DNAプローブ

WordNet

question or examine thoroughly and closely (同)examine
a flexible slender surgical instrument with a blunt end that is used to explore wounds or body cavities
an exploratory action or expedition
an investigation conducted using a flexible surgical instrument to explore an injury or a body cavity
an inquiry into unfamiliar or questionable activities; "there was a congressional probe into the scandal" (同)investigation
examine physically with or as if with a probe; "probe an anthill" (同)dig into, poke_into
in favor of a proposition, opinion, etc.
an argument in favor of a proposal
in favor of (an action or proposal etc.); "a pro vote"
the 4th letter of the Roman alphabet (同)d

PrepTutorEJDIC

(傷の深さを調べる)さぐり針 / (…を)厳密に調べること,精査《+『into』(『for』,『at』)+『名』》 / (また『space probe』)(ロケットの)宇宙探測機 / …‘を'厳密に調べる / 〈傷〉‘を'さぐり針で調べる / (…を)厳密に調べる《+『into』(『for』,『at』)+『名』》
=professional
賛成論;賛成票(者) / 賛成して
deuteriumの化学記号
deoxyribonucleic acidディオキシリボ核酸

Wikipedia preview

出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2015/06/08 23:57:28」(JST)

wiki en

In molecular biology, X hybridization probe is a fragment of DNA or RNA of variable length (usually 100-1000 bases long) which is radioactively labelled used in DNA or RNA samples to detect the presence of nucleotide sequences (the DNA target) that are complementary to the sequence in the probe. The probe thereby hybridizes to single-stranded nucleic acid (DNA or RNA) whose base sequence allows probe-target base pairing due to complementarity between the probe and target. The labeled probe is first denatured (by heating or under alkaline conditions such as exposure to sodium hydroxide) into single stranded DNA (ssDNA) and then hybridized to the target ssDNA (Southern blotting) or RNA (Northern blotting) immobilized on a membrane or in situ.

To detect hybridization of the probe to its target sequence, the probe is tagged (or "labeled") with a molecular marker of either radioactive or (more recently) fluorescent molecules; commonly used markers are ³²P (a radioactive isotope of phosphorus incorporated into the phosphodiester bond in the probe DNA) or Digoxigenin, which is a non-radioactive, antibody-based marker. DNA sequences or RNA transcripts that have moderate to high sequence similarity to the probe are then detected by visualizing the hybridized probe via autoradiography or other imaging techniques. Normally, either X-ray pictures are taken of the filter, or the filter is placed under UV light. Detection of sequences with moderate or high similarity depends on how stringent the hybridization conditions were applied — high stringency, such as high hybridization temperature and low salt in hybridization buffers, permits only hybridization between nucleic acid sequences that are highly similar, whereas low stringency, such as lower temperature and high salt, allows hybridization when the sequences are less similar. Hybridization probes used in DNA microarrays refer to DNA covalently attached to an inert surface, such as coated glass slides or gene chips, to which a mobile cDNA target is hybridized.

Depending on the method, the probe may be synthesized using the phosphoramidite method, or it can be generated and labeled by PCR amplification or cloning (both are older methods). In order to increase the in vivo stability of the probe RNA is not used, instead RNA analogues may be used, in particular morpholino- derivatives. Molecular DNA- or RNA-based probes are now routinely used in screening gene libraries, detecting nucleotide sequences with blotting methods, and in other gene technologies, such as nucleic acid and tissue microarrays.

Examples of probes

Scorpion® probes

Molecular Beacon probes

TaqMan® probes

LNA® (Locked Nucleic Acid) probes

Cycling Probe Technology (CPT)

Uses in Microbial Ecology

Within the field of microbial ecology, oligonucleotide probes are used in order to determine the presence of microbial species, genera, or microorganisms classified on a more broad level, such as bacteria, archaea, and eukaryotes via fluorescence in situ hybridization (FISH).^[1] rRNA probes have enabled scientists to visualize microorganisms, yet to be cultured in laboratory settings, by retrieval of rRNA sequences directly from the environment.^[2] Examples of these types of microorganisms include:

Nevskia ramosa: N. ramosa is a neuston bacterium that forms typical, dichotomically-branching rosettes on the surface of shallow freshwater habitats.^[3]

Achromatium oxaliferum: This huge bacterium (cell length up to >100 µm, diameter up to 50 µm) contains sulfur globules and massive calcite inclusions and inhabits the upper layers of freshwater sediments. It is visible to the naked eye and has, by its resistance to cultivation, puzzled generations of microbiologists.^[4]

Limitations

In some instances, differentiation between species may be problematic when using 16S rRNA sequences due to similarity. In such instances, 23S rRNA may be a better alternative.^[5] The global standard library of rRNA sequences is constantly becoming larger and continuously being updated, and thus the possibility of a random hybridization event between a specifically-designed probe (based on complete and current data from a range of test organisms) and an undesired/unknown target organism cannot be easily dismissed.^[6] On the contrary, it is plausible that there exist microorganisms, yet to be identified, which are phylogenetically members of a probe target group, but have partial or near-perfect target sites. This usually applies when designing group-specific probes.

Probably the greatest practical limitation to this technique is the lack of available automation.^[7]

Use in forensic science

In forensic science, hybridization probes are used, for example, for detection of short tandem repeats (microsatellite) regions and in restriction fragment length polymorphism (RFLP) methods, all of which are widely used as part of DNA profiling analysis.

References

^ Amann R, Ludwig W (2000). "Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology". FEMS Microbiology Reviews 24: 555–565. doi:10.1111/j.1574-6976.2000.tb00557.x.
^ Amann, R., Ludwig, W. and Schleifer, K.-H. (1995). "Phylogenetic identification and in situ detection of individual microbial cells without cultivation". Microbiology Review 59: 143–169.
^ Glöckner, F.O., Babenzien H.D., and Amann R. (1998). "Phylogeny and identification in situ of Nevskia ramosa". Appl. Environ. Microbiol. 64: 1895–1901.
^ Glöckner, F.O., Babenzien H.D., and Amann R. (1999). "Phylogeny and diversity of Achromatium oxaliferum". Syst. Appl. Microbiol. 22: 28–38. doi:10.1016/s0723-2020(99)80025-3.
^ Fox, G.E., Wisotzkey, J.D. and Jurtshuk Jr., P. (1992). "How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity.". Int. J. Syst. Bacteriol. 42: 166–170. doi:10.1099/00207713-42-1-166.
^ Olsen, G.J., Lane, D.J., Giovannoni, S.J., Pace, N.R. and Stahl, D.A. (1986). "Microbial ecology and evolution: a ribosomal RNA approach". Annu. Rev. Microbiol. 40: 337–365. doi:10.1146/annurev.mi.40.100186.002005.
^ Amann R, Ludwig W (2000). "Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology". FEMS Microbiology Reviews 24: 555–565. doi:10.1111/j.1574-6976.2000.tb00557.x.

UpToDate Contents

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1. 成人および思春期における淋菌感染症の臨床症状および診断 clinical manifestations and diagnosis of neisseria gonorrhoeae infection in adults and adolescents
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5. 性感染症：思春期特有の問題の概要 sexually transmitted diseases overview of issues specific to adolescents

English Journal

Surface plasmon resonance technique for directly probing the interaction of DNA and graphene oxide and ultra-sensitive biosensing.

Xue T1, Cui X2, Guan W3, Wang Q1, Liu C1, Wang H1, Qi K1, Singh DJ4, Zheng W5.Author information 1Key Laboratory of Automobile Materials of MOE and State Key Laboratory of Superhard Materials, Department of Materials Science, Jilin University, Changchun 130012, People׳s Republic of China.2Key Laboratory of Automobile Materials of MOE and State Key Laboratory of Superhard Materials, Department of Materials Science, Jilin University, Changchun 130012, People׳s Republic of China. Electronic address: xqcui@jlu.edu.cn.3State Key Laboratory of Advanced Technologies for Comprehensive Utilization of Platinum Metals, Kunming 650106, People׳s Republic of China.4Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6056, United States.5Key Laboratory of Automobile Materials of MOE and State Key Laboratory of Superhard Materials, Department of Materials Science, Jilin University, Changchun 130012, People׳s Republic of China. Electronic address: wtzheng@jlu.edu.cn.AbstractThe binding of DNA with graphene oxide (GO) is important for applications in disease diagnosis, genetic screening, and drug discovery. The standard assay methods are mainly limited to indirect observation via fluorescence labeling. Here we report the use of surface plasmon resonance for direct sensing of DNA/GO binding. We show that this can be used for ultra-sensitive detection of single-stranded DNA (ssDNA). Furthermore, the results provide a more direct probe of DNA/GO binding abilities and confirm that hydrogen bonding plays a key role in the interaction between GO and ssDNA. This enables to a novel biosensor for highly sensitive and selective detection of ssDNA based on indirect competitive inhibition assay (ICIA). We report development of such a sensor with a linear dynamic range of 10(-14)-10(-6)M, a detection limit of 10fM and a high level of stability during repeated regeneration.
Biosensors & bioelectronics.Biosens Bioelectron.2014 Aug 15;58:374-9. doi: 10.1016/j.bios.2014.03.002. Epub 2014 Mar 12.
The binding of DNA with graphene oxide (GO) is important for applications in disease diagnosis, genetic screening, and drug discovery. The standard assay methods are mainly limited to indirect observation via fluorescence labeling. Here we report the use of surface plasmon resonance for direct sensi
PMID 24686149

One-pot approach for examining the DNA methylation patterns using an engineered methyl-probe.

Kim SE, Chang M, Yuan C.Author information School of Chemical Engineering, Purdue University, 480 Stadium Mall Drive, West Lafayette, IN 47907, USA.AbstractAberrant DNA methylation is a common observation in various types of human cancers, i.e., breast and lung cancers. Nevertheless, the current DNA methylation detection approaches require bisulfite treatments and are laborious or costly to perform. To address these challenges, we developed a methyl-probe based on the MBD1 protein. Combined with fluorescence correlation spectroscopy, our probe can sensitively detect the existence of DNA methylation at concentrations above 20nM in a one-pot assay. The probe can quantify the total amount of methylated CG dinucleotides above ~20nM, independent of DNA sequence contexts, concentrations (20-1900nM) and methylation levels (5-100%). Our detection platform offers a simple and cheap alternative DNA methylation detection approach.
Biosensors & bioelectronics.Biosens Bioelectron.2014 Aug 15;58:333-7. doi: 10.1016/j.bios.2014.02.064. Epub 2014 Mar 12.
Aberrant DNA methylation is a common observation in various types of human cancers, i.e., breast and lung cancers. Nevertheless, the current DNA methylation detection approaches require bisulfite treatments and are laborious or costly to perform. To address these challenges, we developed a methyl-pr
PMID 24662063

Magnified fluorescence detection of silver(I) ion in aqueous solutions by using nano-graphite-DNA hybrid and DNase I.

Wei Y1, Li B1, Wang X1, Duan Y2.Author information 1Research Center of Analytical Instrumentation, Analytical & Testing Center, Sichuan University, Chengdu, China.2Research Center of Analytical Instrumentation, Analytical & Testing Center, Sichuan University, Chengdu, China. Electronic address: yduan@scu.edu.cn.AbstractThis paper describes a novel approach utilizing nano-graphite-DNA hybrid and DNase I for the amplified detection of silver(I) ion in aqueous solutions for the first time. Nano-graphite can effectively quench the fluorescence of dye-labeled cytosine-rich single-stranded DNA due to its strong π-π stacking interactions; however, in the presence of Ag(+), C-Ag(+)-C coordination induces the probe to fold into a hairpin structure, which does not adsorb on the surface of nano-graphite and thus retains the dye fluorescence. Meanwhile, the hairpin structure can be cleaved by DNase I, and in such case Ag(+) is delivered from the complex. The released Ag(+) then binds other dye-labeled single-stranded DNA on the nano-graphite surface, and touches off another target recycling, resulting in the successive release of dye-labeled single-stranded DNA from the nano-graphite, which leads to significant amplification of the signal. The present magnification sensing system exhibits high sensitivity toward Ag(+) with a limit of detection of 0.3nM (S/N=3), which is much lower than the standard for Ag(+) in drinking water recommended by the Environmental Protection Agency (EPA). The selectivity of the sensor for Ag(+) against other biologically and environmentally related metal ions is outstanding due to the high specificity of C-Ag(+)-C formation. Moreover, the sensing system is used for the determination of Ag(+) in river water samples with satisfying results. The proposed assay is simple, cost-effective, and might open the door for the development of new assays for other metal ions or biomolecules.
Biosensors & bioelectronics.Biosens Bioelectron.2014 Aug 15;58:276-81. doi: 10.1016/j.bios.2014.02.075. Epub 2014 Mar 12.
This paper describes a novel approach utilizing nano-graphite-DNA hybrid and DNase I for the amplified detection of silver(I) ion in aqueous solutions for the first time. Nano-graphite can effectively quench the fluorescence of dye-labeled cytosine-rich single-stranded DNA due to its strong π-π st
PMID 24657649

Japanese Journal

Study on Nanoparticle Sizing Using Fluorescent Polarization Method with DNA Fluorescen Probe (Special Issue on Laser Metrology for Precision Measurement and Inspection in Industry)

International journal of automation technology 9(5), 534-540, 2015-09
NAID 40020585835

Widespread Distribution and Expression of Gamma A (UMB), an Uncultured, Diazotrophic, γ-Proteobacterial nifH Phylotype

PLOS ONE 10(6), e0128912, 2015-06-23
NAID 120005649213

Improved solid-phase DNA probe method for tRNA purification : large-scale preparation and alteration of DNA fixation

The journal of biochemistry 157(5), 411-418, 2015-05
NAID 40020461535

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