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Kazemzadeh-Beneh H, Safarnejad MR, Norouzi P, Samsampour D, Alavi SM, Shaterreza D. Development of label-free electrochemical OMP-DNA probe biosensor as a highly sensitive system to detect of citrus huanglongbing. Sci Rep 2024; 14:12183. [PMID: 38806617 PMCID: PMC11133464 DOI: 10.1038/s41598-024-63112-w] [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] [Received: 02/01/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024] Open
Abstract
The fabrication of the first label-free electrochemical DNA probe biosensor for highly sensitive detection of Candidatus Liberibacter asiaticus (CLas), as the causal agent of citrus huanglongbing disease, is conducted here. An OMP probe was designed based on the hybridization with its target-specific sequence in the outer membrane protein (OMP) gene of CLas. The characterization of the steps of biosensor fabrication and hybridization process between the immobilized OMP-DNA probe and the target ssDNA oligonucleotides (OMP-complementary and three mismatches OMP or OMP-mutation) was monitored using cyclic voltammetry and electrochemical impedance spectroscopy based on increasing or decreasing in the electron transfer in [Fe (CN)6]3-/4- on the modified gold electrode surface. The biosensor sensitivity indicated that the peak currents were linear over ranges from 20 to 100 nM for OMP-complementary with the detection limit of 0.026 nM (S/N = 3). The absence of any cross-interference with other biological DNA sequences confirmed a high selectivity of fabricated biosensor. Likewise, it showed good specificity in discriminating the mutation oligonucleotides from complementary target DNAs. The functional performance of optimized biosensor was achieved via the hybridization of OMP-DNA probe with extracted DNA from citrus plant infected with CLas. Therefore, fabricated biosensor indicates promise for sensitivity and early detection of citrus huanglongbing disease.
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Affiliation(s)
- Hashem Kazemzadeh-Beneh
- Division of Biotechnology & Plant Molecular Genetic, Department of Horticulture Science, University of Hormozgan, Bandar Abbas, Iran
| | - Mohammad Reza Safarnejad
- Department of Plant Viruses, Agricultural Research Education and Extension Organization, Iranian Research Institute of Plant Protection, P.O. Box 1452-19395, Tehran, Iran.
| | - Parviz Norouzi
- Faculty of Chemistry, Center of Excellence in Electrochemistry, University of Tehran, Tehran, Iran
| | - Davood Samsampour
- Division of Biotechnology & Plant Molecular Genetic, Department of Horticulture Science, University of Hormozgan, Bandar Abbas, Iran
| | - Seyed Mehdi Alavi
- National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Davood Shaterreza
- Faculty of Chemistry, Center of Excellence in Electrochemistry, University of Tehran, Tehran, Iran
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2
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Tukur F, Bagra B, Jayapalan A, Liu M, Tukur P, Wei J. Plasmon-Exciton Coupling Effect in Nanostructured Arrays for Optical Signal Amplification and SARS-CoV-2 DNA Sensing. ACS APPLIED NANO MATERIALS 2023; 6:2071-2082. [PMID: 36789152 PMCID: PMC9888407 DOI: 10.1021/acsanm.2c05063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
A surface plasmon resonance (SPR)-enhanced optical signal using a nanoslit array and acridine orange (AO) dye system at a flexible poly(dimethylsiloxane) (PDMS) substrate was achieved in this work and demonstrated a simple sensing scheme to directly detect SARS-CoV-2 nucleic acid via DNA hybridization. A simple nanoimprinting pattern transfer technique was introduced to form uniform reproducible nanoslit arrays where the dimensions of the slit array were controlled by the thickness of the gold film. The plasmon-exciton coupling effect on the optical enhancement of different dye molecules, i.e., AO, propidium iodide (PI), or dihydroethidium (DHE) attached to the nanoslit surfaces, was examined thoroughly by measuring the surface reflection and fluorescence imaging. The results indicate that the best overlap of the plasmon resonance wavelength to the excitation spectrum of AO presented the largest optical enhancement (∼57×) compared to the signal at flat gold surfaces. Based on this finding, a sensitive assay for detecting DNA hybridization was generated using the interaction of the selected SARS-CoV-2 ssDNA and dsDNA with AO to trigger the metachromatic behavior of the dye at the nanoarray surfaces. We found strong optical signal amplification on the formation of acridine-ssDNA complexes and a quenched signal upon hybridization to the complementary target DNA (ct-DNA) along with a blue shift in the fluorescence of AO-dsDNAs. A quantitative evaluation of the ct-DNA concentration in a range of 100-0.08 nM using both the reflection and emission imaging signals demonstrated two linear regimes with a lowest detection limit of 0.21 nM. The sensing method showed high sensitivity and distinguished signals from 1-, 2-, and 3-base mismatched DNA targets, as well as high stability and reusability. This approach toward enhancing optical signal for DNA sensing offers promise in a general, rapid, and direct vision detection method for nucleic acid analytes.
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3
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Kawaka F. Characterization of symbiotic and nitrogen fixing bacteria. AMB Express 2022; 12:99. [PMID: 35907164 PMCID: PMC9339069 DOI: 10.1186/s13568-022-01441-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/22/2022] [Indexed: 11/10/2022] Open
Abstract
Symbiotic nitrogen fixing bacteria comprise of diverse species associated with the root nodules of leguminous plants. Using an appropriate taxonomic method to confirm the identity of superior and elite strains to fix nitrogen in legume crops can improve sustainable global food and nutrition security. The current review describes taxonomic methods preferred and commonly used to characterize symbiotic bacteria in the rhizosphere. Peer reviewed, published and unpublished articles on techniques used for detection, classification and identification of symbiotic bacteria were evaluated by exploring their advantages and limitations. The findings showed that phenotypic and cultural techniques are still affordable and remain the primary basis of species classification despite their challenges. Development of new, robust and informative taxonomic techniques has really improved characterization and identification of symbiotic bacteria and discovery of novel and new species that are effective in biological nitrogen fixation (BNF) in diverse conditions and environments.
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Affiliation(s)
- Fanuel Kawaka
- Department of Biological Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O. Box 210-40601, Bondo, Kenya.
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4
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Hertel S, Spinney RE, Xu SY, Ouldridge TE, Morris RG, Lee LK. The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure. Nucleic Acids Res 2022; 50:7829-7841. [PMID: 35880577 PMCID: PMC9371923 DOI: 10.1093/nar/gkac590] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/23/2022] [Accepted: 07/25/2022] [Indexed: 11/12/2022] Open
Abstract
The kinetics of DNA hybridization are fundamental to biological processes and DNA-based technologies. However, the precise physical mechanisms that determine why different DNA sequences hybridize at different rates are not well understood. Secondary structure is one predictable factor that influences hybridization rates but is not sufficient on its own to fully explain the observed sequence-dependent variance. In this context, we measured hybridization rates of 43 different DNA sequences that are not predicted to form secondary structure and present a parsimonious physically justified model to quantify our observations. Accounting only for the combinatorics of complementary nucleating interactions and their sequence-dependent stability, the model achieves good correlation with experiment with only two free parameters. Our results indicate that greater repetition of Watson-Crick pairs increases the number of initial states able to proceed to full hybridization, with the stability of those pairings dictating the likelihood of such progression, thus providing new insight into the physical factors underpinning DNA hybridization rates.
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Affiliation(s)
- Sophie Hertel
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Richard E Spinney
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia.,School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Stephanie Y Xu
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Thomas E Ouldridge
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Richard G Morris
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia.,School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, Australia
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5
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Wong KL, Liu J. Factors and methods to modulate DNA hybridization kinetics. Biotechnol J 2021; 16:e2000338. [PMID: 34411451 DOI: 10.1002/biot.202000338] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/09/2022]
Abstract
DNA oligonucleotides are widely used in a diverse range of research fields from analytical chemistry, molecular biology, nanotechnology to drug delivery. In these applications, DNA hybridization is often the most important enabling reaction. Achieving control over hybridization kinetics and a high yield of hybridized products is needed to ensure high-quality and reproducible results. Since DNA strands are highly negatively charged and can also fold upon itself to form various intramolecular structures, DNA hybridization needs to overcome these barriers. Nucleation and diffusion are two main kinetic limiting steps although their relative importance differs in different conditions. The effects of length and sequence, temperature, pH, salt concentration, cationic polymers, organic solvents, freezing and crowding agents are summarized in the context of overcoming these barriers. This article will help researchers in the biotechnology-related fields to better understand and control DNA hybridization, as well as provide a landscape for future work in simulation and experiment to optimize DNA hybridization systems.
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Affiliation(s)
- Kingsley L Wong
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, Canada
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6
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Kumar S, Dhami I, Thadke SA, Ly DH, Taylor RE. Rapid self-assembly of γPNA nanofibers at constant temperature. Biopolymers 2021; 112:e23463. [PMID: 34214178 DOI: 10.1002/bip.23463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 11/07/2022]
Abstract
Peptide nucleic acids (PNAs) have primarily been used to achieve therapeutic gene modulation through antisense strategies since their design in the 1990s. However, the application of PNAs as a functional nanomaterial has been more recent. We recently reported that γ-modified peptide nucleic acids (γPNAs) could be used to enable formation of complex, self-assembling nanofibers in select polar aprotic organic solvent mixtures. Here we demonstrate that distinct γPNA strands, each with a high density of γ-modifications can form complex nanostructures at constant temperatures within 30 minutes. Additionally, we demonstrate DNA-assisted isothermal growth of γPNA nanofibers, thereby overcoming a key hurdle for future scale-up of applications related to nanofiber growth and micropatterning.
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Affiliation(s)
- Sriram Kumar
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Isha Dhami
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Shivaji A Thadke
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Danith H Ly
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Rebecca E Taylor
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.,Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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7
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Lin P, Dinh H, Nakata E, Morii T. Dynamic Shape Transformation of a DNA Scaffold Applied for an Enzyme Nanocarrier. Front Chem 2021; 9:697857. [PMID: 34249866 PMCID: PMC8263910 DOI: 10.3389/fchem.2021.697857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
Structural programmability and accurate addressability of DNA nanostructures are ideal characteristics for the platform of arranging enzymes with the nanoscale precision. In this study, a three-dimensional DNA scaffold was designed to enable a dynamic shape transition from an open plate-like structure to its closed state of a hexagonal prism structure. The two domains in the open state were folded together to transform into the closed state by hybridization of complementary short DNA closing keys at both of the facing edges in over 90% yield. The shape transformation of the DNA scaffold was extensively studied by means of the fluorescence energy transfer measurement, atomic force microscope images, and agarose gel electrophoretic analyses. A dimeric enzyme xylitol dehydrogenase was assembled on the DNA scaffold in its open state in a high-loading yield. The enzyme loaded on the scaffold was subsequently transformed to its closed state by the addition of short DNA closing keys. The enzyme encapsulated in the closed state displayed comparable activity to that in the open state, ensuring that the catalytic activity of the enzyme was well maintained in the DNA nanocarrier. The nanocarrier with efficient encapsulation ability is potentially applicable for drug delivery, biosensing, biocatalytic, and diagnostic tools.
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Affiliation(s)
- Peng Lin
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
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8
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Exploring the most stable aptamer/target molecule complex by the stochastic tunnelling-basin hopping-discrete molecular dynamics method. Sci Rep 2021; 11:11406. [PMID: 34075115 PMCID: PMC8169667 DOI: 10.1038/s41598-021-90907-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 05/07/2021] [Indexed: 11/29/2022] Open
Abstract
The stochastic tunnelling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method was applied to the search for the most stable biomolecular complexes in water by using the MARTINI coarse-grained (CG) model. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as an EpCAM adaptor for an EpA (AptEpA) benchmark target molecule. The effects of two adsorption positions on the EpCAM were analysed, and it is found that the AptEpA adsorption configuration located within the EpCAM pocket-like structure is more stable and the energy barrier is lower due to the interaction with water. By the root mean square deviation (RMSD), the configuration of EpCAM in water is more conservative when the AptEpA binds to EpCAM by attaching to the pocket space of the EpCAM dimer. For AptEpA, the root mean square fluctuation (RMSF) analysis result indicates Nucleobase 1 and Nucleobase 2 display higher flexibility during the CGMD simulation. Finally, from the binding energy contour maps and histogram plots of EpCAM and each AptEpA nucleobase, it is clear that the binding energy adsorbed to the pocket-like structure is more continuous than that energy not adsorbed to the pocket-like structure. This study has proposed a new numerical process for applying the STUN-BH-DMD with the CG model, which can reduce computational details and directly find a more stable AptEpA/EpCAM complex in water.
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9
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Dijkstra M, Luijten E. From predictive modelling to machine learning and reverse engineering of colloidal self-assembly. NATURE MATERIALS 2021; 20:762-773. [PMID: 34045705 DOI: 10.1038/s41563-021-01014-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
An overwhelming diversity of colloidal building blocks with distinct sizes, materials and tunable interaction potentials are now available for colloidal self-assembly. The application space for materials composed of these building blocks is vast. To make progress in the rational design of new self-assembled materials, it is desirable to guide the experimental synthesis efforts by computational modelling. Here, we discuss computer simulation methods and strategies used for the design of soft materials created through bottom-up self-assembly of colloids and nanoparticles. We describe simulation techniques for investigating the self-assembly behaviour of colloidal suspensions, including crystal structure prediction methods, phase diagram calculations and enhanced sampling techniques, as well as their limitations. We also discuss the recent surge of interest in machine learning and reverse-engineering methods. Although their implementation in the colloidal realm is still in its infancy, we anticipate that these data-science tools offer new paradigms in understanding, predicting and (inverse) design of novel colloidal materials.
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Affiliation(s)
- Marjolein Dijkstra
- Soft Condensed Matter, Debye Institute for Nanomaterial Science, Department of Physics, Utrecht University, Utrecht, The Netherlands.
| | - Erik Luijten
- Departments of Materials Science and Engineering, Engineering Sciences & Applied Mathematics, Chemistry and Physics & Astronomy, Northwestern University, Evanston, IL, USA.
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10
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Wang GA, Xie X, Mansour H, Chen F, Matamoros G, Sanchez AL, Fan C, Li F. Expanding detection windows for discriminating single nucleotide variants using rationally designed DNA equalizer probes. Nat Commun 2020; 11:5473. [PMID: 33122648 PMCID: PMC7596233 DOI: 10.1038/s41467-020-19269-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
Combining experimental and simulation strategies to facilitate the design and operation of nucleic acid hybridization probes are highly important to both fundamental DNA nanotechnology and diverse biological/biomedical applications. Herein, we introduce a DNA equalizer gate (DEG) approach, a class of simulation-guided nucleic acid hybridization probes that drastically expand detection windows for discriminating single nucleotide variants in double-stranded DNA (dsDNA) via the user-definable transformation of the quantitative relationship between the detection signal and target concentrations. A thermodynamic-driven theoretical model was also developed, which quantitatively simulates and predicts the performance of DEG. The effectiveness of DEG for expanding detection windows and improving sequence selectivity was demonstrated both in silico and experimentally. As DEG acts directly on dsDNA, it is readily adaptable to nucleic acid amplification techniques, such as polymerase chain reaction (PCR). The practical usefulness of DEG was demonstrated through the simultaneous detection of infections and the screening of drug-resistance in clinical parasitic worm samples collected from rural areas of Honduras.
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Affiliation(s)
- Guan A Wang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 610064, Chengdu, Sichuan, China
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Xiaoyu Xie
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Hayam Mansour
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada
- Department of Cell Biology, National Research Centre, Cairo, 12622, Egypt
| | - Fangfang Chen
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 610064, Chengdu, Sichuan, China
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Gabriela Matamoros
- Department of Health Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
- Microbiology Research Institute, National Autonomous University of Honduras (UNAH), Tegucigalpa, Honduras
| | - Ana L Sanchez
- Department of Health Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
- Microbiology Research Institute, National Autonomous University of Honduras (UNAH), Tegucigalpa, Honduras
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 201240, Shanghai, China
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 610064, Chengdu, Sichuan, China.
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada.
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11
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Li M, Liu M, Ma C, Shi C. Rapid DNA detection and one-step RNA detection catalyzed by Bst DNA polymerase and narrow-thermal-cycling. Analyst 2020; 145:5118-5122. [PMID: 32648859 DOI: 10.1039/d0an00975j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We reported a novel detection method named accelerated strand exchange amplification by employing Bst DNA polymerase and narrow-thermal-cycling for the first time, achieving direct detection of 120 copies of DNA within 15 min and 1.2 × 105 copies of RNA within 20 min and sparking the revolution of the use of routine isothermal polymerases for diverse applications.
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Affiliation(s)
- Mengzhe Li
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, and Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, PR China.
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12
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Kim YJ, Hosokawa K, Maeda M. Sensitivity Enhancement of MicroRNA Detection Using a Power-free Microfluidic Chip. ANAL SCI 2019; 35:1227-1236. [PMID: 31327815 DOI: 10.2116/analsci.19p211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We present a microRNA (miRNA) detection method that achieves enhanced sensitivity by means of a power-free microfluidic chip without the requirement of an external power source. The miRNA detection is completed by sandwich hybridization between probe DNAs and target miRNA with small sample volume (0.5 μL) within 20 min. Fluorescence signals after hybridization were amplified by laminar flow-assisted dendritic amplification (LFDA) using fluorescein isothiocyanate (FITC)-labeled streptavidin (F-SA) and biotinylated anti-streptavidin (B-anti-SA) as amplification reagents. To enhance the sensitivity of on-chip miRNA detection, the hybridization buffer solution was newly optimized with three main components-sodium dodecyl sulfate (SDS), formamide and dextran sulfate-that are known to strongly influence hybridization. An on-chip miRNA detection test in the newly optimized hybridization buffer (0.2% SDS, 5% formamide and 1% dextran sulfate) revealed dramatic increases in both the LFDA signal in the sample channel and the signal-to-background ratio (S/B ratio). Moreover, the LFDA signals in a blank reference channel remained low due to the suppression of non-specific bindings and hybridizations. By changing the hybridization buffer, we obtained an improved limit of detection (LOD) that was 0.045 pM (miRNA-196a) and 0.45 pM (miRNA-331), which are around 30- and 10-fold better than that of when control hybridization buffer was used. The improved performance of our miRNA detection system with short running time and high sensitivity could contribute to future research, including point-of-care diagnostic systems.
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Affiliation(s)
- Young-Jin Kim
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, RIKEN
| | - Kazuo Hosokawa
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, RIKEN
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, RIKEN
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13
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Xiao S, Sharpe DJ, Chakraborty D, Wales DJ. Energy Landscapes and Hybridization Pathways for DNA Hexamer Duplexes. J Phys Chem Lett 2019; 10:6771-6779. [PMID: 31609632 DOI: 10.1021/acs.jpclett.9b02356] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Strand hybridization is not only a fundamental molecular mechanism underlying the biological functions of nucleic acids but is also a key step in the design of efficient nanodevices. Despite recent efforts, the microscopic rules governing the hybridization mechanisms remain largely unknown. In this study, we exploit the energy landscape framework to assess how sequence-specificity modulates the hybridization mechanisms in DNA. We find that GG-tracts hybridize much more rapidly compared to GC-tracts, via either zippering or slithering pathways. For the hybridization of GG-tracts, both zippering and slithering mechanisms appear to be kinetically relevant. In contrast, for the GC-tracts, the zippering mechanism is dominant. Our work reveals that even for the relatively small systems considered, the energy landscapes feature multiple metastable states and kinetic traps, which is at odds with the conventional "all-or-nothing" model of DNA hybridization formulated on the basis of thermodynamic arguments alone. Interestingly, entropic effects are found to play an important role in determining the thermal stability of competing conformational ensembles and in determining the preferred hybridization pathways.
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Affiliation(s)
- Shiyan Xiao
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
| | - Daniel J Sharpe
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
| | - Debayan Chakraborty
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - David J Wales
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
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14
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Bolotsky A, Butler D, Dong C, Gerace K, Glavin NR, Muratore C, Robinson JA, Ebrahimi A. Two-Dimensional Materials in Biosensing and Healthcare: From In Vitro Diagnostics to Optogenetics and Beyond. ACS NANO 2019; 13:9781-9810. [PMID: 31430131 DOI: 10.1021/acsnano.9b03632] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Since the isolation of graphene in 2004, there has been an exponentially growing number of reports on layered two-dimensional (2D) materials for applications ranging from protective coatings to biochemical sensing. Due to the exceptional, and often tunable, electrical, optical, electrochemical, and physical properties of these materials, they can serve as the active sensing element or a supporting substrate for diverse healthcare applications. In this review, we provide a survey of the recent reports on the applications of 2D materials in biosensing and other emerging healthcare areas, ranging from wearable technologies to optogenetics to neural interfacing. Specifically, this review provides (i) a holistic evaluation of relevant material properties across a wide range of 2D systems, (ii) a comparison of 2D material-based biosensors to the state-of-the-art, (iii) relevant material synthesis approaches specifically reported for healthcare applications, and (iv) the technological considerations to facilitate mass production and commercialization.
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Affiliation(s)
| | | | - Chengye Dong
- State Key Lab of Electrical Insulation and Power Equipment , Xi'an Jiaotong University , Xi'an , Shaanxi 710049 , People's Republic of China
| | | | - Nicholas R Glavin
- Materials and Manufacturing Directorate , Air Force Research Laboratory , WPAFB , Ohio 45433 , United States
| | - Christopher Muratore
- Department of Chemical and Materials Engineering , University of Dayton , Dayton , Ohio 45469 , United States
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15
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Cordeiro M, Otrelo-Cardoso AR, Svergun DI, Konarev PV, Lima JC, Santos-Silva T, Baptista PV. Optical and Structural Characterization of a Chronic Myeloid Leukemia DNA Biosensor. ACS Chem Biol 2018; 13:1235-1242. [PMID: 29562136 DOI: 10.1021/acschembio.8b00029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selective base pairing is the foundation of DNA recognition. Here, we elucidate the molecular and structural details of a FRET-based two-component molecular beacon relying on steady-state fluorescence spectroscopy, small-angle X-ray scattering (SAXS), microscale thermophoresis (MST), and differential electrophoretic mobility. This molecular beacon was designed to detect the most common fusion sequences causing chronic myeloid leukemia, e14a2 and e13a2. The emission spectra indicate that the self-assembly of the different components of the biosensor occurs sequentially, triggered by the fully complementary target. We further assessed the structural alterations leading to the specific fluorescence FRET signature by SAXS, MST, and the differential electrophoretic mobility, where the size range observed is consistent with hybridization and formation of a 1:1:1 complex for the probe in the presence of the complementary target and revelator. These results highlight the importance of different techniques to explore conformational DNA changes in solution and its potential to design and characterize molecular biosensors for genetic disease diagnosis.
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Affiliation(s)
- Mílton Cordeiro
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
- LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Ana Rita Otrelo-Cardoso
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Hamburg, Germany, 22067
| | - Petr V. Konarev
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, c/o DESY, Hamburg, Germany, 22067
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, Leninsky prospect 59, 119333 Moscow, Russia
- National Research Centre “Kurchatov Institute”, pl. Kurchatova 1, 123182 Moscow, Russia
| | - João Carlos Lima
- LAQV, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Teresa Santos-Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
| | - Pedro Viana Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, 2829-516 Caparica, Portugal
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