in diagnostics and pharmaceutical research on transmembrane proteins and label free detection.
Collapse
|