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Zhang G, Wang Y, Zhou W, Lei Y, Lu J, Yin W, Zhu Z, Yang C, Zhang P. A Magnetically Driven Tandem Chip Enables Rapid Isolation and Multiplexed Profiling of Extracellular Vesicles. Angew Chem Int Ed Engl 2023; 62:e202315113. [PMID: 37937998 DOI: 10.1002/anie.202315113] [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: 10/08/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/09/2023]
Abstract
The protein phenotypes of extracellular vesicles (EVs) have emerged as promising biomarkers for cancer diagnosis and treatment monitoring. However, the technical challenges in rapid isolation and multiplexed molecular detection of EVs have limited their clinical practice. Herein, we developed a magnetically driven tandem chip to achieve streamlined rapid isolation and multiplexed profiling of surface protein biomarkers of EVs. Driven by magnetic force, the magnetic nanomixers not only act as tiny stir bars to promote mass transfer and enhance reaction efficiency of EVs, but also transport on communicating vessels of the tandem chip continuously and expedite the assay workflow. We designed cyclic surface enhancement of Raman scattering (SERS) tags to bind with target EVs and then release them by exonuclease I, eliminating steric hindrance and amplifying the SERS signal of multiple protein biomarkers on EVs. Due to the excellent assay performance, six breast cancer biomarkers were detected simultaneously on EVs using only 10 μL plasma within 1.5 h. The unweighted SUM signature offers great accuracy in discriminating breast cancer patients from healthy donors. Overall, the dynamic magnetic driving tandem chip offers a new avenue to advance the clinical application of EV-based liquid biopsy.
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Affiliation(s)
- Guihua Zhang
- Institute of Molecular Medicine, Department of Breast Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yaohui Wang
- Institute of Molecular Medicine, Department of Breast Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Weihang Zhou
- Institute of Molecular Medicine, Department of Breast Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yanmei Lei
- Institute of Molecular Medicine, Department of Breast Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Jinsong Lu
- Institute of Molecular Medicine, Department of Breast Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Wenjin Yin
- Institute of Molecular Medicine, Department of Breast Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Zhi Zhu
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Department of Breast Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
- MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Peng Zhang
- Institute of Molecular Medicine, Department of Breast Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
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2
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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: 5] [Impact Index Per Article: 1.7] [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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3
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Xiong Q, Lim AE, Lim Y, Lam YC, Duan H. Dynamic Magnetic Nanomixers for Improved Microarray Assays by Eliminating Diffusion Limitation. Adv Healthc Mater 2019; 8:e1801022. [PMID: 30511823 DOI: 10.1002/adhm.201801022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 10/21/2018] [Indexed: 12/12/2022]
Abstract
Microarrays are widely used in high-throughput analysis of DNA, protein, and small molecules. However, the majority of microarray assays need improved assay speed and sensitivity due to the slow molecular diffusion from bulk solutions to probe surfaces. Here, a new class of magnetic nanomixers in DNA and protein microarray assays is reported to eliminate the diffusion constraint through dynamic mixing. It is demonstrated that the dynamic nanomixers can improve the assay kinetics at least by a factor of 4 and 2 for DNA and protein microarray assays, respectively. By using the dynamic nanomixers, the sensitivities of detecting Escherichia coli O157:H7 DNA and prostate specific antigen increase by more than four-fold. The dynamic mixing also greatly reduces the spot-to-spot variation to below 10% across a broad concentration range, providing more accurate assay results. In comparison with existing methods, this magnetic nanomixer-based approach offers rapid turnaround, improved sensitivity, good accuracy, low cost, simple operation, and excellent compatibility with commercial microarrays.
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Affiliation(s)
- Qirong Xiong
- School of Chemical and Biomedical EngineeringNanyang Technological University 70 Nanyang Drive Singapore 637457 Singapore
| | - An Eng Lim
- School of Mechanical and Aerospace EngineeringNanyang Technological University 50 Nanyang Avenue Singapore 639798 Singapore
| | - Yun Lim
- School of Chemical and Biomedical EngineeringNanyang Technological University 70 Nanyang Drive Singapore 637457 Singapore
| | - Yee Cheong Lam
- School of Mechanical and Aerospace EngineeringNanyang Technological University 50 Nanyang Avenue Singapore 639798 Singapore
| | - Hongwei Duan
- School of Chemical and Biomedical EngineeringNanyang Technological University 70 Nanyang Drive Singapore 637457 Singapore
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4
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He W, Xu D, Wang Z, Wu H, Xiang X, Tang B, Jiang W, Cui Y, Wang H, Jiang N, Sun Y, Chen Y, Li S, Hou M, Zhang Y, Wang L, Ke ZF. Three-dimensional nanostructured substrates enable dynamic detection of ALK-rearrangement in circulating tumor cells from treatment-naive patients with stage III/IV lung adenocarcinoma. J Transl Med 2019; 17:32. [PMID: 30658713 PMCID: PMC6339314 DOI: 10.1186/s12967-019-1779-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 01/11/2019] [Indexed: 12/25/2022] Open
Abstract
Background Circulating tumor cells (CTC) shows great prospect to realize precision medicine in cancer patients. Methods We developed the NanoVelcro Chip integrating three functional mechanisms. NanoVelcro CTC capture efficiency was tested in stage III or IV lung adenocarcinoma. Further, ALK-rearrangement status was examined through fluorescent in situ hybridization in CTCs enriched by NanoVelcro. Results NanoVelcro system showed higher CTC-capture efficiency than CellSearch in stage III or IV lung adenocarcinoma. CTC counts obtained by both methods were positively correlated (r = 0.45, p < 0.05). Further, Correlation between CTC counts and pTNM stage determined by NanoVelcro was more significant than that determined by CellSearch (p < 0.001 VS p = 0.029). All ALK-positive patients had 3 or more ALK-rearranged CTC per ml of blood. Less than 3 ALK-rearranged CTC was detected in ALK-negative patients. NanoVelcro can detect the ALK–rearranged status with consistent sensitivity and specificity compared to biopsy test. Furthermore, the ALK-rearranged CTC ratio correlated to the pTNM stage in ALK-positive patients. Following up showed that CTCs counting by NanoVelcro was more stable and reliable in evaluating the efficacy of Clozotinib both in the short and long run compared with CellSearch. Changing of NanoVlecro CTC counts could accurately reflect disease progression. Conclusion NanoVelcro provides a sensitive method for CTC counts and characterization in advanced NSCLC. ALK-rearrangement can be detected in CTCs collected from advanced NSCLC patients by NanoVelcro, facilitating diagnostic test and prognosis analysis, most importantly offering one noninvasive method for real-time monitoring of treatment reaction. Electronic supplementary material The online version of this article (10.1186/s12967-019-1779-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weiling He
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China.,Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Di Xu
- Department of Thoracic Surgery, The Central Hospital of Wuhan, No.26 Shenli Street, Jiang'an District, Wuhan, 430014, Hubei, China
| | - Zhuo Wang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Hui Wu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Xianhong Xiang
- Department of Interventional Radiology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Bing Tang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Wenting Jiang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Yongmei Cui
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Han Wang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Neng Jiang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Yu Sun
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Yangshan Chen
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Shuhua Li
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Minzhi Hou
- Department of Gyneacology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, People's Republic of China
| | - Yang Zhang
- Biomedical Engineering, University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968, USA
| | - Liantang Wang
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Zun-Fu Ke
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China.
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5
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Huang SH, Chang YS, Juang JMJ, Chang KW, Tsai MH, Lu TP, Lai LC, Chuang EY, Huang NT. An automated microfluidic DNA microarray platform for genetic variant detection in inherited arrhythmic diseases. Analyst 2019; 143:1367-1377. [PMID: 29423467 DOI: 10.1039/c7an01648d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, we developed an automated microfluidic DNA microarray (AMDM) platform for point mutation detection of genetic variants in inherited arrhythmic diseases. The platform allows for automated and programmable reagent sequencing under precise conditions of hybridization flow and temperature control. It is composed of a commercial microfluidic control system, a microfluidic microarray device, and a temperature control unit. The automated and rapid hybridization process can be performed in the AMDM platform using Cy3 labeled oligonucleotide exons of SCN5A genetic DNA, which produces proteins associated with sodium channels abundant in the heart (cardiac) muscle cells. We then introduce a graphene oxide (GO)-assisted DNA microarray hybridization protocol to enable point mutation detection. In this protocol, a GO solution is added after the staining step to quench dyes bound to single-stranded DNA or non-perfectly matched DNA, which can improve point mutation specificity. As proof-of-concept we extracted the wild-type and mutant of exon 12 and exon 17 of SCN5A genetic DNA from patients with long QT syndrome or Brugada syndrome by touchdown PCR and performed a successful point mutation discrimination in the AMDM platform. Overall, the AMDM platform can greatly reduce laborious and time-consuming hybridization steps and prevent potential contamination. Furthermore, by introducing the reciprocating flow into the microchannel during the hybridization process, the total assay time can be reduced to 3 hours, which is 6 times faster than the conventional DNA microarray. Given the automatic assay operation, shorter assay time, and high point mutation discrimination, we believe that the AMDM platform has potential for low-cost, rapid and sensitive genetic testing in a simple and user-friendly manner, which may benefit gene screening in medical practice.
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Affiliation(s)
- Shu-Hong Huang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.
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6
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Abstract
Microfluidic biochips hold great potential for liquid analysis in biomedical research and clinical diagnosis. However, the lack of integrated on-chip liquid mixing, bioseparation and signal transduction presents a major challenge in achieving rapid, ultrasensitive bioanalysis in simple microfluidic configurations. Here we report magnetic nanochain integrated microfluidic chip built upon the synergistic functions of the nanochains as nanoscale stir bars for rapid liquid mixing and as capturing agents for specific bioseparation. The use of magnetic nanochains enables a simple planar design of the microchip consisting of flat channels free of common built-in components, such as liquid mixers and surface-anchored sensing elements. The microfluidic assay, using surface-enhanced Raman scattering nanoprobes for signal transduction, allows for streamlined parallel analysis of multiple specimens with greatly improved assay kinetics and delivers ultrasensitive identification and quantification of a panel of cancer protein biomarkers and bacterial species in 1 μl of body fluids within 8 min. Microfluidic platforms are an attractive setup for performing clinical tests but integrated liquid mixing and bioseparation is difficult at small scales. Here Xiong et al. propose magnetic nanochains which can stir the solution and capture agents and thus enable liquid analysis in a short amount of time.
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7
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Amplification-free detection of microRNAs via a rapid microarray-based sandwich assay. Anal Bioanal Chem 2017; 409:3497-3505. [DOI: 10.1007/s00216-017-0298-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/27/2017] [Accepted: 03/06/2017] [Indexed: 12/16/2022]
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8
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Li Y, Zhao Q, Wang Y, Man T, Zhou L, Fang X, Pei H, Chi L, Liu J. Ultrasensitive Signal-On Detection of Nucleic Acids with Surface-Enhanced Raman Scattering and Exonuclease III-Assisted Probe Amplification. Anal Chem 2016; 88:11684-11690. [DOI: 10.1021/acs.analchem.6b03267] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yingying Li
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Qingcheng Zhao
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Yandong Wang
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Tiantian Man
- School
of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Lu Zhou
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Xu Fang
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Hao Pei
- School
of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Lifeng Chi
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
| | - Jian Liu
- Institute
of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory
for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
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9
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Li J, Zrazhevskiy P, Gao X. Eliminating Size-Associated Diffusion Constraints for Rapid On-Surface Bioassays with Nanoparticle Probes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:1035-1043. [PMID: 26749053 PMCID: PMC4815929 DOI: 10.1002/smll.201503101] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 11/30/2015] [Indexed: 05/21/2023]
Abstract
Nanoparticle probes enable implementation of advanced on-surface assay formats, but impose often underappreciated size-associated constraints, in particular on assay kinetics and sensitivity. The present study highlights substantially slower diffusion-limited assay kinetics due to the rapid development of a nanoprobe depletion layer next to the surface, which static incubation and mixing of bulk solution employed in conventional assay setups often fail to disrupt. In contrast, cyclic solution draining and replenishing yields reaction-limited assay kinetics irrespective of the probe size. Using common surface bioassays, enzyme-linked immunosorbent assays and immunofluorescence, this study shows that this conceptually distinct approach effectively "erases" size-dependent diffusion constraints, providing a straightforward route to rapid on-surface bioassays employing bulky probes and procedures involving multiple labeling cycles, such as multicycle single-cell molecular profiling. For proof-of-concept, the study demonstrates that the assay time can be shortened from hours to minutes with the same probe concentration and, at a typical incubation time, comparable target labeling can be achieved with up to eight times lower nanoprobe concentration. The findings are expected to enable realization of novel assay formats and stimulate development of rapid on-surface bioassays with nanoparticle probes.
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Affiliation(s)
- Junwei Li
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Pavel Zrazhevskiy
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Xiaohu Gao
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
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10
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Abstract
The DNA microarray technology is currently a useful biomedical tool which has been developed for a variety of diagnostic applications. However, the development pathway has not been smooth and the technology has faced some challenges. The reliability of the microarray data and also the clinical utility of the results in the early days were criticized. These criticisms added to the severe competition from other techniques, such as next-generation sequencing (NGS), impacting the growth of microarray-based tests in the molecular diagnostic market.Thanks to the advances in the underlying technologies as well as the tremendous effort offered by the research community and commercial vendors, these challenges have mostly been addressed. Nowadays, the microarray platform has achieved sufficient standardization and method validation as well as efficient probe printing, liquid handling and signal visualization. Integration of various steps of the microarray assay into a harmonized and miniaturized handheld lab-on-a-chip (LOC) device has been a goal for the microarray community. In this respect, notable progress has been achieved in coupling the DNA microarray with the liquid manipulation microsystem as well as the supporting subsystem that will generate the stand-alone LOC device.In this chapter, we discuss the major challenges that microarray technology has faced in its almost two decades of development and also describe the solutions to overcome the challenges. In addition, we review the advancements of the technology, especially the progress toward developing the LOC devices for DNA diagnostic applications.
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Affiliation(s)
| | - Abootaleb Sedighi
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6
| | - Paul C H Li
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada, V5A 1S6.
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11
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Heimer BW, Shatova TA, Lee JK, Kaastrup K, Sikes HD. Evaluating the sensitivity of hybridization-based epigenotyping using a methyl binding domain protein. Analyst 2015; 139:3695-701. [PMID: 24824477 DOI: 10.1039/c4an00667d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hypermethylation of CpG islands in gene promoter regions has been shown to be a predictive biomarker for certain diseases. Most current methods for methylation profiling are not well-suited for clinical analysis. Here, we report the development of an inexpensive device and an epigenotyping assay with a format conducive to multiplexed analysis.
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Affiliation(s)
- Brandon W Heimer
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02129, USA.
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12
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Hoffman JM, Stayton PS, Hoffman AS, Lai JJ. Stimuli-responsive reagent system for enabling microfluidic immunoassays with biomarker purification and enrichment. Bioconjug Chem 2014; 26:29-38. [PMID: 25405605 PMCID: PMC4306508 DOI: 10.1021/bc500522k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Immunoassays
have been translated into microfluidic device formats,
but significant challenges relating to upstream sample processing
still limit their applications. Here, stimuli-responsive polymer–antibody
conjugates are utilized in a microfluidic immunoassay to enable rapid
biomarker purification and enrichment as well as sensitive detection.
The conjugates were constructed by covalently grafting poly(N-isopropylacrylamide) (PNIPAAm), a thermally responsive
polymer, to the lysine residues of anti-prostate specific antigen
(PSA) Immunoglobulin G (IgG) using carbodiimide chemistry via the
polymer end-carboxylate. The antibody-PNIPAAm (capture) conjugates
and antibody-alkaline phosphatase (detection) conjugates formed sandwich
immunocomplexes via PSA binding in 50% human plasma. The complexes
were loaded into a recirculating poly(dimethylsiloxane) microreactor,
equipped with micropumps and transverse flow features, for subsequent
separation, enrichment, and quantification. The immunocomplexes were
captured by heating the solution to 39 °C, mixed over the transverse
features for 2 min, and washed with warm buffer. In one approach,
the assay utilized immunocomplex solution that was contained in an
80 nL microreactor, which was loaded with solution at room temperature
and subsequently heated to 39 °C. The assay took 25 min and resulted
in 37 pM PSA limit of detection (LOD), which is comparable to a plate
ELISA employing the same antibody pair. In another approach, the microreactor
was preheated to 39 °C, and immunocomplex solution was flowed
through the reactor, mixed, and washed. When the specimen volume was
increased to 7.5 μL by repeating the capture process three times,
the higher specimen volume led to immunocomplex enrichment within
the microreactor. The resulting assay LOD was 0.5 pM, which is 2 orders
of magnitude lower than the plate ELISA. Both approaches generate
antigen specific signal over a clinically significant range. The sample
processing capabilities and subsequent utility in a biomarker assay
demonstrate the opportunity for stimuli-responsive polymer–protein
conjugates in novel diagnostic technologies.
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Affiliation(s)
- John M Hoffman
- Department of Bioengineering, University of Washington , Seattle, Washington 98195, United States
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13
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Han CM, Katilius E, Santiago JG. Increasing hybridization rate and sensitivity of DNA microarrays using isotachophoresis. LAB ON A CHIP 2014; 14:2958-67. [PMID: 24921466 DOI: 10.1039/c4lc00374h] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We present an on-chip electrokinetic method to increase the reaction kinetics and sensitivity of DNA microarray hybridization. We use isotachophoresis (ITP) to preconcentrate target molecules in solution and transport them over the immobilized probe sites of a microarray, greatly increasing the binding reaction rate. We show theoretically and experimentally that ITP-enhanced microarrays can be hybridized much faster and with higher sensitivity than conventional methods. We demonstrate our assay using a microfluidic system consisting of a PDMS microchannel superstructure bonded onto a glass slide on which 60 spots of 20-27 nt ssDNA oligonucleotide probes are immobilized. Our 30 min assay results in an 8.2 fold higher signal than the conventional overnight hybridization at 100 fM target concentration. We show rapid and quantitative detection over 4 orders of magnitude dynamic range of target concentration with no increase in the nonspecific signal. Our technique can be further multiplexed for higher density microarrays and extended for other reactions of target-surface immobilized ligands.
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Affiliation(s)
- Crystal M Han
- Department of Mechanical Engineering, Stanford University, CA 94305, USA
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14
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Sedighi A, Li PC. Challenges and Future Trends in DNA Microarray Analysis. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-62651-6.00002-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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15
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Yang F, Zhang Y, Rafeah S, Ji H, Xie S, Ning Y, Zhang GJ. Accelerated DNA recombination on a functionalized microfluidic chip. RSC Adv 2014. [DOI: 10.1039/c4ra02076f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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16
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Lynn NS, Martínez-López JI, Bocková M, Adam P, Coello V, Siller HR, Homola J. Biosensing enhancement using passive mixing structures for microarray-based sensors. Biosens Bioelectron 2013; 54:506-14. [PMID: 24321884 DOI: 10.1016/j.bios.2013.11.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/17/2013] [Accepted: 11/06/2013] [Indexed: 10/26/2022]
Abstract
The combination of microarray technologies with microfluidic sample delivery and real-time detection methods has the capability to simultaneously monitor 10-1000 s of biomolecular interactions in a single experiment. Despite the benefits that microfluidic systems provide, they typically operate in the laminar flow regime under mass transfer limitations, where large analyte depletion layers act as a resistance to analyte capture. By locally stirring the fluid and delivering fresh analyte to the capture spot, the use of passive mixing structures in a microarray environment can reduce the negative effects of these depletion layers and enhance the sensor performance. Despite their large potential, little attention has been given to the integration of these mixing structures in microarray sensing environments. In this study, we use passive mixing structures to enhance the mass transfer of analyte to a capture spot within a microfluidic flow cell. Using numerical methods, different structure shapes and heights were evaluated as means to increase local fluid velocities, and in turn, rates of mass transfer to a capture spot. These results were verified experimentally via the real-time detection of 20-mer ssDNA for an array of microspots. Both numerical and experimental results showed that a passive mixing structure situated directly over the capture spot can significantly enhance the binding rate of analyte to the sensing surface. Moreover, we show that these structures can be used to enhance mass transfer in experiments regarding an array of capture spots. The results of this study can be applied to any experimental system using microfluidic sample delivery methods for microarray detection techniques.
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Affiliation(s)
- N Scott Lynn
- Institute of Photonics and Electronics, Chaberská 57, 18251 Prague, Czech Republic
| | | | - Markéta Bocková
- Institute of Photonics and Electronics, Chaberská 57, 18251 Prague, Czech Republic
| | - Pavel Adam
- Institute of Photonics and Electronics, Chaberská 57, 18251 Prague, Czech Republic
| | - Victor Coello
- Centro de Investigación Científica y de Educación Superior de Ensenada, Unidad Monterrey, Alianza Sur No. 105, Nueva Carretera Aeropuerto Km 9.5, Apodaca 66629, N.L., México.
| | - Héctor R Siller
- Tecnológico de Monterrey, Eugenio Garza Sada 2501 Sur, C.P. 64849 Monterrey, N.L., México.
| | - Jiří Homola
- Institute of Photonics and Electronics, Chaberská 57, 18251 Prague, Czech Republic.
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17
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Fordyce PM, Diaz-Botia CA, DeRisi JL, Gomez-Sjoberg R. Systematic characterization of feature dimensions and closing pressures for microfluidic valves produced via photoresist reflow. LAB ON A CHIP 2012; 12:4287-95. [PMID: 22930180 DOI: 10.1039/c2lc40414a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Multilayer soft lithography (MSL) provides a convenient and low-cost method for fabricating poly(dimethyl siloxane) (PDMS) microfluidic devices with on-chip valves for automated and precise control of fluid flow. MSL casting molds for flow channels typically incorporate small patches of rounded positive photoresist at valve locations to achieve the rounded cross-sectional profile required for these valves to function properly. Despite the importance of these rounded features for device performance, a comprehensive characterization of how the rounding process affects feature dimensions and closing pressures has been lacking. Here, we measure valve dimensions both before and after rounding and closing pressures for 120 different valve widths and lengths at post-rounding heights between 15 and 84 μm, for a total of 1200 different geometries spanning a wide range of useful sizes. We find that valve height and width after rounding depend strongly on valve aspect ratios, with these effects becoming more pronounced for taller and narrower features. Based on the measured data, we provide a simple fitted model and an online tool for estimating the pre-rounding dimensions needed to achieve desired post-rounding dimensions. We also find that valve closing pressures are well explained by modelling valve membranes in a manner analogous to a suspension bridge, shedding new light on device physics and providing a practical model for estimating closing pressures during device design.
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Affiliation(s)
- P M Fordyce
- Department of Biochemistry and Biophysics, University of California San Francisco, 1700 4th Street Byers Hall Room 403, San Francisco, CA 94158, USA.
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18
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Qu X, Wang Y, Shi Z, Fu G, Zeng X, Li X, Chen H. Probe droplet arrays generated in the capillary for microarray analysis. Biosens Bioelectron 2012; 38:342-7. [DOI: 10.1016/j.bios.2012.06.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 06/11/2012] [Accepted: 06/13/2012] [Indexed: 11/16/2022]
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19
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Forbes TP, Kralj JG. Engineering and analysis of surface interactions in a microfluidic herringbone micromixer. LAB ON A CHIP 2012; 12:2634-7. [PMID: 22706612 DOI: 10.1039/c2lc40356k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We developed a computational model and theoretical framework to investigate the geometrical optimization of particle-surface interactions in a herringbone micromixer. The enhancement of biomolecule- and particle-surface interactions in microfluidic devices through mixing and streamline disruption holds promise for a variety of applications. This analysis provides guidelines for optimizing the frequency and specific location of surface interactions based on the flow pattern and relative hydraulic resistance between a groove and the effective channel. The channel bottom, i.e., channel surface between grooves, was identified as the dominant location for surface contact. In addition, geometries that decrease the groove-to-channel hydraulic resistance improve contact with the channel top. Thus, herringbone mixers appear useful for a variety of surface-interaction applications, yet they have largely not been employed in an optimized fashion.
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Affiliation(s)
- Thomas P Forbes
- National Institute of Standards and Technology, Biochemical Science Division, Gaithersburg, MD, USA
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20
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Bercovici M, Han CM, Liao JC, Santiago JG. Rapid hybridization of nucleic acids using isotachophoresis. Proc Natl Acad Sci U S A 2012; 109:11127-32. [PMID: 22733732 PMCID: PMC3396536 DOI: 10.1073/pnas.1205004109] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We use isotachophoresis (ITP) to control and increase the rate of nucleic acid hybridization reactions in free solution. We present a new physical model, validation experiments, and demonstrations of this assay. We studied the coupled physicochemical processes of preconcentration, mixing, and chemical reaction kinetics under ITP. Our experimentally validated model enables a closed form solution for ITP-aided reaction kinetics, and reveals a new characteristic time scale which correctly predicts order 10,000-fold speed-up of chemical reaction rate for order 100 pM reactants, and greater enhancement at lower concentrations. At 500 pM concentration, we measured a reaction time which is 14,000-fold lower than that predicted for standard second-order hybridization. The model and method are generally applicable to acceleration of reactions involving nucleic acids, and may be applicable to a wide range of reactions involving ionic reactants.
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Affiliation(s)
- Moran Bercovici
- Mechanical Engineering, Stanford University, 440 Escondido Mall, Stanford, CA 94305; and
- Department of Urology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305
| | - Crystal M. Han
- Mechanical Engineering, Stanford University, 440 Escondido Mall, Stanford, CA 94305; and
| | - Joseph C. Liao
- Department of Urology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305
| | - Juan G. Santiago
- Mechanical Engineering, Stanford University, 440 Escondido Mall, Stanford, CA 94305; and
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21
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Brody E, Gold L, Mehan M, Ostroff R, Rohloff J, Walker J, Zichi D. Life's simple measures: unlocking the proteome. J Mol Biol 2012; 422:595-606. [PMID: 22721953 DOI: 10.1016/j.jmb.2012.06.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 06/12/2012] [Indexed: 01/22/2023]
Abstract
Using modified nucleotides and selecting for slow off-rates in the SELEX procedure, we have evolved a special class of aptamers, called SOMAmers (slow off-rate modified aptamers), which bind tightly and specifically to proteins in body fluids. We use these in a novel assay that yields 1:1 complexes of the SOMAmers with their cognate proteins in body fluids. Measuring the SOMAmer concentrations of the resultant complexes reflects the concentration of the proteins in the fluids. This is simply done by hybridization to complementary sequences on solid supports, but it can also be done by any other DNA quantification technology (including NexGen sequencing). We use measurements of over 1000 proteins in under 100 μL of serum or plasma to answer important medical questions, two of which are reviewed here. A number of bioinformatics methods have guided our discoveries, including principal component analysis. We use various methods to evaluate sample handling procedures in our clinical samples and can identify many parameters that corrupt proteomics analysis.
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Affiliation(s)
- Edward Brody
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA.
| | - Larry Gold
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - Mike Mehan
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - Rachel Ostroff
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - John Rohloff
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - Jeff Walker
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - Dom Zichi
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
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22
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Antibody-functionalized fluid-permeable surfaces for rolling cell capture at high flow rates. Biophys J 2012; 102:721-30. [PMID: 22385842 DOI: 10.1016/j.bpj.2011.12.044] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 11/14/2011] [Accepted: 12/09/2011] [Indexed: 12/22/2022] Open
Abstract
Adhesion-based cell capture on surfaces in microfluidic devices forms the basis of numerous biomedical diagnostics and in vitro assays. However, the performance of these platforms is partly limited by interfacial phenomena that occur at low Reynolds numbers. In contrast, cell homing to porous vasculature is highly effective in vivo during inflammation, stem cell trafficking, and cancer metastasis. Here, we show that a porous, fluid-permeable surface functionalized with cell-specific antibodies promotes efficient and selective cell capture in vitro. This architecture is advantageous due to enhanced transport as streamlines are diverted toward the surface. Moreover, specific cell-surface interactions are promoted due to reduced shear, allowing gentle cell rolling and arrest. Together, these synergistic effects enable highly effective cell capture at flow rates more than an order of magnitude larger than those provided by existing devices with solid surfaces.
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23
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Abstract
Traditional ‘macroscopic’ pharmacokinetics (PK) investigates the fate of drugs or toxicants administered externally to living organisms, described by the extent and rate of absorption, distribution, metabolism and excretion. However, how a single cell affects a specific pharmaceutical after administration still remains a largely untouched area, primarily due to the technical restrictions imposed by minute amounts of chemicals involved. With the fast development of high-temporal and spatial-resolution detection techniques and single-cell handling techniques, it becomes possible to pursue single-cell PK. This review summarizes useful methodological and experimental techniques to investigate PK at the level of the single cell, including the microfluidics-based single-cell manipulation and the MS and electrochemical methods for single-cell analysis.
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24
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Søe MJ, Okkels F, Sabourin D, Alberti M, Holmstrøm K, Dufva M. HistoFlex--a microfluidic device providing uniform flow conditions enabling highly sensitive, reproducible and quantitative in situ hybridizations. LAB ON A CHIP 2011; 11:3896-3907. [PMID: 21964811 DOI: 10.1039/c1lc20748b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A microfluidic device (the HistoFlex) designed to perform and monitor molecular biological assays under dynamic flow conditions on microscope slide-substrates, with special emphasis on analyzing histological tissue sections, is presented. Microscope slides were reversibly sealed onto a cast polydimethylsiloxane (PDMS) insert, patterned with distribution channels and reaction chambers. Topology optimization was used to design reaction chambers with uniform flow conditions. The HistoFlex provided uniform hybridization conditions, across the reaction chamber, as determined by hybridization to microscope slides of spotted DNA microarrays when applying probe concentrations generally used in in situ hybridization (ISH) assays. The HistoFlex's novel ability in online monitoring of an in situ hybridization assay was demonstrated using direct fluorescent detection of hybridization to 18S rRNA. Tissue sections were not visually damaged during assaying, which enabled adapting a complete ISH assay for detection of microRNAs (miRNA). The effects of flow based incubations on hybridization, antibody incubation and Tyramide Signal Amplification (TSA) steps were investigated upon adapting the ISH assay for performing in the HistoFlex. The hybridization step was significantly enhanced using flow based incubations due to improved hybridization efficiency. The HistoFlex device enabled a fast miRNA ISH assay (3 hours) which provided higher hybridization signal intensity compared to using conventional techniques (5 h 40 min). We further demonstrate that the improved hybridization efficiency using the HistoFlex permits more complex assays e.g. those comprising sequential hybridization and detection of two miRNAs to be performed with significantly increased sensitivity. The HistoFlex provides a new histological analysis platform that will allow multiple and sequential assays to be performed under their individual optimum assay conditions. Images can subsequently be recorded either in combination or sequentially through the ability of the HistoFlex to monitor assays without disassembly.
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25
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Golova JB, Chernov BK, Perov AN, Reynolds J, Linger YL, Kukhtin A, Chandler DP. Nonvolatile copolymer compositions for fabricating gel element microarrays. Anal Biochem 2011; 421:526-33. [PMID: 22033291 DOI: 10.1016/j.ab.2011.09.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 09/27/2011] [Accepted: 09/28/2011] [Indexed: 11/28/2022]
Abstract
By modifying polymer compositions and cross-linking reagents, we have developed a simple yet effective manufacturing strategy for copolymerized three-dimensional gel element arrays. A new gel-forming monomer, 2-(hydroxyethyl) methacrylamide (HEMAA), was used. HEMAA possesses low volatility and improves the stability of copolymerized gel element arrays to on-chip thermal cycling procedures relative to previously used monomers. Probe immobilization efficiency within the new polymer was 55%, equivalent to that obtained with acrylamide (AA) and methacrylamide (MA) monomers. Nonspecific binding of single-stranded targets was equivalent for all monomers. Increasing cross-linker chain length improved hybridization kinetics and end-point signal intensities relative to N,N-methylenebisacrylamide (Bis). The new copolymer formulation was successfully applied to a model orthopox array. Because HEMAA greatly simplifies gel element array manufacture, we expect it (in combination with new cross-linkers described here) to find widespread application in microarray science.
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26
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Hartman RL, McMullen JP, Jensen KF. Pro und kontra Strömungsreaktoren in der Synthese. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201004637] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Hartman RL, McMullen JP, Jensen KF. Deciding whether to go with the flow: evaluating the merits of flow reactors for synthesis. Angew Chem Int Ed Engl 2011; 50:7502-19. [PMID: 21710673 DOI: 10.1002/anie.201004637] [Citation(s) in RCA: 638] [Impact Index Per Article: 49.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Indexed: 11/06/2022]
Abstract
The fine chemicals and pharmaceutical industries are transforming how their products are manufactured, where economically favorable, from traditional batchwise processes to continuous flow. This evolution is impacting synthetic chemistry on all scales-from the laboratory to full production. This Review discusses the relative merits of batch and micro flow reactors for performing synthetic chemistry in the laboratory.
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Affiliation(s)
- Ryan L Hartman
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, 66-350, Cambridge, MA 02139, USA
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28
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Wang X, Chen X, Ma X, Kong X, Xu Z, Wang J. Fast DNA hybridization on a microfluidic mixing device based on pneumatic driving. Talanta 2011; 84:565-71. [DOI: 10.1016/j.talanta.2011.01.065] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 01/24/2011] [Accepted: 01/26/2011] [Indexed: 11/24/2022]
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29
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Wang S, Liu K, Liu J, Yu ZTF, Xu X, Zhao L, Lee T, Lee EK, Reiss J, Lee YK, Chung LWK, Huang J, Rettig M, Seligson D, Duraiswamy KN, Shen CKF, Tseng HR. Highly efficient capture of circulating tumor cells by using nanostructured silicon substrates with integrated chaotic micromixers. Angew Chem Int Ed Engl 2011; 50:3084-8. [PMID: 21374764 PMCID: PMC3085082 DOI: 10.1002/anie.201005853] [Citation(s) in RCA: 468] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2010] [Revised: 11/19/2010] [Indexed: 12/30/2022]
Affiliation(s)
- Shutao Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing (P. R. China),
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging (CIMI), California NanoSystems Institute (CNSI), Institute for Molecular Medicine (IMED), University of California, Los Angeles, 570 Westwood Plaza, Building 114, Los Angeles, CA 90095-1770 (USA)
| | - Kan Liu
- College of Electronics and Information Engineering, Wuhan Textile University, Wuhan (P. R. China)
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging (CIMI), California NanoSystems Institute (CNSI), Institute for Molecular Medicine (IMED), University of California, Los Angeles, 570 Westwood Plaza, Building 114, Los Angeles, CA 90095-1770 (USA)
| | - Jian Liu
- Uro-oncology Research Program, Samuel Oschin Comprehensive Cancer Institute, Cedars Sinai Medical Center, Los Angeles, CA (USA)
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging (CIMI), California NanoSystems Institute (CNSI), Institute for Molecular Medicine (IMED), University of California, Los Angeles, 570 Westwood Plaza, Building 114, Los Angeles, CA 90095-1770 (USA)
| | - Zeta T.-F. Yu
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging (CIMI), California NanoSystems Institute (CNSI), Institute for Molecular Medicine (IMED), University of California, Los Angeles, 570 Westwood Plaza, Building 114, Los Angeles, CA 90095-1770 (USA)
| | - Xiaowen Xu
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging (CIMI), California NanoSystems Institute (CNSI), Institute for Molecular Medicine (IMED), University of California, Los Angeles, 570 Westwood Plaza, Building 114, Los Angeles, CA 90095-1770 (USA)
| | - Libo Zhao
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging (CIMI), California NanoSystems Institute (CNSI), Institute for Molecular Medicine (IMED), University of California, Los Angeles, 570 Westwood Plaza, Building 114, Los Angeles, CA 90095-1770 (USA)
| | - Tom Lee
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging (CIMI), California NanoSystems Institute (CNSI), Institute for Molecular Medicine (IMED), University of California, Los Angeles, 570 Westwood Plaza, Building 114, Los Angeles, CA 90095-1770 (USA)
| | - Eun Kyung Lee
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging (CIMI), California NanoSystems Institute (CNSI), Institute for Molecular Medicine (IMED), University of California, Los Angeles, 570 Westwood Plaza, Building 114, Los Angeles, CA 90095-1770 (USA)
| | - Jean Reiss
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles (USA)
| | - Yi-Kuen Lee
- Department of Mechanical Engineering, The Hong Kong University of Science and Technology (Hong Kong)
| | - Leland W. K. Chung
- Uro-oncology Research Program, Samuel Oschin Comprehensive Cancer Institute, Cedars Sinai Medical Center, Los Angeles, CA (USA)
| | - Jiaoti Huang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles (USA)
| | - Matthew Rettig
- Department of Urology, University of California, Los Angeles (USA)
| | - David Seligson
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles (USA)
| | - Kumaran N. Duraiswamy
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging (CIMI), California NanoSystems Institute (CNSI), Institute for Molecular Medicine (IMED), University of California, Los Angeles, 570 Westwood Plaza, Building 114, Los Angeles, CA 90095-1770 (USA)
| | - Clifton K.-F. Shen
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging (CIMI), California NanoSystems Institute (CNSI), Institute for Molecular Medicine (IMED), University of California, Los Angeles, 570 Westwood Plaza, Building 114, Los Angeles, CA 90095-1770 (USA)
| | - Hsian-Rong Tseng
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging (CIMI), California NanoSystems Institute (CNSI), Institute for Molecular Medicine (IMED), University of California, Los Angeles, 570 Westwood Plaza, Building 114, Los Angeles, CA 90095-1770 (USA)
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30
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Wang S, Liu K, Liu J, Yu ZTF, Xu X, Zhao L, Lee T, Lee EK, Reiss J, Lee YK, Chung LWK, Huang J, Rettig M, Seligson D, Duraiswamy KN, Shen CKF, Tseng HR. Highly Efficient Capture of Circulating Tumor Cells by Using Nanostructured Silicon Substrates with Integrated Chaotic Micromixers. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201005853] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Microfluidic DNA microarray analysis: a review. Anal Chim Acta 2010; 687:12-27. [PMID: 21241842 DOI: 10.1016/j.aca.2010.11.056] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/29/2010] [Accepted: 11/30/2010] [Indexed: 11/21/2022]
Abstract
Microarray DNA hybridization techniques have been used widely from basic to applied molecular biology research. Generally, in a DNA microarray, different probe DNA molecules are immobilized on a solid support in groups and form an array of microspots. Then, hybridization to the microarray can be performed by applying sample DNA solutions in either the bulk or the microfluidic manner. Because the immobilized probe DNA binds and retains its complementary target DNA, detection is achieved through the read-out of the tagged markers on the sample target molecules. The recent microfluidic hybridization method shows the advantages of less sample usage and reduced incubation time. Here, sample solutions are confined in microfabricated channels and flow through the probe microarray area. The high surface-to-volume ratio in microchannels of nanolitre volume greatly enhanced the sensitivity as obtained with the bulk solution method. To generate nanolitre flows, different techniques have been developed, and this including electrokinetic control, vacuum suction and syringe pumping. The latter two are pressure-driven methods which are more flexible without the need of considering the physicochemical properties of solutions. Recently, centrifugal force is employed to drive liquid movement in microchannels. This method utilizes the body force from the liquid itself and there are no additional solution interface contacts such as from electrodes or syringes and tubing. Centrifugal force driven flow also features the ease of parallel hybridizations. In this review, we will summarize the recent advances in microfluidic microarray hybridization and compare the applications of various flow methods.
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32
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Hoffman JM, Ebara M, Lai JJ, Hoffman AS, Folch A, Stayton PS. A helical flow, circular microreactor for separating and enriching "smart" polymer-antibody capture reagents. LAB ON A CHIP 2010; 10:3130-8. [PMID: 20882219 PMCID: PMC3116725 DOI: 10.1039/c004978f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We report a mechanistic study of how flow and recirculation in a microreactor can be used to optimize the capture and release of stimuli-responsive polymer-protein reagents on stimuli-responsive polymer-grafted channel surfaces. Poly(N-isopropylacrylamide) (PNIPAAm) was grafted to polydimethylsiloxane (PDMS) channel walls, creating switchable surfaces where PNIPAAm-protein conjugates would adhere at temperatures above the lower critical solution temperature (LCST) and released below the LCST. A PNIPAAm-streptavidin conjugate that can capture biotinylated antibody-antigen targets was first characterized. The conjugate's immobilization and release were limited by mass transport to and from the functionalized PNIPAAm surface. Transport and adsorption efficiencies were dependent on the aggregate size of the PNIPAAm-streptavidin conjugate above the LCST and also were dependent on whether the conjugates were heated in the presence of the stimuli-responsive surface or pre-aggregated and then flowed across the surface. As conjugate size increased, through the addition of non-conjugated PNIPAAm, recirculation and mixing were shown to markedly improve conjugate immobilization compared to diffusion alone. Under optimized conditions of flow and reagent concentrations, approximately 60% of the streptavidin conjugate bolus could be captured at the surface and subsequently successfully released. The kinetic release profile sharpness was also strongly improved with recirculation and helical mixing. Finally, the concentration of protein-polymer conjugates could be achieved by continuous conjugate flow into the heated recirculator, allowing nearly linear enrichment of the conjugate reagent from larger volumes. This capability was shown with anti-p24 HIV monoclonal antibody reagents that were enriched over 5-fold using this protocol. These studies provide insight into the mechanism of smart polymer-protein conjugate capture and release in grafted channels and show the potential of this purification and enrichment module for processing diagnostic samples.
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33
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Huang S, Li C, Lin B, Qin J. Microvalve and micropump controlled shuttle flow microfluidic device for rapid DNA hybridization. LAB ON A CHIP 2010; 10:2925-2931. [PMID: 20830429 DOI: 10.1039/c005227b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We present a novel microfluidic device integrated with microvalves and micropumps for rapid DNA hybridization using shuttle flow. The device is composed of 48 hybridization units containing 48 microvalves and 96 micropumps for the automation of shuttle flow. We used four serotypes of Dengue Virus genes (18mer) to demonstrate that the automatic shuttle flow shortened the hybridization time to 90 s, reduced sample consumption to 1 μL and lowered detection limit to 100 pM (100 amol in a 1 μL sample). Moreover, we applied this device to realize single base discrimination and analyze 48 samples containing different DNA targets, simultaneously. For kinetic measurements of nucleotide hybridization, on-line monitoring of the processes was carried out. This rapid hybridization device has the ability for accommodating the entire hybridization process (i.e., injection, hybridization, washing, detection, signal acquisition) in an automated and high-throughput fashion.
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Affiliation(s)
- Shuqiang Huang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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34
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Millet LJ, Stewart ME, Nuzzo RG, Gillette MU. Guiding neuron development with planar surface gradients of substrate cues deposited using microfluidic devices. LAB ON A CHIP 2010; 10:1525-35. [PMID: 20390196 PMCID: PMC2930779 DOI: 10.1039/c001552k] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Wiring the nervous system relies on the interplay of intrinsic and extrinsic signaling molecules that control neurite extension, neuronal polarity, process maturation and experience-dependent refinement. Extrinsic signals establish and enrich neuron-neuron interactions during development. Understanding how such extrinsic cues direct neurons to establish neural connections in vitro will facilitate the development of organized neural networks for investigating the development and function of nervous system networks. Producing ordered networks of neurons with defined connectivity in vitro presents special technical challenges because the results must be compliant with the biological requirements of rewiring neural networks. Here we demonstrate the ability to form stable, instructive surface-bound gradients of laminin that guide postnatal hippocampal neuron development in vitro. Our work uses a three-channel, interconnected microfluidic device that permits the production of adlayers of planar substrates through the combination of laminar flow, diffusion and physisorption. Through simple flow modifications, a variety of patterns and gradients of laminin (LN) and fluorescein isothiocyanate-conjugated poly-l-lysine (FITC-PLL) were deposited to present neurons with an instructive substratum to guide neuronal development. We present three variations in substrate design that produce distinct growth regimens for postnatal neurons in dispersed cell cultures. In the first approach, diffusion-mediated gradients of LN were formed on cover slips to guide neurons toward increasing LN concentrations. In the second approach, a combined gradient of LN and FITC-PLL was produced using aspiration-driven laminar flow to restrict neuronal growth to a 15 microm wide growth zone at the center of the two superimposed gradients. The last approach demonstrates the capacity to combine binary lines of FITC-PLL in conjunction with surface gradients of LN and bovine serum albumin (BSA) to produce substrate adlayers that provide additional levels of control over growth. This work demonstrates the advantages of spatio-temporal fluid control for patterning surface-bound gradients using a simple microfluidics-based substrate deposition procedure. We anticipate that this microfluidics-based patterning approach will provide instructive patterns and surface-bound gradients to enable a new level of control in guiding neuron development and network formation.
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Affiliation(s)
- Larry J. Millet
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. ; Tel: +1-217-244-1355
| | - Matthew E. Stewart
- Department of Chemistry and the Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Ralph G. Nuzzo
- Department of Chemistry and the Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Martha U. Gillette
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. ; Tel: +1-217-244-1355
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Wang L, Li PCH. Optimization of a microfluidic microarray device for the fast discrimination of fungal pathogenic DNA. Anal Biochem 2010; 400:282-8. [PMID: 20083083 DOI: 10.1016/j.ab.2010.01.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 01/12/2010] [Accepted: 01/13/2010] [Indexed: 10/20/2022]
Abstract
A microfluidic microarray device, which has been developed for parallel DNA detection, is now further optimized for more rapid and sensitive DNA detection and for the single-base-pair discrimination of two fungal pathogenic PCR products. Two poly(dimethylsiloxane) (PDMS)-based microfluidic chips consist of radial and spiral microchannels in which flexible probe creation and convenient sample delivery have been achieved by centrifugal pumping. The microarray hybridizations occurred at the cross sections within the spiral channels intersecting the preprinted radial probe lines. The centrifugal pumping method showed advantages over the vacuum suction method in terms of parallel solution delivery and less signal variations between replicate samples. The effect of microchannel depth was studied, and hybridization time is predictable at a certain rotation speed. Cy5 dye labels were proved to show much higher hybridization efficiency as well as less photobleaching effect as compared with the fluorescein dye labels used in our previous work. With these optimized conditions, the method was applied to the detection of three fungal pathogenic polymerase chain reaction (PCR) products with a sample load of 0.2 ng (in 1 microl). Furthermore, the single-base-pair discrimination between the PCR products of two relevant Botrytis species (B. cinerea and B. squamosa) was achieved in a duration as short as 3 min.
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Affiliation(s)
- Lin Wang
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
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36
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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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37
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Kim SJ, Wang F, Burns MA, Kurabayashi K. Temperature-programmed natural convection for micromixing and biochemical reaction in a single microfluidic chamber. Anal Chem 2009; 81:4510-6. [PMID: 19419189 PMCID: PMC2727855 DOI: 10.1021/ac900512x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Micromixing is a crucial step for biochemical reactions in microfluidic networks. A critical challenge is that the system containing micromixers needs numerous pumps, chambers, and channels not only for the micromixing but also for the biochemical reactions and detections. Thus, a simple and compatible design of the micromixer element for the system is essential. Here, we propose a simple, yet effective, scheme that enables micromixing and a biochemical reaction in a single microfluidic chamber without using any pumps. We accomplish this process by using natural convection in conjunction with alternating heating of two heaters for efficient micromixing, and by regulating capillarity for sample transport. As a model application, we demonstrate micromixing and subsequent polymerase chain reaction (PCR) for an influenza viral DNA fragment. This process is achieved in a platform of a microfluidic cartridge and a microfabricated heating-instrument with a fast thermal response. Our results will significantly simplify micromixing and a subsequent biochemical reaction that involves reagent heating in microfluidic networks.
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Affiliation(s)
- Sung-Jin Kim
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
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38
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Xie H, Li B, Zhong R, Qin J, Zhu Y, Lin B. Microfluidic device for integrated restriction digestion reaction and resulting DNA fragment analysis. Electrophoresis 2009; 29:4956-63. [PMID: 19130575 DOI: 10.1002/elps.200800490] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A microfluidic system combining temperature-controlled reactor, analyte delivery, chip electrophoresis (CE) separation, and fluorescence detection was developed, in which the heaters, resistance temperature detectors, enzymatic reactors, CE channels, and pneumatic valves/pumps were integrated onto a single glass-PDMS chip. The microdevice was used to perform the digestion reaction, followed by on-line electrophoresis separation and detection of the resulting fragments with endonuclease BamHI and FokI as models. Pneumatic valves/pumps served not only for isolating the reaction region from the separation medium to prevent contamination, but also for delivering and quantitatively diluting the fluid from the reaction chamber to the CE section. Thus enzymatic reaction and electrophoresis separation could be insulated and connected as needed. A dynamic coating procedure with the use of PVP and mannitol was firstly adopted for glass-PDMS hybrid chip-based DNA separations, leading to an improved separation efficiency with reproducible migration time and theoretical plates. The expected 263- and 287-bp digestion products of BamHI and FokI were definitely verified by the size-based electrophoretic separation and detection. The whole integrated reaction-CE system can be manipulated in a simple manner with good reproducibility, which is expected to be applied in other on-line analysis of various biochemical reactions.
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Affiliation(s)
- Hua Xie
- Dalian Institute of Chemical Physics, Dalian, PR China
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39
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Ohno KI, Tachikawa K, Manz A. Microfluidics: Applications for analytical purposes in chemistry and biochemistry. Electrophoresis 2008; 29:4443-53. [DOI: 10.1002/elps.200800121] [Citation(s) in RCA: 296] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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40
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Cheong R, Wang CJ, Levchenko A. High content cell screening in a microfluidic device. Mol Cell Proteomics 2008; 8:433-42. [PMID: 18953019 DOI: 10.1074/mcp.m800291-mcp200] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A comprehensive, systems level understanding of cell signaling networks requires methods to efficiently assay multiple signaling species, at the level of single cells, responding to a variety of stimulation protocols. Here we describe a microfluidic device that enables quantitative interrogation of signaling networks in thousands of individual cells using immunofluorescence-based readouts. The device is especially useful for measuring the signaling activity of kinases, transcription factors, and/or target genes in a high throughput, high content manner. We demonstrate how the device may be used to measure detailed time courses of signaling responses to one or more soluble stimuli and/or chemical inhibitors as well as responses to a complex temporal pattern of multiple stimuli. Furthermore we show how the throughput and resolution of the device may be exploited in investigating the differences, if any, of signaling at the level of a single cell versus at the level of the population. In particular, we show that NF-kappaB activity dynamics in individual cells are not asynchronous and instead resemble the dynamics of the population average in contrast to studies of cells overexpressing p65-EGFP.
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Affiliation(s)
- Raymond Cheong
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, Maryland 21218, USA
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41
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Foley JO, Mashadi-Hossein A, Fu E, Finlayson BA, Yager P. Experimental and model investigation of the time-dependent 2-dimensional distribution of binding in a herringbone microchannel. LAB ON A CHIP 2008; 8:557-564. [PMID: 18369510 DOI: 10.1039/b713644g] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A microfluidic device known to mix bulk solutions, the herringbone microchannel, was incorporated into a surface-binding assay to determine if the recirculation of solution altered the binding of a model protein (streptavidin) to the surface. Streptavidin solutions were pumped over surfaces functionalized with its ligand, biotin, and the binding of streptavidin to those surfaces was monitored using surface plasmon resonance imaging. Surface binding was compared between a straight microchannel and herringbone microchannels in which the chevrons were oriented with and against the flow direction. A 3-dimensional finite-element model of the surface binding reaction was developed for each of the geometries and showed strong qualitative agreement with the experimental results. Experimental and model results indicated that the forward and reverse herringbone microchannels substantially altered the distribution of protein binding (2-dimensional binding profile) as a function of time when compared to a straight microchannel. Over short distances (less than 1.5 mm) down the length of the microchannel, the model predicted no additional protein binding in the herringbone microchannel compared to the straight microchannel, consistent with previous findings in the literature.
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Affiliation(s)
- Jennifer O Foley
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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42
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Sorokin NV, Yurasov DY, Cherepanov AI, Kozhekbaeva JM, Chechetkin VR, Gra OA, Livshits MA, Nasedkina TV, Zasedatelev AS. Effects of external transport on discrimination between perfect and mismatch duplexes on gel-based oligonucleotide microchips. J Biomol Struct Dyn 2007; 24:571-8. [PMID: 17508779 DOI: 10.1080/07391102.2007.10507146] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Using hydrogel-based oligonucleotide microchips developed previously for the choice of drugs during leukemia treatment and the other diseases, it is shown that the acceleration of external transport by mixing buffer solution with peristaltic pump not only enhances the observable fluorescence signals, but also improves significantly the discrimination between perfect and mismatch duplexes at the intermediate stage of hybridization on the oligonucleotide microchips. The discrimination efficiency for a given hybridization time grows monotonously with the frequency of flow pulsations. The mixing with frequency 10 Hz accelerates the hybridization rate approximately thrice and improves the discrimination efficiency 1.5-2.5 times higher for overnight hybridization. To study these effects, we have developed the special peristaltic pump mixing solution in a hybridization chamber of 35 mul in volume (area approximately 1 x 1 cm(2) and height 0.3 mm). We present also the brief theoretical summary for the interpretation and assessment of the observed experimental features.
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Affiliation(s)
- N V Sorokin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow, Russia 119991
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Melin J, Quake SR. Microfluidic large-scale integration: the evolution of design rules for biological automation. ACTA ACUST UNITED AC 2007; 36:213-31. [PMID: 17269901 DOI: 10.1146/annurev.biophys.36.040306.132646] [Citation(s) in RCA: 344] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microfluidic large-scale integration (mLSI) refers to the development of microfluidic chips with thousands of integrated micromechanical valves and control components. This technology is utilized in many areas of biology and chemistry and is a candidate to replace today's conventional automation paradigm, which consists of fluid-handling robots. We review the basic development of mLSI and then discuss design principles of mLSI to assess the capabilities and limitations of the current state of the art and to facilitate the application of mLSI to areas of biology. Many design and practical issues, including economies of scale, parallelization strategies, multiplexing, and multistep biochemical processing, are discussed. Several microfluidic components used as building blocks to create effective, complex, and highly integrated microfluidic networks are also highlighted.
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Affiliation(s)
- Jessica Melin
- Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford, California 94305, USA.
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44
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Song S, Li B, Wang L, Wu H, Hu J, Li M, Fan C. A cancer protein microarray platform using antibody fragments and its clinical applications. MOLECULAR BIOSYSTEMS 2006; 3:151-8. [PMID: 17245494 DOI: 10.1039/b608973a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Antibody microarrays have shown great potential for measurement of either a spectrum of target proteins in proteomics or disease-associated antigens in molecular diagnostics. Despite its importance, the applications of antibody microarrays are still limited by a variety of fundamental problems. Among them, cross-reactivity significantly limits the multiplexing ability in parallel sandwich immunoassays. As a result, it is very important to design new capture probes in order to incorporate a universal label into the assay configuration. In this report, an antibody fragments (F(ab')2) microarray platform for serum tumor markers was developed. Each antigen was detected at different concentrations to assemble its calibration curve, and combinations of different markers were tested to examine the specificity of simultaneous detection based on the F(ab')2 microarrays. Diagnostics of serum samples with this cancer antibody microarray platform and immunoradiometric assays (IRMA) were also performed. Wide range calibration curves (0-1280 U mL(-1)) were obtained for each tumor marker. Comparative studies demonstrated that such F(ab')2 microarrays exhibited both moderately improved sensitivity and better specificity than full-sized monoclonal antibody microarrays. It is also demonstrated that this microarray platform is quantitative, highly specific and reasonably sensitive. More importantly, clinical applications of our F(ab')2 microarray platform for upwards of 100 patient serum samples clearly show its potential in cancer diagnostics.
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Affiliation(s)
- Shiping Song
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China.
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