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Wu S, Fu T, Qiu R, Xu L. DNA fragmentation in complicated flow fields created by micro-funnel shapes. SOFT MATTER 2021; 17:9047-9056. [PMID: 34570150 DOI: 10.1039/d1sm00984b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Micro-funnels have been widely applied to produce extensionally dominant flows for DNA manipulation, such as DNA extension for DNA mapping and DNA fragmentation for gene sequencing. However, it still lacks a systematic understanding of DNA fragmentation behaviors in complicated flow fields regulated by different funnel shapes with high flow rates. This limits the rational design and application scope of related microfluidic devices. In this study, fragmentation experiments of λ DNA were carried out in microfluidic chips with four different micro-funnel shapes, namely a sudden finish, a linear contraction, a constant acceleration, and an increasing extension rate funnel. The experimental results demonstrated a significant effect of the micro-funnel shape on the produced DNA fragment size. Then, the dynamical behaviors of DNA molecules in flow fields created by different micro-funnels were simulated using a numerical method of Brownian dynamics-computational fluid dynamics. The numerical simulation revealed that both the magnitude and distribution of the extension rate of flow fields were drastically altered by the funnel shape, and the extension rate at the micro-scale was the dominant factor of DNA fragmentation. The different DNA fragmentation behaviors in four micro-funnels were investigated from the perspectives including the fragment size distribution, fragmentation location, percentage of broken molecules, conformational type and stretched length of DNA before fragmentation. The results elucidated the significant impact of funnel shape on the dynamical behaviors of DNA fragmentation. This study offers insights into the rational design of microfluidic chips for DNA manipulation.
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Affiliation(s)
- Shuyi Wu
- College of Transportation and Civil Engineering, Fujian Agriculture and Forestry University, Fuzhou, 350108, China
| | - Tengfei Fu
- College of Transportation and Civil Engineering, Fujian Agriculture and Forestry University, Fuzhou, 350108, China
| | - Renhui Qiu
- College of Transportation and Civil Engineering, Fujian Agriculture and Forestry University, Fuzhou, 350108, China
| | - Luping Xu
- Center for Nano and Micro Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, 100084, China.
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Ni Y, Zhao Y, Chen Q, Yamaguchi Y, Dou X. Study of the peak broadening due to detection in the electrophoretic separation of DNA by CE and microchip CE and the application of image sensor for ultra-small detection cell length. J Sep Sci 2019; 42:2280-2288. [PMID: 31038284 DOI: 10.1002/jssc.201900051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/20/2019] [Accepted: 04/24/2019] [Indexed: 11/12/2022]
Abstract
Narrow peaks are important to high-resolution and high-speed separation of DNA fragments by capillary electrophoresis and microchip capillary electrophoresis. Detection cell length is one of the broadening factors, which is often ignored in experiments. However, is it always safe to neglect detection cell length under any condition? To answer this question, we investigated the influence of detection cell length by simulation and experiments. A parameter named as detection cell length ratio was proposed to directly compare the detection cell length and the spatial length of sample band. Electrophoretic peaks generated by various detection cell length ratios were analyzed. A simple rule to evaluate the peak broadening due to detection cell length was obtained. The current states of the detection cell length of detection system and their reliabilities in capillary electrophoresis and microchip capillary electrophoresis were analyzed. Microchip capillary electrophoresis detection with an ultra-small detection cell length of 0.36 μm was easily achieved by using an image sensor.
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Affiliation(s)
- Yi Ni
- Institute of Photonics and Bio-medicine, Graduate School of Science, East China University of Science and Technology, Shanghai, P. R. China
| | - Yubin Zhao
- Institute of Photonics and Bio-medicine, Graduate School of Science, East China University of Science and Technology, Shanghai, P. R. China
| | - Qinmiao Chen
- Institute of Photonics and Bio-medicine, Graduate School of Science, East China University of Science and Technology, Shanghai, P. R. China
| | - Yoshinori Yamaguchi
- Institute of Photonics and Bio-medicine, Graduate School of Science, East China University of Science and Technology, Shanghai, P. R. China.,Department of Applied Physics, Graduate School of Engineering, Osaka University, Yamadaoka, Suita-city, Osaka, Japan
| | - Xiaoming Dou
- Institute of Photonics and Bio-medicine, Graduate School of Science, East China University of Science and Technology, Shanghai, P. R. China.,Department of Applied Physics, Graduate School of Engineering, Osaka University, Yamadaoka, Suita-city, Osaka, Japan.,School of Optoelectronic Engineering, ChangZhou Institute of Technology, Changzhou, Jiangsu, P. R. China
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Wu S, Li C, Zheng Q, Xu L. Modelling DNA extension and fragmentation in contractive microfluidic devices: a Brownian dynamics and computational fluid dynamics approach. SOFT MATTER 2018; 14:8780-8791. [PMID: 30338769 DOI: 10.1039/c8sm00863a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fragmenting DNA into short pieces is an essential manipulation in many biological studies, ranging from genome sequencing to molecular diagnosis. Among various DNA fragmentation methods, microfluidic hydrodynamic DNA fragmentation has huge advantages especially in terms of handling small-volume samples and being integrated into automatic and all-in-one DNA analysis equipment. Despite the fast progress in experimental studies and applications, a systematic understanding of how DNA molecules are distributed, stretched and fragmented in a confined microfluidic field is still lacking. In this work, we investigate the extension and fragmentation of DNA in a typical contractive microfluidic field, which consists of a shear flow-dominated area and an elongational flow-dominated area, using the Brownian dynamics-computational fluid dynamics method. Our results show that the shear flow at the straight part of the microfluidic channel and the elongational flow at the contractive bottleneck together determine the performance of DNA fragmentation. The average fragment size of DNA decreases with the increase of the strain rate of the elongational flow, and the upstream shear flow can significantly precondition the conformation of DNA to produce shorter and more uniform fragments. A systematic study of the dynamics of DNA fragmentation shows that DNA tends to break at the mid-point when the strain rate of elongational flow is small, and the breakage point largely deviates from the midpoint as the strain rate increases. Our simulation of the thorough DNA fragmentation process in a realistic microfluidic field agrees well with experimental results. We expect that our study can shed new light on the development of future microfluidic devices for DNA fragmentation and integrated DNA analysis devices.
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Affiliation(s)
- Shuyi Wu
- Center for Nano and Micro Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, China.
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Oliver-Calixte NJ, Uba FI, Battle KN, Weerakoon-Ratnayake KM, Soper SA. Immobilization of lambda exonuclease onto polymer micropillar arrays for the solid-phase digestion of dsDNAs. Anal Chem 2014; 86:4447-54. [PMID: 24628008 PMCID: PMC4018173 DOI: 10.1021/ac5002965] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
The
process of immobilizing enzymes onto solid supports for bioreactions
has some compelling advantages compared to their solution-based counterpart
including the facile separation of enzyme from products, elimination
of enzyme autodigestion, and increased enzyme stability and activity.
We report the immobilization of λ-exonuclease onto poly(methylmethacrylate)
(PMMA) micropillars populated within a microfluidic device for the
on-chip digestion of double-stranded DNA. Enzyme immobilization was
successfully accomplished using 3-(3-dimethylaminopropyl) carbodiimide/N-hydroxysuccinimide (EDC/NHS) coupling to carboxylic acid
functionalized PMMA micropillars. Our results suggest that the efficiency
for the catalysis of dsDNA digestion using λ-exonuclease, including
its processivity and reaction rate, were higher when the enzyme was
attached to a solid support compared to the free solution digestion.
We obtained a clipping rate of 1.0 × 103 nucleotides
s–1 for the digestion of λ-DNA (48.5 kbp)
by λ-exonuclease. The kinetic behavior of the solid-phase reactor
could be described by a fractal Michaelis–Menten model with
a catalytic efficiency nearly 17% better than the homogeneous solution-phase
reaction. The results from this work will have important ramifications
in new single-molecule DNA sequencing strategies that employ free
mononucleotide identification.
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Affiliation(s)
- Nyoté J Oliver-Calixte
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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Arora A, Simone G, Salieb-Beugelaar GB, Kim JT, Manz A. Latest Developments in Micro Total Analysis Systems. Anal Chem 2010; 82:4830-47. [PMID: 20462185 DOI: 10.1021/ac100969k] [Citation(s) in RCA: 372] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Arun Arora
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
| | - Giuseppina Simone
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
| | - Georgette B. Salieb-Beugelaar
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
| | - Jung Tae Kim
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
| | - Andreas Manz
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
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Fan Y, Scriba GKE. Advances in capillary electrophoretic enzyme assays. J Pharm Biomed Anal 2010; 53:1076-90. [PMID: 20439145 DOI: 10.1016/j.jpba.2010.04.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 03/26/2010] [Accepted: 04/05/2010] [Indexed: 01/25/2023]
Abstract
In recent years, capillary electrophoresis (CE) has become a frequently used tool for enzyme assays due to its well-recognized advantages such as high separation efficiency, short analysis time, small sample and chemicals consumption. The published applications cover all aspects of enzyme characterization and analysis including the determination of the enzyme activity, substrate and modulator characterization and identification, as well as the investigation of enzyme-mediated metabolic pathways of bioactive molecules. The CE assays may be classified into two general categories: (1) pre-capillary assays where the reactions are performed offline followed by CE analysis of the substrates and products and (2) online assays when the enzyme reaction and separation of the analytes are performed in the same capillary. In online assays, the enzyme may be either immobilized or in solution. The latter is also referred to as electrophoretically mediated microanalysis (EMMA). The present review will highlight the literature of CE-based enzyme assays from 2006 to November 2009. One section will be devoted to applications of microfluidic devices.
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Affiliation(s)
- Yi Fan
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Jena, Philosophenweg 14, D-07743 Jena, Germany
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7
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Zhang Y, Yu H, Qin J, Lin B. A microfluidic DNA computing processor for gene expression analysis and gene drug synthesis. BIOMICROFLUIDICS 2009; 3:44105. [PMID: 20216967 PMCID: PMC2835285 DOI: 10.1063/1.3259628] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 10/17/2009] [Indexed: 05/08/2023]
Abstract
Boolean logic performs a logical operation on one or more logic input and produces a single logic output. Here, we describe a microfluidic DNA computing processor performing Boolean logic operations for gene expression analysis and gene drug synthesis. Multiple cancer-related genes were used as input molecules. Their expression levels were identified by interacting with the computing related DNA strands, which were designed according to the sequences of cancer-related genes and the suicide gene. When all the expressions of the cancer-related genes fit in with the diagnostic criteria, positive diagnosis would be confirmed and then a complete suicide gene (gene drug) could be synthesized as an output molecule. Microfluidic chip was employed as an effective platform to realize the computing process by integrating multistep biochemical reactions involving hybridization, displacement, denaturalization, and ligation. By combining the specific design of the computing related molecules and the integrated functions of the microfluidics, the microfluidic DNA computing processor is able to analyze the multiple gene expressions simultaneously and realize the corresponding gene drug synthesis with simplicity and fast speed, which demonstrates the potential of this platform for DNA computing in biomedical applications.
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Xie H, Li B, Qin J, Huang Z, Zhu Y, Lin B. A splicing model-based DNA-computing approach on microfluidic chip. Electrophoresis 2009; 30:3514-8. [DOI: 10.1002/elps.200900323] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Zhang M, Gong X, Wen W. Manipulation of microfluidic droplets by electrorheological fluid. Electrophoresis 2009; 30:3116-23. [DOI: 10.1002/elps.200900119] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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10
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Akamine R, Yatsushiro S, Yamamura S, Kido JI, Shinohara Y, Baba Y, Kataoka M. Direct endonuclease digestion and multi-analysis of restriction fragment length polymorphisms by microchip electrophoresis. J Pharm Biomed Anal 2009; 50:947-53. [PMID: 19616912 DOI: 10.1016/j.jpba.2009.06.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 06/15/2009] [Accepted: 06/17/2009] [Indexed: 11/15/2022]
Abstract
A high-performance multi-analysis system for genotypic mutation by means of restriction fragment length polymorphisms (RFLP) involving endonuclease treatment of PCR-amplified DNA on a microchip and subsequent analysis by microchip electrophoresis for DNA sizing was developed. A Hitachi SV1210 system, with which 12 samples can be analyzed on a plastic chip with good accuracy as to DNA sizing between 25 and 300 bp, was employed for RFLP analysis. We performed RFLP analysis of the ABO genotypes of blood donors for whom the ABO type was known. Six blood samples were analyzed by PCR to amplify two different regions of the genomic DNA, each of the amplified DNAs containing a different nucleotide polymorphism. To analyze the genes at polymorphic sites 261 and 526, restriction endonucleases Kpn I and Ban I were employed, respectively. When an amplified DNA was digested with each endonuclease on a microchip for 20 min, sequential analysis revealed the presence or absence of the respective restriction site. This analysis was performed within 7 min using a 1/10 volume of a DNA sample in comparison with the conventional method, and the estimated DNA size differed from the predicted size by less than 10 bp. The results indicate the potential of microchip electrophoresis for RFLP with on-chip direct endonuclease digestion and sequential analysis, offering high resolution in a short time.
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Affiliation(s)
- Rie Akamine
- Health Technology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Hayashi-cho 2217-14, Takamatsu 761-0395, Japan
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