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Saito Y, Komatsu K. Functional Role of NBS1 in Radiation Damage Response and Translesion DNA Synthesis. Biomolecules 2015; 5:1990-2002. [PMID: 26308066 PMCID: PMC4598784 DOI: 10.3390/biom5031990] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/11/2015] [Accepted: 08/13/2015] [Indexed: 12/15/2022] Open
Abstract
Nijmegen breakage syndrome (NBS) is a recessive genetic disorder characterized by increased sensitivity to ionizing radiation (IR) and a high frequency of malignancies. NBS1, a product of the mutated gene in NBS, contains several protein interaction domains in the N-terminus and C-terminus. The C-terminus of NBS1 is essential for interactions with MRE11, a homologous recombination repair nuclease, and ATM, a key player in signal transduction after the generation of DNA double-strand breaks (DSBs), which is induced by IR. Moreover, NBS1 regulates chromatin remodeling during DSB repair by histone H2B ubiquitination through binding to RNF20 at the C-terminus. Thus, NBS1 is considered as the first protein to be recruited to DSB sites, wherein it acts as a sensor or mediator of DSB damage responses. In addition to DSB response, we showed that NBS1 initiates Polη-dependent translesion DNA synthesis by recruiting RAD18 through its binding at the NBS1 C-terminus after UV exposure, and it also functions after the generation of interstrand crosslink DNA damage. Thus, NBS1 has multifunctional roles in response to DNA damage from a variety of genotoxic agents, including IR.
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Affiliation(s)
- Yuichiro Saito
- Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Kenshi Komatsu
- Genome Repair Dynamics, Radiation Biology Center, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan.
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2
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Hakenberg S, Hügle M, Meyer P, Behrmann O, Dame G, Urban G. Fenton fragmentation for faster electrophoretic on chip purification of amplifiable genomic DNA. Biosens Bioelectron 2015; 67:49-52. [DOI: 10.1016/j.bios.2014.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/22/2014] [Accepted: 06/01/2014] [Indexed: 12/01/2022]
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3
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Corrigan DK, Schulze H, Henihan G, Hardie A, Ciani I, Giraud G, Terry JG, Walton AJ, Pethig R, Ghazal P, Crain J, Campbell CJ, Templeton KE, Mount AR, Bachmann TT. Development of a PCR-free electrochemical point of care test for clinical detection of methicillin resistant Staphylococcus aureus (MRSA). Analyst 2014; 138:6997-7005. [PMID: 24093127 DOI: 10.1039/c3an01319g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An MRSA assay requiring neither labeling nor amplification of target DNA has been developed. Sequence specific binding of fragments of bacterial genomic DNA is detected at femtomolar concentrations using electrochemical impedance spectroscopy (EIS). This has been achieved using systematic optimisation of probe chemistry (PNA self-assembled monolayer film on gold electrode), electrode film structure (the size and nature of the chemical spacer) and DNA fragmentation, as these are found to play an important role in assay performance. These sensitivity improvements allow the elimination of the PCR step and DNA labeling and facilitate the development of a simple and rapid point of care test for MRSA. Assay performance is then evaluated and specific direct detection of the MRSA diagnostic mecA gene from genomic DNA, extracted directly from bacteria without further treatment is demonstrated for bacteria spiked into saline (10(6) cells per mL) on gold macrodisc electrodes and into human wound fluid (10(4) cells per mL) on screen printed gold electrodes. The latter detection level is particularly relevant to clinical requirements and point of care testing where the general threshold for considering a wound to be infected is 10(5) cells per mL. By eliminating the PCR step typically employed in nucleic acid assays, using screen printed electrodes and achieving sequence specific discrimination under ambient conditions, the test is extremely simple to design and engineer. In combination with a time to result of a few minutes this means the assay is well placed for use in point of care testing.
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Affiliation(s)
- D K Corrigan
- Division of Pathway Medicine, Medical School, The University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, Scotland, UK.
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4
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Flexible programming of cell-free protein synthesis using magnetic bead-immobilized plasmids. PLoS One 2012; 7:e34429. [PMID: 22470570 PMCID: PMC3314631 DOI: 10.1371/journal.pone.0034429] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 03/01/2012] [Indexed: 01/23/2023] Open
Abstract
The use of magnetic bead-immobilized DNA as movable template for cell-free protein synthesis has been investigated. Magnetic microbeads containing chemically conjugated plasmids were used to direct cell-free protein synthesis, so that protein generation could be readily programmed, reset and reprogrammed. Protein synthesis by using this approach could be ON/OFF-controlled through repeated addition and removal of the microbead-conjugated DNA and employed in sequential expression of different genes in a same reaction mixture. Since the incubation periods of individual template plasmids are freely controllable, relative expression levels of multiple proteins can be tuned to desired levels. We expect that the presented results will find wide application to the flexible design and execution of synthetic pathways in cell-free chassis.
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Tsuchida K, Komatsu K. Impaired removal of DNA interstrand cross-link in Nijmegen breakage syndrome and Fanconi anemia, but not in BRCA-defective group. Cancer Sci 2008; 99:2238-43. [PMID: 18771529 PMCID: PMC11159798 DOI: 10.1111/j.1349-7006.2008.00915.x] [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: 11/26/2022] Open
Abstract
Human diseases characterized by a high sensitivity to DNA interstrand cross-links (ICL) and predisposition to malignance include Nijmegen breakage syndrome (NBS) and Fanconi anemia (FA), which is further classified to three groups: (1) FA core-complex group; (2) FA-ID complex group; and (3) breast cancer (BRCA)-defective group. The relationships between these four groups and the basic defect in ICL repair remain unclear. To study the details of ICL repair in NBS and FA, a highly sensitive PPB (psoralen-polyethylene oxide-biotin) dot blot assay was developed to provide sensitive quantitative measurements of ICL during the removal process. Studies utilizing this assay demonstrated a decreased rate of ICL removal in cells belonging to the FA core-complex group (e.g. groups A and G) and FA-ID complex group (group D2), while ICL removal was restored to normal levels after these cells were complemented with wt-FANCA, wt-FANCG and wt-FANCD2. Conversely, FA-D1 cells with a defective BRCA2 protein displayed normal ICL removal, although they were compromised with respect to recombination. This normal ICL removal rate in recombination-deficient cells was confirmed by using XRCC3-defective Chinese hamster cells, which are similarly compromised with respect to recombination and are sensitive to mitomycin C. The present study also showed that cells from patients with Nijmegen breakage syndrome were defective in ICL removal, while they were impaired in the recombination. These results indicate an obvious defect of FA and NBS in the ICL repair process, except in the BRCA-defective group, and a separate step of recombination-mediated repair pathway between the BRCA group and NBS.
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Affiliation(s)
- Ken Tsuchida
- Radiation Biology Center, Kyoto University, Yoshida-Konoecho, Kyoto, Japan
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6
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Suzuki S, Ono N, Furusawa C, Kashiwagi A, Yomo T. Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays. BMC Genomics 2007; 8:373. [PMID: 17939865 PMCID: PMC2180184 DOI: 10.1186/1471-2164-8-373] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2007] [Accepted: 10/16/2007] [Indexed: 11/10/2022] Open
Abstract
Background High-density oligonucleotide arrays are widely used for analysis of genome-wide expression and genetic variation. Affymetrix GeneChips – common high-density oligonucleotide arrays – contain perfect match (PM) and mismatch (MM) probes generated by changing a single nucleotide of the PMs, to estimate cross-hybridization. However, a fraction of MM probes exhibit larger signal intensities than PMs, when the difference in the amount of target specific hybridization between PM and MM probes is smaller than the variance in the amount of cross-hybridization. Thus, pairs of PM and MM probes with greater specificity for single nucleotide mismatches are desirable for accurate analysis. Results To investigate the specificity for single nucleotide mismatches, we designed a custom array with probes of different length (14- to 25-mer) tethered to the surface of the array and all possible single nucleotide mismatches, and hybridized artificially synthesized 25-mer oligodeoxyribonucleotides as targets in bulk solution to avoid the effects of cross-hybridization. The results indicated the finite availability of target molecules as the probe length increases. Due to this effect, the sequence specificity of the longer probes decreases, and this was also confirmed even under the usual background conditions for transcriptome analysis. Conclusion Our study suggests that the optimal probe length for specificity is 19–21-mer. This conclusion will assist in improvement of microarray design for both transcriptome analysis and mutation screening.
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Affiliation(s)
- Shingo Suzuki
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Suzuki S, Furusawa C, Ono N, Kashiwagi A, Urabe I, Yomo T. Insight into the sequence specificity of a probe on an Affymetrix GeneChip by titration experiments using only one oligonucleotide. Biophysics (Nagoya-shi) 2007; 3:47-56. [PMID: 27857566 PMCID: PMC5036658 DOI: 10.2142/biophysics.3.47] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 07/20/2007] [Indexed: 12/01/2022] Open
Abstract
High-density oligonucleotide arrays are powerful tools for the analysis of genome-wide expression of genes and for genome-wide screens of genetic variation in living organisms. One of the critical problems in high-density oligonucleotide arrays is how to identify the actual amounts of a transcript due to noise and cross-hybridization involved in the observed signal intensities. Although mismatch (MM) probes are spotted on Affymetrix GeneChips to evaluate the noise and cross-hybridization embedded in perfect match (PM) probes, the behavior of probe-level signal intensities remains unclear. In the present study, we hybridized only one complement 25-mer oligonucleotide to characterize the behavior of duplex formation between target and probe in the complete absence of cross-hybridization. Titration experiments using only one oligonucleotide demonstrated that a substantial amount of intact target was hybridized not only to the PM but also the MM probe and that duplex formation between intact target and MM probe was efficiently reduced by increasing the stringency of hybridization conditions and shortening probe length. In addition, we discuss the correlation between potential for secondary structure of target oligonucleotide and hybridization intensity. These findings will be useful for the development of genome-wide analysis of gene expression and genetic variations by optimization of hybridization and probe conditions.
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Affiliation(s)
- Shingo Suzuki
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Chikara Furusawa
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Complex Systems Biology Project, ERATO, Japan Science and Technology Corporation, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naoaki Ono
- Complex Systems Biology Project, ERATO, Japan Science and Technology Corporation, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Akiko Kashiwagi
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Itaru Urabe
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Yomo
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Complex Systems Biology Project, ERATO, Japan Science and Technology Corporation, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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8
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Strommenger B, Schmidt C, Werner G, Roessle-Lorch B, Bachmann TT, Witte W. DNA microarray for the detection of therapeutically relevant antibiotic resistance determinants in clinical isolates of Staphylococcus aureus. Mol Cell Probes 2007; 21:161-70. [PMID: 17123780 DOI: 10.1016/j.mcp.2006.10.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Revised: 10/07/2006] [Accepted: 10/12/2006] [Indexed: 11/20/2022]
Abstract
An oligonucleotide microarray was constructed for the rapid and sensitive molecular detection of antibiotic resistance determinants in Staphylococcus aureus. The array is equipped with oligonucleotide capture probes for the detection of 10 clinically and therapeutically relevant antibiotic resistance genes and -mutations (mecA, aacA-aphD, tetK, tetM, vat(A), vat(B), vat(C), erm(A), erm(C), grlA-mutation) as well as several control probes. A microarray concept was established including multiplexed PCR amplification, DNA labeling, hybridization and data processing. This concept was applied to clinical Staphylococcus aureus isolates and results were concordant with those from standard genotypic and phenotypic resistance testing. Our microarray concept offers rapid and accurate identification of antibiotic resistance profiles. It is easily expandable and thus can be adapted to changing clinical and epidemiological requirements in clinical diagnosis as well as in epidemiological studies.
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Affiliation(s)
- Birgit Strommenger
- Robert Koch Institute, Wernigerode Branch, Burgstr. 37, D-38855 Wernigerode, Germany.
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9
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Thazhathveetil AK, Liu ST, Indig FE, Seidman MM. Psoralen conjugates for visualization of genomic interstrand cross-links localized by laser photoactivation. Bioconjug Chem 2007; 18:431-7. [PMID: 17373769 DOI: 10.1021/bc060309t] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA interstrand cross-links are formed by chemotherapy drugs as well as by products of normal oxidative metabolism. Despite their importance, the pathways of cross-link metabolism are poorly understood. Laser confocal microscopy has become a powerful tool for studying the repair of DNA lesions that can be detected by immunofluorescent reagents. In order to apply this approach to cross-link repair, we have synthesized conjugates of 4,5',8-trimethylpsoralen (TMP) and easily detected compounds such as Lissamine rhodamine B sulfonyl chloride (LRB-SC), biotin, and digoxigenin. These conjugates are activated by UVA, and we have analyzed the intracellular localization of DNA damage and DNA reactivity by confocal and immunofluorescence microscopy. The LRB-SC-TMP conjugate 2 appeared mainly in the mitochondria, while the biotin-TMP conjugate 4 preferentially localized in the cytoplasm. Adducts formed by UVA and digoxigenin conjugates of TMP 7a and 4,5'-dimethylangelicin (DMA) 7b, which forms only monoadducts, were largely localized to the nucleus. Exposure of cells incubated with 7a and 7b to a 364 nm UV laser directed toward defined nuclear regions of interest resulted in localized adduct formation which could be visualized by immunofluorescence. Repair-proficient cells were able to remove the photoadducts, while repair-deficient cells were unable to repair the damage. The results indicated that the digoxigenin-TMP conjugate 7a and digoxigenin-DMA conjugate 7b can be used for studying the repair of laser localized DNA monoadducts and cross-links.
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Affiliation(s)
- Arun Kalliat Thazhathveetil
- Laboratory of Molecular Gerontology, National Institute on Aging, 5600 Nathan Shock Drive, Baltimore, Maryland 21224, USA
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10
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Vinogradova OA, Pyshnaya IA, Zarytova VF, Ivanova EM, Pyshnyi DV. Enhancement of a hybridization analysis efficiency by the controlled DNA fragmentation. Mol Biol 2007. [DOI: 10.1134/s0026893307010190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Ozsolak F, Song JS, Liu XS, Fisher DE. High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol 2007; 25:244-8. [PMID: 17220878 DOI: 10.1038/nbt1279] [Citation(s) in RCA: 250] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Accepted: 11/28/2006] [Indexed: 11/08/2022]
Abstract
Our understanding of how chromatin structure influences cellular processes such as transcription and replication has been limited by a lack of nucleosome-positioning data in human cells. We describe a high-resolution microarray approach combined with an analysis algorithm to examine nucleosome positioning in 3,692 promoters within seven human cell lines. Unlike unexpressed genes without transcription-preinitiation complexes at their promoters, expressed genes or genes containing preinitiation complexes exhibit characteristic nucleosome-free regions at their transcription start sites. The combination of these nucleosome data with chromatin immunoprecipitation-chip analyses reveals that the melanocyte master regulator microphthalmia-associated transcription factor (MITF) predominantly binds nucleosome-free regions, supporting the model that nucleosomes limit sequence accessibility. This study presents a global view of human nucleosome positioning and provides a high-throughput tool for analyzing chromatin structure in development and disease.
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Affiliation(s)
- Fatih Ozsolak
- Melanoma Program in Medical Oncology, and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Children's Hospital Boston, Harvard Medical School, 44 Binney Street, Boston, Massachusetts 02115, USA
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12
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Yang Q, Xu J, Qian X, Zhang K, Lei X. Eliminating nucleic acids contaminants by hydrogen peroxide-induced free radicals during the preparation of proteins. Biochem Eng J 2006. [DOI: 10.1016/j.bej.2005.02.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Abstract
High throughput and automation of nucleic acid analysis are required in order to exploit the information that has been accumulated from the Human Genome Project. Microfabricated analytical systems enable parallel sample processing, reduced analysis-times, low consumption of sample and reagents, portability, integration of various analytical procedures and automation. This review article discusses miniaturized analytical systems for nucleic acid amplification, separation by capillary electrophoresis, sequencing and hybridization. Microarrays are also covered as a new analytical tool for global analysis of gene expression. Thus. instead of studying the expression of a single gene or a few genes at a time we can now obtain the expression profiles of thousands of genes in a single experiment.
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Affiliation(s)
- Pierre J Obeid
- Department of Chemistry, University of Patras, Patras, Greece
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14
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Preininger C, Bodrossy L, Sauer U, Pichler R, Weilharter A. ARChip epoxy and ARChip UV for covalent on-chip immobilization of pmoA gene-specific oligonucleotides. Anal Biochem 2005; 330:29-36. [PMID: 15183758 DOI: 10.1016/j.ab.2003.12.037] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2003] [Indexed: 10/26/2022]
Abstract
ARChip Epoxy and ARChip UV are presented as novel chip platforms for oligonucleotide immobilization. ARChip Epoxy is made of reactive epoxy resin available commercially. ARChip UV consists of photoactivatable poly(styrene-co-4-vinylbenzylthiocyanate). Both ARChip surfaces are tested in a model assay based on oligonucleotide probes from a real-life genotyping project and are evaluated in comparison with five commercial chip surfaces based on nitrocellulose, epoxy, and aldehyde polymer, and two different aminosilanes. Optimum print buffer, spotter compatibility, and data normalization are discussed.
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Affiliation(s)
- Claudia Preininger
- Division of Environmental and Life Sciences, ARC Seibersdorf Research GmbH, Biotechnology Unit, A-2444 Seibersdorf, Austria.
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15
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Booth SA, Drebot MA, Martin IE, Ng LK. Design of oligonucleotide arrays to detect point mutations: molecular typing of antibiotic resistant strains of Neisseria gonorrhoeae and hantavirus infected deer mice. Mol Cell Probes 2003; 17:77-84. [PMID: 12788028 DOI: 10.1016/s0890-8508(03)00005-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microarrays are promising tools for use in molecular diagnostics due to their ability to perform a multitude of tests simultaneously. In the case of genotyping many such tests will require discrimination of sequence at the single nucleotide level. A number of challenges exist including binding of optimal quantities of probe to the chip surface, the use of uniform hybridization conditions across the chip and the generation of labeled target. We investigated two model systems to test out the efficacy and ease with which probes can be designed for this purpose. In the first of these we designed primers to identify five mutations found in two genes from N. gonohorroeae, gyrA and parC that have been implicated in ciprofloxacin resistance. In the second system we used a similar strategy to identify four mutations in AT rich mitochondrial DNA from deer mice. These mutations are associated with deer mice subspecies that originate from different geographical regions of Canada and harbor different hantavirus strains. In every case we were able to design probes that could discriminate mutations in the target sequences under uniform hybridization conditions, even when targets were fairly long in length, up to 400 bp. Our results suggest that microarray analysis of point mutations might be very useful for automated identification and characterization of pathogens and their hosts.
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Affiliation(s)
- Stephanie A Booth
- National Microbiology Laboratory, Population and Public Health Branch, Health Canada, Winnipeg, Man, Canada
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16
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Li G, Shu X, Ma HH, Chen W, Chen WS, Chen Q, Jiang YS, Yao JL. Detection of HBV, HCV and HBV YMDD mutants by DNA microarray. Shijie Huaren Xiaohua Zazhi 2003; 11:178-181. [DOI: 10.11569/wcjd.v11.i2.178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the effect of DNA microarray in detection of hepatitis B virus (HBV), hepatitis C virus (HCV) and HBV YMDD mutants.
METHODS: HBV and HCV in 40 serum samples were detected by mixed microarray and quantitative determination method as well; 20 serum samples from patients with hepatitis B treated with lamivudine were detected by microarray loaded HBV YMDD mutants gene, and were simultaneously tested with mismatched PCR and DNA sequencing for comparison.
RESULTS: The coincident rate of mixed microarray and quantitative determination of HBV DNA was 85% (34/40). The detectable rate of HBV by mixed microarray was 83% (19/23); 2 of 17 samples showed false positive reaction. The coincident rate of mixed microarray and HCV RNA quantitative determination was 85% (34/40). The detectable rate of HCV by mixed microarray was 58% (7/12). One of 28 samples showed false positive reaction. The coincident rate of HBV YMDD mutants microarray and mismatched PCR was 70% (14/20). Mixed infection of wild and mutant HBV or different mutants were detected by microarray.
CONCLUSION: Mixed microarray has high sensitivity and low non-specificity in detection of HBV, but has lower sensitivity and higher specificity in detection of HCV. Detection of HBV YMDD mutants and mixed infection with microarray had higher sensitivity and specificity.
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17
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Li ES, Liu WT. DNA Microarray Technology in Microbial Ecology Studies-Principle, Applications and Current Limitations. Microbes Environ 2003. [DOI: 10.1264/jsme2.18.175] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Emily S.Y. Li
- Department of Civil Engineering, National University of Singapore
| | - Wen-Tso Liu
- Department of Civil Engineering, National University of Singapore
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18
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Abstract
In this review, recent advances in DNA microarray technology and their applications are examined. The many varieties of DNA microarray or DNA chip devices and systems are described along with their methods for fabrication and their use. This includes both high-density microarrays for high-throughput screening applications and lower-density microarrays for various diagnostic applications. The methods for microarray fabrication that are reviewed include various inkjet and microjet deposition or spotting technologies and processes, in situ or on-chip photolithographic oligonucleotide synthesis processes, and electronic DNA probe addressing processes. The DNA microarray hybridization applications reviewed include the important areas of gene expression analysis and genotyping for point mutations, single nucleotide polymorphisms (SNPs), and short tandem repeats (STRs). In addition to the many molecular biological and genomic research uses, this review covers applications of microarray devices and systems for pharmacogenomic research and drug discovery, infectious and genetic disease and cancer diagnostics, and forensic and genetic identification purposes. Additionally, microarray technology being developed and applied to new areas of proteomic and cellular analysis are reviewed.
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Affiliation(s)
- Michael J Heller
- Department of Bioengineering/Electronic, University of California, San Diego, La Jolla 92093, USA.
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Makrigiorgos GM, Chakrabarti S, Zhang Y, Kaur M, Price BD. A PCR-based amplification method retaining the quantitative difference between two complex genomes. Nat Biotechnol 2002; 20:936-9. [PMID: 12161758 DOI: 10.1038/nbt724] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
With the increasing emergence of genome-wide analysis technologies (including comparative genomic hybridization (CGH), expression profiling on microarrays, differential display (DD), subtractive hybridization, and representational difference analysis (RDA)), there is frequently a need to amplify entire genomes or cDNAs by PCR to obtain enough material for comparisons among target and control samples. A major problem with PCR is that amplification occurs in a nonlinear manner and reproducibility is influenced by stray impurities. As a result, when two complex DNA populations are amplified separately, the quantitative relationship between two genes after amplification is generally not the same as their relation before amplification. Here we describe balanced PCR, a procedure that faithfully retains the difference among corresponding amplified genes by using a simple principle. Two distinct genomic DNA samples are tagged with oligonucleotides containing both a common and a unique DNA sequence. The genomic DNA samples are pooled and amplified in a single PCR tube using the common DNA tag. By mixing the two genomes, PCR loses the ability to discriminate among the different alleles and the influence of impurities is eliminated. The PCR-amplified pooled samples can be separated using the DNA tag unique to each individual genomic DNA sample. The principle of this method has been validated with synthetic DNA, genomic DNA, and cDNA applied on microarrays. By removing the bias of PCR, this method allows a balanced amplification of allelic fragments from two complex DNAs even after three sequential rounds of PCR. This balanced PCR approach should allow genetic analysis in minute laser-microdissected tissues, paraffin-embedded archived material, or single cells.
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Affiliation(s)
- G Mike Makrigiorgos
- Department of Radiation Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
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