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Gao F, Tie C, Zhang XX, Niu Z, He X, Ma Y. Star-shaped polymers for DNA sequencing by capillary electrophoresis. J Chromatogr A 2011; 1218:3037-41. [DOI: 10.1016/j.chroma.2011.03.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 03/08/2011] [Accepted: 03/13/2011] [Indexed: 10/18/2022]
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2
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Jiang SY, Ramachandran S. Natural and artificial mutants as valuable resources for functional genomics and molecular breeding. Int J Biol Sci 2010; 6:228-51. [PMID: 20440406 PMCID: PMC2862397 DOI: 10.7150/ijbs.6.228] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 04/20/2010] [Indexed: 12/31/2022] Open
Abstract
With the completion of rice genome sequencing, large collection of expression data and the great efforts in annotating rice genomes, the next challenge is to systematically assign functions to all predicted genes in the genome. The generations and collections of mutants at the genome-wide level form technological platform of functional genomics. In this study, we have reviewed currently employed tools to generate such mutant populations. These tools include natural, physical, chemical, tissue culture, T-DNA, transposon or gene silencing based mutagenesis. We also reviewed how these tools were used to generate a large collection of mutants and how these mutants can be screened and detected for functional analysis of a gene. The data suggested that the current population of mutants might be large enough to tag all predicted genes. However, the collection of flanking sequencing tags (FSTs) is limited due to the relatively higher cost. Thus, we have proposed a new strategy to generate gene-silencing mutants at the genome-wide level. Due to the large collection of insertion mutants, the next step to rice functional genomics should be focusing on functional characterization of tagged genes by detailed survey of corresponding mutants. Additionally, we also evaluated the utilization of these mutants as valuable resources for molecular breeding.
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Affiliation(s)
| | - Srinivasan Ramachandran
- Rice Functional Genomics Group, Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604
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3
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Abstract
Analysis and detection of DNA variation is important in any field of biology. Hence, numerous methods have been developed to analyze DNA. A simple yet effective way of analyzing DNA is by denaturant capillary electrophoresis (DCE). The method is in theory applicable to 95% of the human genome. The method involves three steps; fragment design, PCR amplification and allele separation. The allele separation can in principle be performed with any DNA capillary sequencing instrument.
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4
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Ekstrøm PO, Khrapko K, Li-Sucholeiki XC, Hunter IW, Thilly WG. Analysis of mutational spectra by denaturing capillary electrophoresis. Nat Protoc 2008; 3:1153-66. [PMID: 18600220 PMCID: PMC2742298 DOI: 10.1038/nprot.2008.79] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The point mutational spectrum over nearly any 75- to 250-bp DNA sequence isolated from cells, tissues or large populations may be discovered using denaturing capillary electrophoresis (DCE). A modification of the standard DCE method that uses cycling temperature (e.g., +/-5 degrees C), CyDCE, permits optimal resolution of mutant sequences using computer-defined target sequences without preliminary optimization experiments. The protocol consists of three steps: computer design of target sequence including polymerase chain reaction (PCR) primers, high-fidelity DNA amplification by PCR and mutant sequence separation by CyDCE and takes about 6 h. DCE and CyDCE have been used to define quantitative point mutational spectra relating to errors of DNA polymerases, human cells in development and carcinogenesis, common gene-disease associations and microbial populations. Detection limits are about 5 x 10(-3) (mutants copies/total copies) but can be as low as 10(-6) (mutants copies/total copies) when DCE is used in combination with fraction collection for mutant enrichment. No other technological approach for unknown mutant detection and enumeration offers the sensitivity, generality and efficiency of the approach described herein.
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Affiliation(s)
- Per O Ekstrøm
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA. or
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5
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Affiliation(s)
- Karel Klepárník
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
| | - Petr Boček
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
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Issaq HJ. THIRTY-FIVE YEARS OF CAPILLARY ELECTROPHORESIS: ADVANCES AND PERSPECTIVES. J LIQ CHROMATOGR R T 2007. [DOI: 10.1081/jlc-120004015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Haleem J. Issaq
- a Analytical Chemistry Laboratory, SAIC-Frederick, Inc. , National Cancer Institute at Frederick , P.O.Box B, Frederick , MD , 21702 , U.S.A
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7
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Kang D, Hamasaki N. Mitochondrial disease: maintenance of mitochondrial genome and molecular diagnostics. Adv Clin Chem 2006; 42:217-54. [PMID: 17131628 DOI: 10.1016/s0065-2423(06)42006-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mitochondrial DNA (mtDNA) is essential for the aerobic ATP synthesis system that is responsible for about 80% of normal cellular energy demands. In addition to rare genetic disorders causing neuromyopathy, alterations of mtDNA have been found also in so-called common diseases such as heart failure, diabetes, and cancer. Although some of these alterations are inherited, some are considered to be generated and/or accumulated in somatic cells with age. One reason for the somatic mutations is that mtDNA is more vulnerable than is nuclear DNA. For example, mitochondrial respiratory chain produces a large amount of reactive oxygen species as inevitable byproducts of oxidative phosphorylation. However, the molecular mechanisms for maintenance of mitochondrial genome are much less elucidated than those for nuclear genome. In spite of its increasing importance, the molecular diagnosis of mitochondrial DNA-related diseases is well done only in very limited expert laboratories. In this chapter, we focus on maintenance of mtDNA in somatic cells, its clinical importance, and recent developments of molecular tests.
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Affiliation(s)
- Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
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8
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Sang F, Ren H, Ren J. Genetic mutation analysis by CE with LIF detection using inverse-flow derivatization of DNA fragments. Electrophoresis 2006; 27:3846-55. [PMID: 16941450 DOI: 10.1002/elps.200600160] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Inverse-flow derivatization is a novel approach to obtain fluorescent DNA derivatives in DNA analysis based on CE with LIF detection. In the present work, we want to explore the feasibility of the application of this method into the mutation detection based on constant denaturant capillary electrophoresis (CDCE) and SSCP analysis. The DNA fragments were first amplified by PCR using a pair of common primers without fluorescent label, and then the mutations were determined by CDCE or SSCP analysis based on CE-LIF with inverse-flow derivatization of DNA fragments. The experimental conditions were investigated systematically, and different labeling modes including inverse-flow derivatization, on-column derivatization and fluorescent labeled primer technique were compared. The inverse-flow derivatization was successfully used in the detection of C677T mutation in the methylenetetrahydrofolate reductase gene by CDCE or SSCP analysis. Our preliminary results demonstrate that inverse-flow derivatization is very simple, inexpensive and sensitive and well suitable for the genetic analysis in clinical diagnosis.
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Affiliation(s)
- Fuming Sang
- College of Chemistry and Chemical Engineering, Shanghai Jiaotong University, Shanghai, P. R. China
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9
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Peters T, Sedlmeier R. Current methods for high-throughput detection of novel DNA polymorphisms. DRUG DISCOVERY TODAY. TECHNOLOGIES 2006; 3:123-129. [PMID: 24980398 DOI: 10.1016/j.ddtec.2006.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
For research varying from the identification of specific disease loci to the investigation of protein function, the detection of DNA sequence variations requires reliable methods. Technologies enabling rapid and cost effective identification of novel genetic polymorphisms will significantly impact future work in genetic mapping studies, drug target discovery and validation and pharmacogenomics.:
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Affiliation(s)
- Thomas Peters
- Ingenium Pharmaceuticals AG, Fraunhoferstr. 13, 82152 Martinsried, Germany
| | - Reinhard Sedlmeier
- Ingenium Pharmaceuticals AG, Fraunhoferstr. 13, 82152 Martinsried, Germany.
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Li Q, Deka C, Glassner BJ, Arnold K, Li-Sucholeiki XC, Tomita-Mitchell A, Thilly WG, Karger BL. Design of an automated multicapillary instrument with fraction collection for DNA mutation discovery by constant denaturant capillary electrophoresis (CDCE). J Sep Sci 2005; 28:1375-89. [PMID: 16138690 DOI: 10.1002/jssc.200500023] [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: 12/16/2022]
Abstract
A fundamental goal ingenomics is the discovery of genetic variation that contributes to disease states or to differential drug responses. Single nucleotide polymorphism (SNP) detection has been the focus of much attention in the study of genetic variation over the last decade. These SNPs typically occur at a frequency greater than 1% in the human genome. Recently, low-frequency alleles are also being increasingly recognized as critical to obtain an improved understanding of the correlation between genetic variation and disease. Although many methods have been reported for the discovery and scoringof SNPs, sensitive, automated, and cost-effective methods and platforms for the discovery of low-frequency alleles are not yet readily available. We describe here an automated multicapillary instrument for high-throughput detection of low-frequency alleles from pooled samples using constant denaturant capillary electrophoresis. The instrument features high optical sensitivity (1 x 10(-12) M fluorescein detection limit), precise and stable temperature control (+/- 0.01degrees C), and automation for sample delivery, injection, matrix replacement, and fraction collection. The capillary array is divided into six groups of four capillaries, each of which can be independently set at any temperature ranging from room temperature to 90 degrees C. The key performance characteristics of the instrument are reported.
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Affiliation(s)
- Qingbo Li
- SpectruMedix LLC, State College, PA, USA.
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11
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Bjørheim J, Ekstrøm PO. Review of denaturant capillary electrophoresis in DNA variation analysis. Electrophoresis 2005; 26:2520-30. [PMID: 15934053 DOI: 10.1002/elps.200410403] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Analyses of germline and somatic single-nucleotide DNA variations are important in both population genetics research and clinical practice. Reliable and inexpensive methods that are flexible and designed for automation are required for these analyses. Present day DNA sequencing technology is too expensive for testing all 22-25 000 human genes in populations genetics studies or in scanning large numbers of tumors for novel mutations. Denaturant capillary electrophoresis (DCE) has the potential to meet the need for large-scale analysis of DNA variants. Several different analyses can be performed by DCE, including mutation analysis, single-nucleotide polymorphism (SNP) discovery in individual and pooled samples, detection of allelic imbalance, and determination of microhaplotypes. Here we review the theoretical background of the method, its sensitivity, specificity, detection limit, throughput, and repeatability in the light of current literature in the field.
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Affiliation(s)
- Jens Bjørheim
- Section for Immunotherapy, Department of Immunology, Institute for Cancer Research, University of Oslo, Oslo, Norway
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12
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Li-Sucholeiki XC, Tomita-Mitchell A, Arnold K, Glassner BJ, Thompson T, Murthy JV, Berk L, Lange C, Leong-Morgenthaler PM, MacDougall D, Munro J, Cannon D, Mistry T, Miller A, Deka C, Karger B, Gillespie KM, Ekstrøm PO, Todd JA, Thilly WG. Detection and frequency estimation of rare variants in pools of genomic DNA from large populations using mutational spectrometry. Mutat Res 2005; 570:267-80. [PMID: 15708585 DOI: 10.1016/j.mrfmmm.2004.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Accepted: 11/29/2004] [Indexed: 11/21/2022]
Abstract
DNA variants underlying the inheritance of risk for common diseases are expected to have a wide range of population allele frequencies. The detection and scoring of the rare alleles (at frequencies of <0.01) presents significant practical problems, including the requirement for large sample sizes and the limitations inherent in current methodologies for allele discrimination. In the present report, we have applied mutational spectrometry based on constant denaturing capillary electrophoresis (CDCE) to DNA pools from large populations in order to improve the prospects of testing the role of rare variants in common diseases on a large scale. We conducted a pilot study of the cytotoxic T lymphocyte-associated antigen-4 gene (CTLA4) in type 1 diabetes (T1D). A total of 1228 bp, comprising 98% of the CTLA4 coding sequence, all adjacent intronic mRNA splice sites, and a 3' UTR sequence were scanned for unknown point mutations in pools of genomic DNA from a control population of 10,464 young American adults and two T1D populations, one American (1799 individuals) and one from the United Kingdom (2102 individuals). The data suggest that it is unlikely that rare variants in the scanned regions of CTLA4 represent a significant proportion of T1D risk and illustrate that CDCE-based mutational spectrometry of DNA pools offers a feasible and cost-effective means of testing the role of rare variants in susceptibility to common diseases.
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13
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Hsieh MM, Chang PL, Chang HT. The impact of a plug of salts on the analysis of large volumes of dsDNA by capillary electrophoresis. Electrophoresis 2002; 23:2388-93. [PMID: 12210193 DOI: 10.1002/1522-2683(200208)23:15<2388::aid-elps2388>3.0.co;2-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A partially filling technique for the analysis of DNA markers and polymerase chain reaction (PCR) products by capillary electrophoresis in the presence of electroosmotic flow using polymer solutions is presented. Either after or prior to the sample injection, a plug of salts at high pH was hydrodynamically injected. During the separation, poly(ethylene oxide) (PEO) solution entered the capillary. We have found that the position, length, and composition of the plugs affect the sensitivity, resolution, and speed on the analysis of PhiX-174/HaeIII DNA restriction fragments or a DNA mixture (pBR 322/HaeIII digest, pBR 328/BglI digest and pBR 328/HinfI digest) with different degrees. Through careful evaluation of the impact of anions and cations on the analysis of DNA, we have suggested that the optimal condition is applying a plug consisting of 32 mM NaCl and 0.01 M NaOH at 30 cm height for 60 s after sample injection. In the presence of such a plug, PEO adsorption reduces, and thus the separation is faster, as well as the sensitivity improves. Using this condition, the analysis of a DNA mixture (injected at 30 cm for 360 s) containing ten different PCR products amplified after 17 cycles was complete in 25 min. About a 2000-fold improvement in the sensitivity was achieved when compared to that by a conventional method (10 s injection) without applying a plug.
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Affiliation(s)
- Ming-Mu Hsieh
- Department of Chemistry, National Taiwan University, Taipei, Taiwan, ROC
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14
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Bjørheim J, Gaudernack G, Ekstrøm PO. Melting gel techniques in single nucleotide polymorphism and mutation detection: From theory to automation. J Sep Sci 2002. [DOI: 10.1002/1615-9314(20020701)25:10/11<637::aid-jssc637>3.0.co;2-l] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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15
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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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Nekhaeva E, Bodyak ND, Kraytsberg Y, McGrath SB, Van Orsouw NJ, Pluzhnikov A, Wei JY, Vijg J, Khrapko K. Clonally expanded mtDNA point mutations are abundant in individual cells of human tissues. Proc Natl Acad Sci U S A 2002; 99:5521-6. [PMID: 11943860 PMCID: PMC122802 DOI: 10.1073/pnas.072670199] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Using single-cell sequence analysis, we discovered that a high proportion of cells in tissues as diverse as buccal epithelium and heart muscle contain high proportions of clonal mutant mtDNA expanded from single initial mutant mtDNA molecules. We demonstrate that intracellular clonal expansion of somatic point mutations is a common event in normal human tissues. This finding implies efficient homogenization of mitochondrial genomes within individual cells. Significant qualitative differences observed between the spectra of clonally expanded mutations in proliferating epithelial cells and postmitotic cardiomyocytes suggest, however, that either the processes generating these mutations or mechanisms driving them to homoplasmy are likely to be fundamentally different between the two tissues. Furthermore, the ability of somatic mtDNA mutations to expand (required for their phenotypic expression), as well as their apparently high incidence, reinforces the possibility that these mutations may be involved actively in various physiological processes such as aging and degenerative disease. The abundance of clonally expanded point mutations in individual cells of normal tissues also suggests that the recently discovered accumulation of mtDNA mutations in tumors may be explained by processes that are similar or identical to those operating in the normal tissue.
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Affiliation(s)
- Ekaterina Nekhaeva
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115, USA
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17
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Abstract
A continuous spatial temperature gradient was established in capillary electrophoresis by using a simple temperature control device. The temperature profile along the capillary was predicted by theoretical calculations. A nearly linear spatial temperature gradient was established and applied to DNA mutation detection. By spanning a wide temperature range, it was possible to perform simultaneous heteroduplex analysis for various mutation types that have different melting temperatures.
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Affiliation(s)
- L Zhu
- Department of Chemistry National University of Singapore, Republic of Singapore
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18
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Ren J, Fang ZF. Separation of DNA fragments and single strand conformation polymorphism analysis in bare capillaries using poly(acrylamide-dimethylacrylamide) as a separation medium. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 2001; 761:139-45. [PMID: 11587343 DOI: 10.1016/s0378-4347(01)00234-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A short chain poly(acrylamide-dimethylacrylamide) (PADMA) was synthesized in aqueous phase using isopropanol as a chain transfer agent, and was characterized according to the chemical composition and molecular mass. This polymer can form a stable dynamic coating on the inner surface of the capillary, thereby suppressing the electroosmotic flow and DNA-capillary wall interaction. The sieving medium has low viscosity and capillary filling with this medium and medium replacement were conveniently carried out by commercial capillary electrophoresis instruments. The effects of components and concentration of copolymers on the separation of DNA fragments were investigated. Highly efficient separation of DNA fragments, successful single strand conformation polymorphism (SSCP) analysis and good reproducibility of the migration time were obtained in bare capillaries using these copolymers as sieving media. Our preliminary results demonstrate that PADMA will become an alternative matrix for DNA separation by capillary electrophoresis.
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Affiliation(s)
- J Ren
- College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, PR China.
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McCallum CM, Comai L, Greene EA, Henikoff S. Targeting induced local lesions IN genomes (TILLING) for plant functional genomics. PLANT PHYSIOLOGY 2000; 123:439-42. [PMID: 10859174 PMCID: PMC1539256 DOI: 10.1104/pp.123.2.439] [Citation(s) in RCA: 422] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
- C M McCallum
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
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Abstract
Since the introduction of the first commercial capillary electrophoresis (CE) instrument a decade ago, CE applications have become widespread. Today, CE is a versatile analytical technique which is successfully used for the separation of small ions, neutral molecules, and large biomolecules and for the study of physicochemical parameters. It is being utilized in widely different fields, such as analytical chemistry, forensic chemistry, clinical chemistry, organic chemistry, natural products, pharmaceutical industry, chiral separations, molecular biology, and others. It is not only used as a separation technique but to answer physicochemical questions. In this review, we will discuss different modes of CE such as capillary zone electrophoresis, micellar electrokinetic chromatography, capillary gel electrophoresis, capillary isoelectric focusing, and capillary electrochromatography, and will comment on the future direction of CE, including array capillary electrophoresis and array microchip separations.
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21
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Kwok PY. Finding a Needle in a Haystack: Detection and Quantification of Rare Mutant Alleles Are Coming of Age. Clin Chem 2000. [DOI: 10.1093/clinchem/46.5.593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Pui-Yan Kwok
- Departments of Dermatology and Genetics, Washington University School of Medicine, 660 S. Euclid Ave., Box 8123, St. Louis, MO 63110, Fax 314-362-8159, E-mail
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Abstract
With the accumulation of large-scale sequence data, emphasis in genomics has shifted from determining gene structure to testing gene function, and this relies on reverse genetic methodology. Here we explore the feasibility of screening for chemically induced mutations in target sequences in Arabidopsis thaliana. Our TILLING (Targeting Induced Local Lesions IN Genomes) method combines the efficiency of ethyl methanesulfonate (EMS)-induced mutagenesis with the ability of denaturing high-performance liquid chromatography (DHPLC) to detect base pair changes by heteroduplex analysis. Importantly, this method generates a wide range of mutant alleles, is fast and automatable, and is applicable to any organism that can be chemically mutagenized.
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Affiliation(s)
- C M McCallum
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
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