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Gudagunti FD, Velmanickam L, Nawarathna D, Lima IT. Nucleotide Identification in DNA Using Dielectrophoresis Spectroscopy. MICROMACHINES 2019; 11:mi11010039. [PMID: 31905617 PMCID: PMC7019800 DOI: 10.3390/mi11010039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 11/27/2022]
Abstract
We show that negative dielectrophoresis (DEP) spectroscopy is an effective transduction mechanism of a biosensor for the detection of single nucleotide polymorphism (SNP) in a short DNA strand. We observed a frequency dependence of the negative DEP force applied by interdigitated electrodes to polystyrene microspheres (PM) with respect to changes in both the last and the second-to-last nucleotides of a single-strand DNA bound to the PM. The drift velocity of PM functionalized to single-strand DNA, which is proportional to the DEP force, was measured at the frequency range from 0.5 MHz to 2 MHz. The drift velocity was calculated using a custom-made automated software using real time image processing technique. This technology for SNP genotyping has the potential to be used in the diagnosis and the identification of genetic variants associated with diseases.
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Abstract
When individuals are exposed to stressful environmental challenges, the response varies widely in one or more of three components: psychology, behavior and physiology. This variability among individuals can be defined as temperament. In recent years, an increasing large body of evidence suggests that the dimensions of temperament, as well as personality, psychological disorders and behavioral traits, are influenced by genetic factors, and much of the variation appears to involve variation in genes or gene polymorphisms in the hypothalamic-pituitary-adrenocortical (HPA) axis and the behavior-controlling neurotransmitter networks. Here, we review our current understanding of the probabilistic impact of a number of candidate gene polymorphisms that control temperament, psychological disorders and behavioral traits in animals and human, including the gene polymorphisms related to corticotrophin-releasing hormone (CRH) production and adrenal cortisol production involved in the HPA axis, and a large number of gene polymorphisms in the dopaminergic and serotonergic neurotransmitter networks. It will very likely to assist in diagnosis and treatment of human relevant disorders, and provide useful contributions to our understanding of evolution, welfare and conservation, for animals in the wild and in production systems. Additionally, investigations of gene-gene and gene-environment complex interactions in humans and animals need further clear illustration.
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Affiliation(s)
- Xiaoyan Qiu
- a College of Animal Science and Technology, Southwest University , Chong Qing , PR China.,b UWA Institute of Agriculture and School of Animal Biology M082, Faculty of Sciences , University of Western Australia , Crawley , WA , Australia
| | - Graeme B Martin
- b UWA Institute of Agriculture and School of Animal Biology M082, Faculty of Sciences , University of Western Australia , Crawley , WA , Australia.,c Nuffield Department of Obstetrics and Gynecology , University of Oxford , Oxford , UK
| | - Dominique Blache
- b UWA Institute of Agriculture and School of Animal Biology M082, Faculty of Sciences , University of Western Australia , Crawley , WA , Australia
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Chen X, Zhou D, Shen H, Chen H, Feng W, Xie G. A universal probe design for colorimetric detection of single-nucleotide variation with visible readout and high specificity. Sci Rep 2016; 6:20257. [PMID: 26830326 PMCID: PMC4735751 DOI: 10.1038/srep20257] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/31/2015] [Indexed: 01/02/2023] Open
Abstract
Single-nucleotide variation (SNV) is a crucial biomarker for drug resistance-related detection in cancer and bacterial infection. However, the unintended binding of DNA probes limits the specificity of SNV detection, and the need for redesigned sequences compromise the universality of SNV assay. Herein, we demonstrated a universal and low-cost assay for the colorimetric discrimination of drug-resistance related point mutation. By the use of a universal DNA probe and a split G-quadruplex, the signal could be recognized by naked eye at room temperature. The DNA probe was used as a signal reporter which not only improved the universality, but also enabled high specificity of probe hybridization. This assay was successfully applied in the detection of cancer-related SNV in the epidermal growth factor receptor (EGFR) gene, kirsten rat sarcoma viral oncogene homologue (KRAS), and tuberculosis drug-resistance related point mutation in RNA polymerase beta subunit gene (rpoB) with high specificity and visible readout. This method was simple, rapid, high-throughput and effective, which was suitable for point-of-care applications.
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Affiliation(s)
- Xueping Chen
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Dandan Zhou
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Huawei Shen
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Hui Chen
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Wenli Feng
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Guoming Xie
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
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Huang CW, Lin YT, Ding ST, Lo LL, Wang PH, Lin EC, Liu FW, Lu YW. Efficient SNP Discovery by Combining Microarray and Lab-on-a-Chip Data for Animal Breeding and Selection. ACTA ACUST UNITED AC 2015; 4:570-95. [PMID: 27600241 PMCID: PMC4996412 DOI: 10.3390/microarrays4040570] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/16/2015] [Accepted: 10/28/2015] [Indexed: 11/16/2022]
Abstract
The genetic markers associated with economic traits have been widely explored for animal breeding. Among these markers, single-nucleotide polymorphism (SNPs) are gradually becoming a prevalent and effective evaluation tool. Since SNPs only focus on the genetic sequences of interest, it thereby reduces the evaluation time and cost. Compared to traditional approaches, SNP genotyping techniques incorporate informative genetic background, improve the breeding prediction accuracy and acquiesce breeding quality on the farm. This article therefore reviews the typical procedures of animal breeding using SNPs and the current status of related techniques. The associated SNP information and genotyping techniques, including microarray and Lab-on-a-Chip based platforms, along with their potential are highlighted. Examples in pig and poultry with different SNP loci linked to high economic trait values are given. The recommendations for utilizing SNP genotyping in nimal breeding are summarized.
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Affiliation(s)
- Chao-Wei Huang
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Yu-Tsung Lin
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Shih-Torng Ding
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Ling-Ling Lo
- Department of Animal Science, Chinese Culture University, Taipei 11114, Taiwan.
| | - Pei-Hwa Wang
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - En-Chung Lin
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Fang-Wei Liu
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Yen-Wen Lu
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
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Chin YT, Liao EC, Wu CC, Wang GJ, Tsai JJ. Detection of haplotype mutations of the MD-2 gene promoter associated with Der p2-induced allergy using a nanostructured biosensor. Int J Nanomedicine 2014; 9:1403-12. [PMID: 24648737 PMCID: PMC3958545 DOI: 10.2147/ijn.s59151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Group 2 allergens (Der p2) have been reported to be a major cause of the human immune response to dust mite allergens. In this study, we have demonstrated for the first time the effective differentiation between haplotype mutation and normal genes in the MD-2 gene promoter using a nanostructured biosensor. A 70-mer gene fragment containing the haplotype of two single nucleotide polymorphisms in the MD-2 gene promoter region was used as a probe to detect haplotype mutations associated with Der p2-induced allergy. Discrimination was achieved using electrochemical impedance spectroscopy. The discrimination experiments employed 30 haplotype mutation samples and 30 normal target samples. The haplotype mutation samples and normal target samples could be clearly discriminated, even using samples produced by a five-cycle polymerase chain reaction process. The time and cost of sample preparation for the polymerase chain reaction process in the clinical setting can thus be reduced.
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Affiliation(s)
- Yu-Ting Chin
- Department of Mechanical Engineering, National Chung-Hsing University, Taichung, Taiwan
| | - En-Chih Liao
- Department of Medical Education and Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chia-Che Wu
- Department of Mechanical Engineering, National Chung-Hsing University, Taichung, Taiwan
| | - Gou-Jen Wang
- Department of Mechanical Engineering, National Chung-Hsing University, Taichung, Taiwan ; Graduate Institute of Biomedical Engineering, Taichung, Taiwan ; PhD Program in Tissue Engineering and Regenerative Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Jaw-Ji Tsai
- Department of Medical Education and Research, Taichung Veterans General Hospital, Taichung, Taiwan
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Hou G, Jiang X, Yang Y, Jia F, Li Q, Zhao J, Guo F, Liu L. A 21-locus autosomal SNP multiplex and its application in forensic science. J Forensic Sci 2013; 59:5-14. [PMID: 24400826 DOI: 10.1111/1556-4029.12259] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 08/06/2012] [Accepted: 10/14/2012] [Indexed: 02/06/2023]
Abstract
To develop a cost-effective technique for single-nucleotide polymorphism (SNP) genotyping and improve the efficiency to analyze degraded DNA, we have established a novel multiplex system including 21-locus autosomal SNPs and amelogenin locus, which was based on allele-specific amplification (ASA) and universal reporter primers (URP). The target amplicons for each of the 21 SNPs arranged from 63 base pair (bp) to 192 bp. The system was tested in 539 samples from three ethnic groups (Han, Mongolian, and Zhuang population) in China, and the total power of discrimination (TPD) and cumulative probability of exclusion (CPE) were more than 0.99999999 and 0.98, respectively. The system was further validated with forensic samples and full profiles could be achieved from degraded DNA and 63 case-type samples. In summary, the multiplex system offers an effective technique for individual identification of forensic samples and is much more efficient in the analysis of degraded DNA compared with standard STR typing.
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Affiliation(s)
- Guangwei Hou
- Department of Forensic DNA, Criminal Science and Technology Institute of Liaoning province, Shenyang, 110032, China
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Zhu J, Palla M, Ronca S, Warpner R, Ju J, Lin Q. A MEMS-Based Approach to Single Nucleotide Polymorphism Genotyping. SENSORS AND ACTUATORS. A, PHYSICAL 2013; 195:175-182. [PMID: 24729659 PMCID: PMC3979494 DOI: 10.1016/j.sna.2012.07.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Genotyping of single nucleotide polymorphisms (SNPs) allows diagnosis of human genetic disorders associated with single base mutations. Conventional SNP genotyping methods are capable of providing either accurate or high-throughput detection, but are still labor-, time-, and resource-intensive. Microfluidics has been applied to SNP detection to provide fast, low-cost, and automated alternatives, although these applications are still limited by either accuracy or throughput issues. To address this challenge, we present a MEMS-based SNP genotyping approach that uses solid-phase-based reactions in a single microchamber on a temperature control chip. Polymerase chain reaction (PCR), allele specific single base extension (SBE), and desalting on microbeads are performed in the microchamber, which is coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze the SBE product. Experimental results from genotyping of the SNP on exon 1 of the HBB gene, which causes sickle cell anemia, demonstrate the potential of the device for rapid, accurate, multiplexed and high-throughput detection of SNPs.
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Affiliation(s)
- Jing Zhu
- Department of Mechanical Engineering, Columbia University,
New York, NY, USA
| | - Mirkó Palla
- Department of Mechanical Engineering, Columbia University,
New York, NY, USA
- Department of Chemical Engineering, Columbia University,
New York, NY, USA
| | - Stefano Ronca
- Department of Mechanical Engineering, Columbia University,
New York, NY, USA
- Department of Mechanical and Industrial Engineering,
University of Brescia, Brescia, BS, Italy
| | - Ronald Warpner
- Department of Obstetrics and Gynecology, Columbia
University, New York, NY, USA
| | - Jingyue Ju
- Department of Chemical Engineering, Columbia University,
New York, NY, USA
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University,
New York, NY, USA
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Wang Y, Zhan R, Li T, Pu KY, Wang Y, Tan YC, Liu B. Fluorescence and visual detection of single nucleotide polymorphism using cationic conjugated polyelectrolyte. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:889-895. [PMID: 22047010 DOI: 10.1021/la203714e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We report a simple assay for visual detection of single nucleotide polymorphisms (SNPs) with good sensitivity and selectivity. The selectivity is determined by Escherichia coli (E. coli) DNA ligase mediated circular formation upon recognition of the point mutation on DNA targets. Rolling cycle amplification (RCA) of the perfect-matched DNA target is then initiated using the in situ formed circular template in the presence of Phi29 enzyme. Due to amplification of the DNA target, the RCA product has a tandem-repeated sequence, which is significantly longer than that for the SNP strand. Direct addition of a cationic conjugated polymer of poly[9,9'-bis(6'-(N,N,N-trimethylammonium)hexyl)fluorene-co-9,9'-bis(2-(2-(2-(N,N,N-trimethylammonium)ethoxyl)-ethoxy)-ethyl)fluorene tetrabromide] containing 20 mol% 2,1,3-benzothiadiazole (PFBT(20)) into the RCA solution leads to blue-whitish fluorescent color for SNP strand and yellowish fluorescent color for amplified DNA, due to PFBT(20)/DNA complexation induced intrachain/interchain energy transfer. To further improve the contrast for visual detection, FAM-labeled peptide nucleic acid (PNA) was hybridized to each amplified sequence, which is followed by the addition of poly{2,7-[9,9-bis(6'-N,N,N-trimethylammoniumhexyl)]fluorene-co-2,5-difluoro-1,4-phenylene dibromide} (PFP). The PNA/DNA hybridization brings PFP and FAM-PNA into close proximity for energy transfer, and the solution fluorescent color appears green in the presence of target DNA with a detection limit of 1 nM, which is significantly improved as compared to that for most reported visual SNP assay.
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Affiliation(s)
- Yifan Wang
- Department of Chemical and Biomolecular Engineering, 4 Engineering Drive 4, National University of Singapore, Singapore 117567, Singapore
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Li J, Zhao GH, Chen F, Song HQ, Zhu XQ, Zhao GH, Li J, Chen F, Lin RQ, Weng YB, Mahmoud MS, Zou FC. A cleaved amplified polymorphic sequence (CAPS) method for the identification of geographical isolates of Schistosoma japonicum in China. ANNALS OF TROPICAL MEDICINE AND PARASITOLOGY 2011; 105:531-6. [PMID: 22185948 PMCID: PMC4100313 DOI: 10.1179/2047773211y.0000000004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 10/21/2011] [Accepted: 10/24/2011] [Indexed: 10/31/2022]
Affiliation(s)
- J Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou 730046, China
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AL-Othman ZA, Ali I. NANO CAPILLARY ELECTROPHORESIS IN MICROCHIPS: A NEED OF THE PRESENT CENTURY. J LIQ CHROMATOGR R T 2011. [DOI: 10.1080/10826076.2011.566031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Zeid A. AL-Othman
- a Department of Chemistry, College of Science , King Saud University , Riyadh, Kingdom of Saudi Arabia
| | - Imran Ali
- b Department of Chemistry , Jamia Millia Islamia, (Central University) , New Delhi, India
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11
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Lien KY, Lee GB. Miniaturization of molecular biological techniques for gene assay. Analyst 2010; 135:1499-518. [PMID: 20390199 DOI: 10.1039/c000037j] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The rapid diagnosis of various diseases is a critical advantage of many emerging biomedical tools. Due to advances in preventive medicine, tools for the accurate analysis of genetic mutation and associated hereditary diseases have attracted significant interests in recent years. The entire diagnostic process usually involves two critical steps, namely, sample pre-treatment and genetic analysis. The sample pre-treatment processes such as extraction and purification of the target nucleic acids prior to genetic analysis are essential in molecular diagnostics. The genetic analysis process may require specialized apparatus for nucleic acid amplification, sequencing and detection. Traditionally, pre-treatment of clinical biological samples (e.g. the extraction of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)) and the analysis of genetic polymorphisms associated with genetic diseases are typically a lengthy and costly process. These labor-intensive and time-consuming processes usually result in a high-cost per diagnosis and hinder their practical applications. Besides, the accuracy of the diagnosis may be affected owing to potential contamination from manual processing. Alternatively, due to significant advances in micro-electro-mechanical-systems (MEMS) and microfluidic technology, there are numerous miniature systems employed in biomedical applications, especially for the rapid diagnosis of genetic diseases. A number of advantages including automation, compactness, disposability, portability, lower cost, shorter diagnosis time, lower sample and reagent consumption, and lower power consumption can be realized by using these microfluidic-based platforms. As a result, microfluidic-based systems are becoming promising platforms for genetic analysis, molecular biology and for the rapid detection of genetic diseases. In this review paper, microfluidic-based platforms capable of identifying genetic sequences and diagnosis of genetic mutations are surveyed and reviewed. Some critical issues with the use of microfluidic-based systems for diagnosis of genetic diseases are also highlighted.
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Affiliation(s)
- Kang-Yi Lien
- Institute of Nanotechnology and Microsystems Engineering, National Cheng Kung University, Tainan, 701, Taiwan
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Thuy NTB, Yokogawa R, Yoshimura Y, Fujimoto K, Koyano M, Maenosono S. Surface-enhanced Raman spectroscopy for facile DNA detection using gold nanoparticle aggregates formed via photoligation. Analyst 2010; 135:595-602. [PMID: 20174716 DOI: 10.1039/b919969a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present a new type of nanoparticle-based DNA sensor using surface-enhanced Raman scattering (SERS) on gold nanoparticle (Au NP) aggregates formed by DNA photoligation. The DNA sensor exploits the photoligation reaction between oligodeoxynucleotides (ODNs) attached to the surfaces of Au NPs in the presence of target DNA (T-DNA). When hybridization takes place between the ODNs and T-DNA, Au NPs are covalently crosslinked to form aggregates via photoligation. Once the NP aggregates are formed, the interspace between Au NPs in the aggregate act as a stable "hot spot", and a SERS signal from the Raman-active molecules (sodium cacodylate) present in the hot spot is easily and sensitively detected. In contrast, a SERS signal is not detected if the hybridization is unsuccessful, because the stable hot spot does not form. This DNA sensor does not require an enzymatic reaction, fluorescent dye, precise temperature control, or complicated operating procedures.
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Affiliation(s)
- Nguyen T B Thuy
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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Jin X, Fei Y, Zhang L, Liu X, Shen G, Yu R. An electrochemical molecular switch for one-step, reusable detection of a single-base mutation of DNA. Analyst 2009; 135:121-6. [PMID: 20024191 DOI: 10.1039/b911672a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new strategy for one-step, reusable and sensitive detection of a single-base mutation based on an electrochemical molecular switch is developed in the present work. When the hybridization reaction takes place in the presence of target DNA, the Fc-labeled terminal of the open switch molecule can be captured by the probe through the predesigned complementary bases of both sequences. By this method, a signal-on sensor featuring both generalizability and simplicity towards reagentless detection of DNA with sensitivity and selectivity electrochemical system is built on. The approach had been demonstrated with the identification of a single-base mutation of alpha-thalassemia point mutation in Hb Constant Spring codon 142 (TAA --> CAA). The wild-type and mutant-type of the synthetic 16 mer DNA sequences as the model targets were successfully discriminated. The results showed that the response signal was linear to the logarithm of the target concentration in the range from 0.01 to 100 pM with a detection limit of 0.01 pM. The regeneration experiment demonstrated that the sensor interface can be easily and successfully regenerated. All these revealed that the present system is a promising candidate for single-base mutation discrimination.
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Affiliation(s)
- Xiaoyong Jin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Chemistry and Chemical Engineering College, Hunan University, Changsha 410082, PR China.
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Wang WP, Zhang RH, Wu P, Wang S, Li R. Estimation of allele frequency in pooled DNA by using PCR–RFLP combined with microchip electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:1603-6. [DOI: 10.1016/j.jchromb.2009.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 03/28/2009] [Accepted: 04/01/2009] [Indexed: 11/25/2022]
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Mohanty SK, Warrick J, Gorski J, Beebe DJ. An accessible micro-capillary electrophoresis device using surface-tension-driven flow. Electrophoresis 2009; 30:1470-81. [PMID: 19425002 PMCID: PMC2842211 DOI: 10.1002/elps.200800595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We present a rapidly fabricated micro-capillary electrophoresis chip that utilizes surface-tension-driven flow for sample injection and extraction of DNA. Surface-tension-driven flow (i.e. passive pumping) [G. M. Walker et al., Lab. Chip. 2002, 2, 131-134] injects a fixed volume of sample that can be predicted mathematically. Passive pumping eliminates the need for tubing, valves, syringe pumps, and other equipment typically needed for interfacing with microelectrophoresis chips. This method requires a standard micropipette to load samples before separation, and remove the resulting bands after analysis. The device was made using liquid phase photopolymerization to rapidly fabricate the chip without the need of special equipment typically associated with the construction of microelectrophoresis chips (e.g. cleanroom) [A. K. Agarwal et al., J. Micromech. Microeng. 2006, 16, 332-340; S. K. Mohanty et al., Electrophoresis 2006, 27, 3772-3778]. Batch fabrication time for the device presented here was 1.5 h including channel coating time to suppress electroosmotic flow. Devices were constructed out of poly-isobornyl acrylate and glass. A standard microscope with a UV source was used for sample detection. Separations were demonstrated using Promega BenchTop 100 bp ladder in hydroxyl ethyl cellulose (HEC) and oligonucleotides of 91 and 118 bp were used to characterize sample injection and extraction of DNA bands. The end result was an inexpensive micro-capillary electrophoresis device that uses tools (e.g. micropipette, electrophoretic power supplies, and microscopes) already present in most labs for sample manipulation and detection, making it more accessible for potential end users.
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Affiliation(s)
- Swomitra K Mohanty
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA.
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16
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Design of allele-specific primers and detection of the human ABO genotyping to avoid the pseudopositive problem. Electrophoresis 2009; 29:4130-40. [PMID: 18991264 DOI: 10.1002/elps.200800097] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PCR experiments using DNA primers forming mismatch pairing with template lambda DNA at the 3' end were carried out in order to develop allele-specific primers capable of detecting SNP in genomes without generating pseudopositive amplification products, and thus avoiding the so-called pseudopositive problem. Detectable amounts of PCR products were obtained when primers forming a single or two mismatch pairings at the 3' end were used. In particular, 3' terminal A/C or T/C (primer/template) mismatches tended to allow PCR amplification to proceed, resulting in pseudopositive results in many cases. While less PCR product was observed for primers forming three terminal mismatch pairings, target DNA sequences were efficiently amplified by primers forming two mismatch pairings next to the terminal G/C base pairing. These results indicate that selecting a primer having a 3' terminal nucleotide that recognizes the SNP nucleotide and the next two nucleotides that form mismatch pairings with the template sequence can be used as an allele-specific primer that eliminates the pseudopositive problem. Trials with the human ABO genes demonstrated that this primer design is also useful for detecting a single base pair difference in gene sequences with a signal-to-noise ratio of at least 45.
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17
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Ali I, Aboul-Enein HY, Gupta VK. Microchip-Based Nano Chromatography and Nano Capillary Electrophoresis in Genomics and Proteomics. Chromatographia 2008. [DOI: 10.1365/s10337-008-0813-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Dewald AH, Poe BL, Landers JP. Electrophoretic microfluidic devices for mutation detection in clinical diagnostics. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2008; 2:963-977. [PMID: 23495869 DOI: 10.1517/17530059.2.8.963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BACKGROUND In an era of growing interest in personalized medicine - where ubiquitous patient genotyping holds unprecedented clinical utility - rapid, sensitive and low-cost methodologies will be required for the detection of genetic variants correlative with disease. Electrophoretic microfluidic devices have emerged as a promising platform for such analyses, inherently offering faster analysis, excellent reagent economy, a small laboratory footprint and potentially seamless integration of multiple analytical steps. OBJECTIVE Although glass and polymeric microchips have recently been developed for a wide variety of medical applications, this review focuses on their application to the detection of clinically relevant genomic DNA mutations and polymorphisms. METHOD Mutation analysis techniques, including direct gene sizing, enzyme-based assays, heteroduplex analysis, single-strand conformational polymorphism analysis, and multiplex, allele-specific and methylation-specific PCR are included. CONCLUSION Further development of 'lab-on-a-chip' or 'micro total analysis system' technologies ultimately aims to streamline and miniaturize the entire genetic analysis process, enabling rapid, point-of-care analysis for molecular diagnostics.
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Affiliation(s)
- Alison H Dewald
- University of Virginia, Department of Chemistry, McCormick Road, Charlottesville, VA 22904, USA +1 434 243 8658 ; +1 434 924 3048 ;
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Chen YT, Hsu CL, Hou SY. Detection of single-nucleotide polymorphisms using gold nanoparticles and single-strand-specific nucleases. Anal Biochem 2008; 375:299-305. [PMID: 18211817 DOI: 10.1016/j.ab.2007.12.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 12/21/2007] [Accepted: 12/21/2007] [Indexed: 12/24/2022]
Abstract
The current study reports an assay approach that can detect single-nucleotide polymorphisms (SNPs) and identify the position of the point mutation through a single-strand-specific nuclease reaction and a gold nanoparticle assembly. The assay can be implemented via three steps: a single-strand-specific nuclease reaction that allows the enzyme to truncate the mutant DNA; a purification step that uses capture probe-gold nanoparticles and centrifugation; and a hybridization reaction that induces detector probe-gold nanoparticles, capture probe-gold nanoparticles, and the target DNA to form large DNA-linked three-dimensional aggregates of gold nanoparticles. At high temperature (63 degrees C in the current case), the purple color of the perfect match solution would not change to red, whereas a mismatched solution becomes red as the assembled gold nanoparticles separate. Using melting analysis, the position of the point mutation could be identified. This assay provides a convenient colorimetric detection that enables point mutation identification without the need for expensive mass spectrometry. To our knowledge, this is the first report concerning SNP detection based on a single-strand-specific nuclease reaction and a gold nanoparticle assembly.
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Affiliation(s)
- Yen-Ting Chen
- Institute of Biotechnology, National Taipei University of Technology, Taipei 106, Taiwan
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20
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Cho M, Han MS, Ban C. Detection of mismatched DNAs via the binding affinity of MutS using a gold nanoparticle-based competitive colorimetric method. Chem Commun (Camb) 2008:4573-5. [DOI: 10.1039/b811346g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Zhang P, Chu X, Xu X, Shen G, Yu R. Electrochemical detection of point mutation based on surface ligation reaction and biometallization. Biosens Bioelectron 2007; 23:1435-41. [PMID: 18242973 DOI: 10.1016/j.bios.2007.12.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 12/10/2007] [Accepted: 12/13/2007] [Indexed: 12/20/2022]
Abstract
A highly sensitive electrochemical method for point mutation detection based on surface enzymatic ligation reaction and biometallization is demonstrated. In this method the surface-immobilized allele-specific probe, complementary to the mutant target, undergoes allele-specific ligation with the 5'-phosphorylated ligation probe in the presence of the mutant oligonucleotide target and E. coli DNA ligase. If there is an allele mismatch, no ligation takes place. After thermal treatment at 90 degrees C, the formed duplex melts apart, which merely allows the ligation product to remain on the electrode surface. Then, biotinylated detection probes hybridize with the ligation product. With the binding of streptavidin-alkaline phosphatase (SA-ALP) to the biotinylated probes, a non-reductive substrate of alkaline phosphatase, ascorbic acid 2-phosphate (AA-P), can be converted into ascorbic acid (AA) at the electrode surface. Silver ions in solution are then reduced by AA, resulting in the deposition of silver metal onto the electrode surface. Linear sweep voltammetry (LSV) is used to detect the amount of deposited silver. The proposed approach has been successfully implemented for the identification of single base mutation in codon 12 of K-ras oncogene target with a detection limit of 80fM, demonstrating that this method provides a highly specific, sensitive and cost-efficient approach for point mutation detection.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Chemo/Bio-sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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22
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Deng T, Li J, Jiang JH, Shen GL, Yu RQ. A sensitive fluorescence anisotropy method for point mutation detection by using core-shell fluorescent nanoparticles and high-fidelity DNA ligase. Chemistry 2007; 13:7725-30. [PMID: 17607685 DOI: 10.1002/chem.200700195] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The present study reports a proof-of-principle for a sensitive genotyping assay approach that can detect single nucleotide polymorphisms (SNPs) based on fluorescence anisotropy measurements through a core-shell fluorescent nanoparticles assembly and ligase reaction. By incorporating the core-shell fluorescent nanoparticles into fluorescence anisotropy measurements, this assay provided a convenient and sensitive detection assay that enabled straightforward single-base discrimination without the need of complicated operational steps. The assay was implemented via two steps: first, the hybridization reaction that allowed two nanoparticle-tagged probes to hybridize with the target DNA strand and the ligase reaction that generated the ligation between perfectly matched probes while no ligation occurred between mismatched ones were implemented synchronously in the same solution. Then, a thermal treatment at a relatively high temperature discriminated the ligation of probes. When the reaction mixture was heated to denature the duplex formed, the fluorescence anisotropy value of the perfect-match solution does not revert to the initial value, while that of the mismatch again comes back as the assembled fluorescent nanoparticles dispart. The present approach has been demonstrated with the discrimination of a single base mutation in codon 12 of a K-ras oncogene that is of significant value for colorectal cancers diagnosis, and the wild type and mutant type were successfully scored. Due to its ease of operation and high sensitivity, it was expected that the proposed detection approach might hold great promise in practical clinical diagnosis.
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Affiliation(s)
- Ting Deng
- State Key Laboratory of Chem/Biosensing and Chemometrics, Chemistry and Chemical Engineering College, Hunan University, Changsha 410082, China
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23
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24
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Horsman KM, Bienvenue JM, Blasier KR, Landers JP. Forensic DNA Analysis on Microfluidic Devices: A Review. J Forensic Sci 2007; 52:784-99. [PMID: 17553097 DOI: 10.1111/j.1556-4029.2007.00468.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The advent of microfluidic technology for genetic analysis has begun to impact forensic science. Recent advances in microfluidic separation of short-tandem-repeat (STR) fragments has provided unprecedented potential for improving speed and efficiency of DNA typing. In addition, the analytical processes associated with sample preparation--which include cell sorting, DNA extraction, DNA quantitation, and DNA amplification--can all be integrated with the STR separation in a seamless manner. The current state of these microfluidic methods as well as their advantages and potential shortcomings are detailed. Recent advances in microfluidic device technology, as they pertain to forensic DNA typing, are discussed with a focus on the forensic community.
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Affiliation(s)
- Katie M Horsman
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
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25
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Alonso A, Albarran C, Martín P, García P, Capilla J, García O, de la Rua C, Izaguirre N, Pereira F, Pereira L, Amorim A, Sancho M. Usefulness of microchip electrophoresis for the analysis of mitochondrial DNA in forensic and ancient DNA studies. Electrophoresis 2006; 27:5101-9. [PMID: 17120261 DOI: 10.1002/elps.200600331] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We evaluate the usefulness of a commercially available microchip CE (MCE) device in different genetic identification studies performed with mitochondrial DNA (mtDNA) targets, including the haplotype analysis of HVR1 and HVR2 and the study of interspecies diversity of cytochrome b (Cyt b) and 16S ribosomal RNA (16S rRNA) mitochondrial genes in forensic and ancient DNA samples. The MCE commercial system tested in this study proved to be a fast and sensitive detection method of length heteroplasmy in cytosine stretches produced by 16 189T>C transitions in HVR1 and by 309.1 and 309.2 C-insertions in HVR2. Moreover, the quantitative analysis of PCR amplicons performed by LIF allowed normalizing the amplicon input in the sequencing reactions, improving the overall quality of sequence data. These quantitative data in combination with the quantification of genomic mtDNA by real-time PCR has been successfully used to evaluate the PCR efficiency and detection limit of full sequencing methods of different mtDNA targets. The quantification of amplicons also provided a method for the rapid evaluation of PCR efficiency of multiplex-PCR versus singleplex-PCR to amplify short HV1 amplicons (around 100 bp) from severely degraded ancient DNA samples. The combination of human-specific (Cyt b) and universal (16S rRNA) mtDNA primer sets in a single PCR reaction followed by MCE detection offers a very rapid and simple screening test to differentiate between human and nonhuman hair forensic samples. This method was also very efficient with degraded DNA templates from forensic hair and bone samples, because of its applicability to detect small amplicon sizes. Future possibilities of MCE in forensic DNA typing, including nuclear STRs and SNP profiling are suggested.
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MESH Headings
- Animals
- Bone and Bones/chemistry
- Cattle
- Cytochromes b/genetics
- DNA Fingerprinting/methods
- DNA, Mitochondrial/analysis
- DNA, Mitochondrial/genetics
- Dogs
- Electrophoresis, Microchip/methods
- Forensic Anthropology/methods
- Forensic Genetics/methods
- Hair/chemistry
- Haplotypes
- Humans
- Mice
- RNA, Ribosomal, 16S/genetics
- Rats
- Receptors, Vasoactive Intestinal Peptide, Type II/genetics
- Receptors, Vasoactive Intestinal Polypeptide, Type I/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Antonio Alonso
- Instituto Nacional de Toxicología y Ciencias Forenses, Servicio de Biología, Madrid, Spain.
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26
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Feng K, Li J, Jiang JH, Shen GL, Yu RQ. QCM detection of DNA targets with single-base mutation based on DNA ligase reaction and biocatalyzed deposition amplification. Biosens Bioelectron 2006; 22:1651-7. [PMID: 16963256 DOI: 10.1016/j.bios.2006.07.023] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 07/04/2006] [Accepted: 07/19/2006] [Indexed: 11/17/2022]
Abstract
A novel biosensing technique for highly specific identification of gene with single-base mutation is proposed based on the implementation of the DNA ligase reaction and the biocatalyzed deposition of an insoluble product. The target gene mediated deposition of an insoluble precipitate is then transduced by quartz crystal microbalance (QCM) measurements. In this method, the DNA target hybridizes with a capture DNA probe tethered onto the gold electrode and then with a biotinylated allele-specific detection DNA. A ligase reaction is performed to generate the ligation between the capture and the detection probes, provided there is perfect match between the DNA target and the detection probe. Otherwise even when there is an allele mismatch between them, no ligation would take place. After thermal treatment at an elevated temperature, the formed duplex melts apart that merely allows the detection probe perfectly matched with the target to remain on the electrode surface. The presence of the biotinylated allele-matched probe is then detected by the QCM via the binding to streptavidin-peroxide horseradish (SA-HRP), which catalyzes the oxidative precipitation of 3,3-diaminobenzidine (DAB) by H2O2 on the electrode and provides an amplified frequency response. The proposed approach has been successfully implemented for the identification of single-base mutation in -28 site of the beta-thalassemia gene with a detection limit of 0.1 nM, demonstrating that this method provides a highly specific and cost-efficient approach for point mutation detection.
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Affiliation(s)
- Kejun Feng
- State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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27
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Ng JKK, Liu WT. Miniaturized platforms for the detection of single-nucleotide polymorphisms. Anal Bioanal Chem 2006; 386:427-34. [PMID: 16821029 DOI: 10.1007/s00216-006-0552-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Revised: 04/29/2006] [Accepted: 05/12/2006] [Indexed: 01/03/2023]
Abstract
Conventional methods for detecting single-nucleotide polymorphisms (SNPs), the most common form of genetic variation in human beings, are mostly limited by their analysis time and throughputs. In contrast, advances in microfabrication technology have led to the development of miniaturized platforms that can potentially provide rapid high-throughput analysis at small sample volumes. This review highlights some of the recent developments in the miniaturization of SNP detection platforms, including microarray-based, bead-based microfluidic and microelectrophoresis-based platforms. Particular attention is paid to their ease of fabrication, analysis time, and level of throughput.
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Affiliation(s)
- Johnson Kian-Kok Ng
- Division of Environmental Science and Engineering, National University of Singapore, 21 Lower Kent Ridge Road, 119077, Singapore, Singapore
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28
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Bienvenue JM, Duncalf N, Marchiarullo D, Ferrance JP, Landers JP. Microchip-based cell lysis and DNA extraction from sperm cells for application to forensic analysis. J Forensic Sci 2006; 51:266-73. [PMID: 16566759 DOI: 10.1111/j.1556-4029.2006.00054.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The current backlog of casework is among the most significant challenges facing crime laboratories at this time. While the development of next-generation microchip-based technology for expedited forensic casework analysis offers one solution to this problem, this will require the adaptation of manual, large-volume, benchtop chemistry to small volume microfluidic devices. Analysis of evidentiary materials from rape kits where semen or sperm cells are commonly found represents a unique set of challenges for on-chip cell lysis and DNA extraction that must be addressed for successful application. The work presented here details the development of a microdevice capable of DNA extraction directly from sperm cells for application to the analysis of sexual assault evidence. A variety of chemical lysing agents are assessed for inclusion in the extraction protocol and a method for DNA purification from sperm cells is described. Suitability of the extracted DNA for short tandem repeat (STR) analysis is assessed and genetic profiles shown. Finally, on-chip cell lysis methods are evaluated, with results from fluorescence visualization of cell rupture and DNA extraction from an integrated cell lysis and purification with subsequent STR amplification presented. A method for on-chip cell lysis and DNA purification is described, with considerations toward inclusion in an integrated microdevice capable of both differential cell sorting and DNA extraction. The results of this work demonstrate the feasibility of incorporating microchip-based cell lysis and DNA extraction into forensic casework analysis.
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Affiliation(s)
- Joan M Bienvenue
- Department of Chemistry, McCormick Road, University of Virginia, Charlottesville, VA 22904, USA
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29
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Legendre LA, Bienvenue JM, Roper MG, Ferrance JP, Landers JP. A Simple, Valveless Microfluidic Sample Preparation Device for Extraction and Amplification of DNA from Nanoliter-Volume Samples. Anal Chem 2006; 78:1444-51. [PMID: 16503592 DOI: 10.1021/ac0516988] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A glass microdevice has been constructed for the on-line integration of solid-phase extraction (SPE) of DNA and polymerase chain reaction (PCR) on a single chip. The chromatography required for SPE in the microfluidic sample preparation device (muSPD) was carried out in a silica bead/sol-gel SPE bed, where the purified DNA was eluted directly into a downstream chamber where conventional thermocycling allowed for PCR amplification of specific DNA target sequences. Through rapid, simple passivation of the PCR chamber with a silanizing reagent, reproducible DNA extraction and amplification was demonstrated from complex biological matrixes in a manner amenable to any research laboratory, using only a syringe pump and a conventional thermocycler. The muSPD allowed for SPE concentration of DNA from 600 nL of blood coupled to subsequent on-chip amplification that yielded a detectable amplicon; this simple device can be applied to a variety of routine genetic analyses without the need for sophisticated instrumentation. In addition, the applicability of these developments to nonconventional thermocycling was demonstrated through the use of noncontact, IR-mediated heating. This was exemplified with the isolation of DNA from an anthrax spore-spiked nasal swab and the subsequent on-chip amplification of target DNA sequences in a total processing time of only 25 min.
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Affiliation(s)
- Lindsay A Legendre
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
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30
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Fixe F, Chu V, Prazeres DMF, Conde JP. Single base mismatch detection by microsecond voltage pulses. Biosens Bioelectron 2005; 21:888-93. [PMID: 16257657 DOI: 10.1016/j.bios.2005.02.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Revised: 02/14/2005] [Accepted: 02/15/2005] [Indexed: 11/26/2022]
Abstract
A single square voltage pulse applied to metal electrodes underneath a silicon dioxide film upon which DNA probes are immobilized allows the discrimination of DNA targets with a single base mismatch during hybridization. Pulse duration, magnitude and slew rate of the voltage pulse are all key factors controlling the rates of electric field assisted hybridization. Although pulses with 1 V, lasting less than 1 ms and with a rise/fall times of 4.5 ns led to maximum hybridization of fully complementary strands, lack of stringency did not allow the discrimination of single base mismatches. However, by choosing pulse conditions that are slightly off the optimum, the selectivity for discriminating single base mismatches could be improved up to a factor approximately 5 when the mismatch was in the middle of the strand and up to approximately 1.5 when the mismatch was on the 5'-end and. These results demonstrate that hybridization with the appropriate electric field pulse provides a new, site-specific, approach to the discrimination of single nucleotide polymorphisms in the sub-millisecond time scale, for addressable DNA microarrays.
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Affiliation(s)
- F Fixe
- INESC-Microsistemas and Nanotecnologias, INESC MN, Rua Alves Redol, 9, 1000-029 Lisboa, Portugal
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31
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Xu B, Tubbs RR, Kottke-Marchant K. Molecular Genetic Testing of Polymorphisms Associated With Venous Thrombosis. ACTA ACUST UNITED AC 2005; 14:193-202. [PMID: 16319689 DOI: 10.1097/01.pas.0000177796.73583.ml] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The growing knowledge of genetic polymorphisms predisposing to venous thrombosis has increased the demand for genetic testing of associated risk factors. This has prompted the need for simple, fast, reliable, and cost-effective genotyping methods for identification of those mutations. In the past decade, a large variety of DNA mutation analysis methods have been developed for detection of genetic variants associated with venous thrombosis, including PCR-based and PCR-independent technologies. Each of these technologies possesses unique advantages, but all have a common goal of simplifying and expediting mutation analysis. This review describes some of the commonly used technologies and commercially available platforms employed in clinical laboratories for genetic testing of thrombophilia. The choice of a technology for each individual laboratory would primarily depend on the specific requirements for the assay's accuracy, reliability, speed, throughput, and cost-effectiveness.
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Affiliation(s)
- Bo Xu
- Department of Clinical Pathology, The Cleveland Clinic Foundation. Cleveland, OH 44195, USA
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Li J, Chu X, Liu Y, Jiang JH, He Z, Zhang Z, Shen G, Yu RQ. A colorimetric method for point mutation detection using high-fidelity DNA ligase. Nucleic Acids Res 2005; 33:e168. [PMID: 16257979 PMCID: PMC1275593 DOI: 10.1093/nar/gni163] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The present study reported proof-of-principle for a genotyping assay approach that can detect single nucleotide polymorphisms (SNPs) through the gold nanoparticle assembly and the ligase reaction. By incorporating the high-fidelity DNA ligase (Tth DNA ligase) into the allele-specific ligation-based gold nanoparticle assembly, this assay provided a convenient yet powerful colorimetric detection that enabled a straightforward single-base discrimination without the need of precise temperature control. Additionally, the ligase reaction can be performed at a relatively high temperature, which offers the benefit for mitigating the non-specific assembly of gold nanoparticles induced by interfering DNA strands. The assay could be implemented via three steps: a hybridization reaction that allowed two gold nanoparticle-tagged probes to hybrid with the target DNA strand, a ligase reaction that generates the ligation between perfectly matched probes while no ligation occurred between mismatched ones and a thermal treatment at a relatively high temperature that discriminate the ligation of probes. When the reaction mixture was heated to denature the formed duplex, the purple color of the perfect-match solution would not revert to red, while the mismatch gave a red color as the assembled gold nanoparticles disparted. The present approach has been demonstrated with the identification of a single-base mutation in codon 12 of a K-ras oncogene that is of significant value for colorectal cancers diagnosis, and the wild-type and mutant type were successfully scored. To our knowledge, this was the first report concerning SNP detection based on the ligase reaction and the gold nanoparticle assembly. Owing to its ease of operation and high specificity, it was expected that the proposed procedure might hold great promise in practical clinical diagnosis of gene-mutant diseases.
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Affiliation(s)
| | | | - Yali Liu
- Clinical Pharmacology Laboratory, Tumor Hospital of Hunan ProvinceChangsha 410012, P. R. China
| | - Jian-Hui Jiang
- To whom correspondence should be addressed. Tel: +86 731 8821355; Fax: +86 731 8821355; or
| | - Zhimin He
- Cancer Research Institute, Xiangya School of Medicine, Central South UniversityChangsha 410078, P. R. China
| | - Zhiwei Zhang
- Cancer Research Institute, Xiangya School of Medicine, Central South UniversityChangsha 410078, P. R. China
| | - Guoli Shen
- To whom correspondence should be addressed. Tel: +86 731 8821355; Fax: +86 731 8821355; or
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Abstract
CE on microchip is an emerging separation technique that has attracted wide attention and gained considerable popularity. Because of miniaturization of the separation format, CE on chip typically offers shorter analysis time and lower reagent consumption with potential development of portable analytical instrumentation. This review with 143 references is focused on proteins and peptides analysis, DNA separation including fragment sizing, genotyping, mutation detection and sequencing, and also the analysis of low-molecular-weight compounds, namely explosive residues and warfare agents, pharmaceuticals and drugs of abuse, and various small molecules in body fluids.
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Szantai E, Ronai Z, Szilagyi A, Sasvari-Szekely M, Guttman A. Haplotyping by capillary electrophoresis. J Chromatogr A 2005; 1079:41-9. [PMID: 16038289 DOI: 10.1016/j.chroma.2005.03.078] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The investigation of the genetic background and phenotype structures of complex diseases, such as cardiovascular or psychiatric disorders and tumors, is one of the most scrutinized fields of the post genomic era. Besides the multiplex analysis of genetic markers and polymorphisms throughout the whole genome, more and more attention is focused on the interaction between the etiological factors of these traits. Haplotype determination, rather than multiplex genotyping seems to be one of the first building blocks of this endeavor. This review focuses on the importance and theoretical background of haplotyping, and summarizes the recent examples of novel and emerging haplotyping techniques by capillary gel electrophoresis based DNA fragment analysis, a powerful tool for the examination of the inheritance of complex traits.
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Affiliation(s)
- Eszter Szantai
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
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35
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Rangel-López A, Maldonado-Rodríguez R, Salcedo-Vargas M, Espinosa-Lara JM, Méndez-Tenorio A, Beattie KL. Low density DNA microarray for detection of most frequent TP53 missense point mutations. BMC Biotechnol 2005; 5:8. [PMID: 15713227 PMCID: PMC553977 DOI: 10.1186/1472-6750-5-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2004] [Accepted: 02/15/2005] [Indexed: 11/13/2022] Open
Abstract
Background We have developed an oligonucleotide microarray (genosensor) utilizing a double tandem hybridization technique to search for 9 point mutations located in the most frequently altered codons of the TP53 gene. Isolated and multiplexed PCR products, 108 and 92 bp long, from exons 7 and 8, respectively, were obtained from 24 different samples. Single-stranded target DNA was then prepared from isolated or multiplexed PCR products, through cyclic DNA synthesis. Independent ssDNA's were annealed with the corresponding pairs of labeled stacking oligonucleotides to create partially duplex DNA having a 7-nt gap, which contains the sequence that will be interrogated by the capture probes forming double tandem hybridization. In the case of multiplexed ssPCR products, only two stacking oligonucleotides were added per target, therefore the gap for the PCR products having two consecutive codons to be interrogated in exon 7 was 12 nt long, so only single tandem hybridization was produced with these respective probes. Results 18 codon substitutions were found by DNA sequencing. In 13 of them a perfect correlation with the pattern of hybridization was seen (In 5 no signal was seen with the wt probe while a new signal was seen with the appropriate mutant probe, and in 8 more, as expected, no signal was seen with any probe due to the absence of the corresponding probe in the array). In 3 other cases a mutation was falsely suggested by the combination of the absence of the wild type signal along with a false signal in the other probe. In the other 2 cases the presence of the mutation was not detected due to the production of a false hybridization signal with the wild type probe. In both cases (false mutation or no mutation detected) relatively stable mismatched target/probe duplexes should be formed. These problems could be avoided by the addition of probes to improve the performance of the array. Conclusion Our results demonstrate that a simple TP53 microarray employing short (7-mer) probes, used in combination with single or double tandem hybridization approach and a simple or multiplex target preparation method, can identify common TP53 missense mutations from a variety of DNA sources with good specificity.
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Affiliation(s)
- Angélica Rangel-López
- Escuela Nacional de Ciencias Biológicas IPN, México, 11340, D. F., México, 11340, D. F., México
- Unidad de Investigación Médica en Enfermedades Oncológicas. Hospital de Oncología. Centro Médico Nacional S XXI. IMSS, México, D. F., México
| | | | - Mauricio Salcedo-Vargas
- Unidad de Investigación Médica en Enfermedades Oncológicas. Hospital de Oncología. Centro Médico Nacional S XXI. IMSS, México, D. F., México
| | | | - Alfonso Méndez-Tenorio
- Escuela Nacional de Ciencias Biológicas IPN, México, 11340, D. F., México, 11340, D. F., México
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Footz T, Somerville MJ, Tomaszewski R, Sprysak KA, Backhouse CJ. Heteroduplex-based genotyping with microchip electrophoresis and dHPLC. ACTA ACUST UNITED AC 2004; 7:283-93. [PMID: 15000804 DOI: 10.1089/109065703322783635] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This work compares the methods of mutation detection via denaturing high-performance liquid chromatography (dHPLC) and a microchip-based heteroduplex analysis (HA) method. The mutations analyzed were 185delAG and 5382insC in BRCA1 and 6174delT in BRCA2 with, as additional examples, 188del11 and 5396 + 1G --> A in BRCA1. Our HA method is based upon the use of a replaceable, highly denaturing sieving matrix that has dynamic coating capabilities, rendering our method relatively insensitive to contamination. We have found significant advantages in the microchip analysis in terms of reagent consumption, ease of use, versatility, simplicity of the protocol, the lack of constraints upon sample preparation or content, and the lack of parameters that need be adjusted. Although HA methods have a lower sensitivity than that of dHPLC, the electropherograms of the present HA method appear to provide more information and may allow mutations within the same amplicon to be distinguished. Although the dHPLC method has a remarkably high sensitivity, with this sensitivity there come constraints that may prevent it, in its present form, from being used in some applications, particularly those involving higher levels of integration. The advantages of the present HA method, along with recent developments in microchip-based single-nucleotide polymorphism (SNP) detection and high-throughput arrays, suggest that microchip-based systems could provide compact and integrated platforms capable of large-scale genotyping or mutational screening.
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Affiliation(s)
- Tim Footz
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta, Canada T6G 2V4
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Xu H, Roddy ES, Roddy TP, Lapos JA, Ewing AG. Parallel separations of oligonucleotides with optically gated sample introduction on multichannel microchips. J Sep Sci 2004; 27:7-12. [PMID: 15335051 DOI: 10.1002/jssc.200301593] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
With the release of the human genome sequence, there has been increasing attention given to other genetic analyses, including the detection of genetic variations and fast sequencing of multiple samples for pharmacogenomics studies. Rapid injections of samples in multiplexed separation channels by optically gated sample introduction are shown here for DNA separation. Serial separations of four amino acids are shown in less than four seconds on a microchip with four multiplexed channels. Five short oligonucleotides have also been rapidly separated in 2% LPA with four channels using this technique. In addition, multiple unique samples have been simultaneously separated and five-base resolution has been demonstrated.
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Affiliation(s)
- Hongwei Xu
- Department of Chemistry, Pennsylvania State University, University, PA 16801, USA
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Ugaz VM, Elms RD, Lo RC, Shaikh FA, Burns MA. Microfabricated electrophoresis systems for DNA sequencing and genotyping applications: current technology and future directions. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2004; 362:1105-29. [PMID: 15306487 DOI: 10.1098/rsta.2003.1365] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Many routine genomic-analysis assays rely on gel electrophoresis to perform size-selective fractionation of DNA fragments in the size range below 1 kb in length. Over the past decade, impressive progress has been made towards the development of microfabricated electrophoresis systems to conduct these assays in a microfluidic lab-on-a-chip format. Since these devices are inexpensive, require only nanolitre sample volumes, and do not rely on the availability of a pre-existing laboratory infrastructure, they are readily deployable in remote field locations for use in a variety of medical and biosensing applications. The design and construction of microfabricated electrophoresis devices poses a variety of challenges, including the need to achieve high-resolution separations over distances of a few centimetres or less, and the need to easily interface with additional microfluidic components to produce self-contained integrated DNA-analysis systems. In this paper, we review recent efforts to develop devices to satisfy these requirements and live up to the promise of fulfilling the growing need for inexpensive portable genomic-analysis equipment.
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Affiliation(s)
- Victor M Ugaz
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA
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40
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Russom A, Tooke N, Andersson H, Stemme G. Single nucleotide polymorphism analysis by allele-specific primer extension with real-time bioluminescence detection in a microfluidic device. J Chromatogr A 2004; 1014:37-45. [PMID: 14558610 DOI: 10.1016/s0021-9673(03)01033-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A microfluidic approach for rapid bioluminescent real-time detection of single nucleotide polymorphism (SNP) is presented. The method is based on single-step primer extension using pyrosequencing chemistry to monitor nucleotide incorporations in real-time. The method takes advantage of the fact that the reaction kinetics differ between matched and mismatched primer-template configurations. We show here that monitoring the initial reaction in real time accurately scores SNPs by comparing the initial reaction kinetics between matched and mismatched configurations. Thus, no additional treatment is required to improve the sequence specificity of the extension, which has been the case for many allele-specific extension assays. The microfluidic approach was evaluated using four SNPs. Three of the SNPs included primer-template configurations that have been previously reported to be difficult to resolve by allele-specific primer extension. All SNPs investigated were successfully scored. Using the microfluidic device, the volume for the bioluminescent assay was reduced dramatically, thus offering a cost-effective and fast SNP analysis method.
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Affiliation(s)
- Aman Russom
- Department of Signals, Sensors and Systems, Microsystem Technology, Royal Institute of Technology, SE-100 44 Stockholm, Sweden.
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41
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Liu Y, Garcia CD, Henry CS. Recent progress in the development of muTAS for clinical analysis. Analyst 2003; 128:1002-8. [PMID: 12964597 DOI: 10.1039/b306278n] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Yan Liu
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
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Affiliation(s)
- James P Landers
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA.
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Li ZP, Tsunoda H, Okano K, Nagai K, Kambara H. Microchip Electrophoresis of Tagged Probes Incorporated with One-Colored ddNTP for Analyzing Single-Nucleotide Polymorphisms. Anal Chem 2003; 75:3345-51. [PMID: 14570183 DOI: 10.1021/ac020624i] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We demonstrate a simple and rapid method for SNP typing, allele frequency determination, and trace mutant analysis that works with even an inexpensive detection system. This method is based on microchip electrophoresis of tagged probes incorporated with one-colored ddNTP (METPOC). The assay uses dye terminator incorporation into a pair of probes of different lengths specific to wild- and mutant-type targets, respectively. They are hybridized to the targets prior to ddNTP-Cy-5 incorporation, which occurs only for a matched probe-target duplex. Because the extension reactions for the two probes are carried out simultaneously in one tube and the products from both probes are analyzed in one channel by one-color fluorescence detection, an accurate comparative analysis of SNPs is possible. SNP typing as well as allele frequency determination in the range above 0.1% can easily be carried out using a commercial microchip electrophoresis system in a few minutes.
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Affiliation(s)
- Zheng-ping Li
- Hitachi Ltd., Central Research Laboratory, 1-280 Higashi-koigakubo, Kokubunji, Tokyo 185-8601, Japan
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Abstract
Currently, there is no single method to collect, process, and analyze a water sample for all pathogenic microorganisms of interest. Some of the difficulties in developing a universal method include the physical differences between the major pathogen groups (viruses, bacteria, protozoa), efficiently concentrating large volume water samples to detect low target concentrations of certain pathogen groups, removing co-concentrated inhibitors from the sample, and standardizing a culture-independent endpoint detection method. Integrating the disparate technologies into a single, universal, simple method and detection system would represent a significant advance in public health and microbiological water quality analysis. Recent advances in sample collection, on-line sample processing and purification, and DNA microarray technologies may form the basis of a universal method to detect known and emerging waterborne pathogens. This review discusses some of the challenges in developing a universal pathogen detection method, current technology that may be employed to overcome these challenges, and the remaining needs for developing an integrated pathogen detection and monitoring system for source or finished water.
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Affiliation(s)
- Timothy M Straub
- Analytical Microbiology Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999 MSIN P7-50, Richland, WA 99352, USA.
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Tullo A, D'Erchia AM, Sbisà E. Methods for screening tumors for p53 status and therapeutic exploitation. Expert Rev Mol Diagn 2003; 3:289-301. [PMID: 12779005 DOI: 10.1586/14737159.3.3.289] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mutations in the p53 oncosuppressor gene occur in most human cancers and regulation of the protein is defective in a variety of others. Novel strategies are emerging for the treatment of tumors that have p53 mutations. In this context, the analysis of p53 status is useful in diagnosis and prognosis, and could serve to evaluate the effectiveness of a cancer treatment. In this review, we report an overview of major methods for screening tumors for p53 status and the major strategies suggested for restoring p53 function.
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Affiliation(s)
- Apollonia Tullo
- Sezione di Bioinformatica e Genomica di Bari, Istituto di Tecnologie Biomediche, CNR, via Amendola 165/A, 70126 Bari, Italy.
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Abstract
Miniaturized instruments have developed very quickly in the last decade. This review is focused on the microchip electrophoresis-based separation of DNA. Fundamentals, including the chip format, substrates and fabrication technologies, fluid control, as well as various detection methods, are summarized. Array electrophoresis microchip and the on-chip integration of electrophoresis with other systems are introduced as well. In addition, the application of microchip electrophoresis in DNA sizing, genetic analysis and DNA sequencing are also presented in this paper.
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Affiliation(s)
- Lihua Zhang
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, The University of Tokushima, CREST, Japan Science and Technology Corporation (JST), Shomachi, Tokushima 770-8505, Japan.
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Babon JJ, McKenzie M, Cotton RGH. The use of resolvases T4 endonuclease VII and T7 endonuclease I in mutation detection. Mol Biotechnol 2003; 23:73-81. [PMID: 12611271 DOI: 10.1385/mb:23:1:73] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Mutation and polymorphism detection is of increasing importance in the field of molecular genetics. This is reflected by the plethora of chemical, enzymatic, and physically based methods of mutation detection. The ideal method would detect mutations in large fragments of DNA and position them to single base-pair (bp) accuracy. Few methods are able to quickly screen kilobase lengths of DNA and position the mutation at the same time. The Enzyme Mismatch Cleavage (EMC) method of mutation detection is able to reliably detect nearly 100% of mutations in DNA fragments as large as 2 kb and position them to within 6 bp. This method exploits the activity of a resolvase enzyme from T4, T4 endonuclease VII, and, more recently, a second bacteriophage resolvase, T7 endonuclease I. The technique uses these enzymes to digest heteroduplex DNA formed by annealing wild-type and mutant DNA. Digestion fragments indicate the presence, and the position, of any mutations. The method is robust and reliable and much faster and cheaper than sequencing. These attributes have resulted in its increasing use in the field of mutation detection.
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Affiliation(s)
- J J Babon
- National Institute Medical Research, Mill Hill, London NW7 1AA, UK.
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Xue MZ, Bonny O, Morgenthaler S, Bochud M, Mooser V, Thilly WG, Schild L, Leong-Morgenthaler PM. Use of Constant Denaturant Capillary Electrophoresis of Pooled Blood Samples to Identify Single-Nucleotide Polymorphisms in the Genes (Scnn1a and Scnn1b) Encoding the α and β Subunits of the Epithelial Sodium Channel. Clin Chem 2002. [DOI: 10.1093/clinchem/48.5.718] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Background: The epithelial sodium channel (ENaC) is composed of three homologous subunits: α, β, and γ. Mutations in the Scnn1b and Scnn1g genes, which encode the β and the γ subunits of ENaC, cause a severe form of hypertension (Liddle syndrome). The contribution of genetic variants within the Scnn1a gene, which codes for the α subunit, has not been investigated.
Methods: We screened for mutations in the COOH termini of the α and β subunits of ENaC. Blood from 184 individuals from 31 families participating in a study on the genetics of hypertension were analyzed. Exons 13 of Scnn1a and Scnn1b, which encode the second transmembrane segment and the COOH termini of α- and β-ENaC, respectively, were amplified from pooled DNA samples of members of each family by PCR. Constant denaturant capillary electrophoresis (CDCE) was used to detect mutations in PCR products of the pooled DNA samples.
Results: The detection limit of CDCE for ENaC variants was 1%, indicating that all members of any family or up to 100 individuals can be analyzed in one CDCE run. CDCE profiles of the COOH terminus of α-ENaC in pooled family members showed that the 31 families belonged to four groups and identified families with genetic variants. Using this approach, we analyzed 31 rather than 184 samples. Individual CDCE analysis of members from families with different pooled CDCE profiles revealed five genotypes containing 1853G→T and 1987A→G polymorphisms. The presence of the mutations was confirmed by DNA sequencing. For the COOH terminus of β-ENaC, only one family showed a different CDCE profile. Two members of this family (n = 5) were heterozygous at 1781C→T (T594M).
Conclusion: CDCE rapidly detects point mutations in these candidate disease genes.
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Affiliation(s)
- Ming-Zhan Xue
- Institute of Pharmacology and Toxicology, Rue du Bugnon 27, 1005 Lausanne, Switzerland
| | - Olivier Bonny
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois (CHUV), 1005 Lausanne, Switzerland
| | - Stephan Morgenthaler
- Department of Mathematics, Swiss Federal Institute of Technology-Lausanne, 1015 Lausanne, Switzerland
| | - Murielle Bochud
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois (CHUV), 1005 Lausanne, Switzerland
| | - Vincent Mooser
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois (CHUV), 1005 Lausanne, Switzerland
| | - William G Thilly
- Program in Epidemiology and Human Genetics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Laurent Schild
- Institute of Pharmacology and Toxicology, Rue du Bugnon 27, 1005 Lausanne, Switzerland
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Item C, Hagerty BP, Mühl A, Greber-Platzer S, Stöckler-Ipsiroglu S, Strobl W. Mutations at the galactose-1-p-uridyltransferase gene in infants with a positive galactosemia newborn screening test. Pediatr Res 2002; 51:511-6. [PMID: 11919338 DOI: 10.1203/00006450-200204000-00018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Newborn screening for galactosemia yields a high number of false-positive results. Confirmatory DNA testing for unknown galactosemia mutations on the initial positive sample using novel techniques of mutation detection tenders itself to reduce the recall rate. The potential benefits of confirmatory DNA testing, however, could be offset by the detection of a high percentage of galactosemia carriers, Duarte/galactosemia compound heterozygotes, and infants with benign sequence changes in the galactose-1-phosphate uridyltransferase (GALT) gene among infants with a positive biochemical screening test. Our aim was to determine the frequency and allelic distribution of all sequence changes in the GALT gene in 110 newborns with a positive total galactose screening test among 43,688 Austrian newborns screened consecutively. We found that only 20 of the 110 probands carried at least one known or novel candidate galactosemia mutation (one galactosemia homozygote, 7 Duarte/galactosemia compounds, 12 carriers) as judged by denaturing gradient gel electrophoresis and cleavage fragment length polymorphism analysis. Four novel galactosemia candidate mutations (Q9H, A46fsdelCAGCT, M129T, L342I) were identified. Sixty-seven probands had no detectable sequence changes and 23 carried only the benign Duarte or Los Angeles variant alleles or silent mutations. We conclude that a rapid and automatable confirmation test for unknown GALT mutations, e.g. on a high-density oligonucleotide array basis, has the potential to lower the recall rate of galactosemia screening in our population by about five-fold from 0.25 to 0.046%. Further research, however, will be required before the development of such a test can be advocated.
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Affiliation(s)
- Chike Item
- Department of Pediatrics, University of Vienna, Austria
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Fielden MR, Matthews JB, Fertuck KC, Halgren RG, Zacharewski TR. In silico approaches to mechanistic and predictive toxicology: an introduction to bioinformatics for toxicologists. Crit Rev Toxicol 2002; 32:67-112. [PMID: 11951993 DOI: 10.1080/20024091064183] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Bioinformatics, or in silico biology, is a rapidly growing field that encompasses the theory and application of computational approaches to model, predict, and explain biological function at the molecular level. This information rich field requires new skills and new understanding of genome-scale studies in order to take advantage of the rapidly increasing amount of sequence, expression, and structure information in public and private databases. Toxicologists are poised to take advantage of the large public databases in an effort to decipher the molecular basis of toxicity. With the advent of high-throughput sequencing and computational methodologies, expressed sequences can be rapidly detected and quantitated in target tissues by database searching. Novel genes can also be isolated in silico, while their function can be predicted and characterized by virtue of sequence homology to other known proteins. Genomic DNA sequence data can be exploited to predict target genes and their modes of regulation, as well as identify susceptible genotypes based on single nucleotide polymorphism data. In addition, highly parallel gene expression profiling technologies will allow toxicologists to mine large databases of gene expression data to discover molecular biomarkers and other diagnostic and prognostic genes or expression profiles. This review serves to introduce to toxicologists the concepts of in silico biology most relevant to mechanistic and predictive toxicology, while highlighting the applicability of in silico methods using select examples.
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Affiliation(s)
- Mark R Fielden
- Department of Biochemistry and Molecular Biology, National Food Safety and Toxicology Center, Michigan State University, East Lansing 48824, USA
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