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Welcome to the Pubget Medical Subject Headings (MESH) browser. Click on a topic or subtopic below to explore related papers. In the gold box is the most recent paper about the current MESH term, and below are 20 related papers.
Nucleic Acid Probes (4):
Recent article
Nucleic Acid Probes
Journal of Parasitology (96)3 2010
Abstract
We originally published a physical map of this chromosome and, now, using the sequence data from 46 chromosome-specific probes, have produced a sequence map of the 2 Mb chromosome. Comparison of the probe sequences with the Giardia genome database (http://GiardiaDB.org) has identified 4 scaffolds (C...
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PMID: 20557214
PDF is available here.
PDF is available here.
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Abstract
We have developed a colorimetric assay for DNA detection based on the aggregation of unmodified metallic nanoparticles. Charge neutral peptide nucleic acids (PNA) are used as a "coagulant" of citrate anion-coated particles and as hybridization probe. In the absence of a complementary target DNA, fre...
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PMID: 20337394
PDF is available here.
PDF is available here.
Abstract
We report the design of a new MB that overcomes some of the limitations of MBs for surface immobilization. Essentially, this new design adds locked nucleic acid bases (LNAs) to the beacon structure, resulting in a LNA molecular beacon (LMB) with robust stability after surface immobilization. To test...
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PMID: 19351140
PDF is available here.
PDF is available here.
Phytopathology (99)3 2009
Abstract
Severe isolates of Citrus tristeza virus (CTV) inducing seedling yellows (SY) and/or stem pitting (SP) in grapefruit or sweet orange are a major threat for the citrus industry worldwide. Identification of these CTV variants was achieved by quantitative real-time reverse transcription-polymerase chai...
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PMID: 19203284
PDF is available here.
PDF is available here.
Abstract
Numerous molecular assays have been developed recently using a variety of technologies. Direct hybridization techniques have allowed analysis of blood culture bottles for organisms such as methicillin-resistant Staphylococcus aureus. Target amplification methods allow postamplification analysis usin...
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PMID: 19242246
PDF is available here.
PDF is available here.
Abstract
We describe a method to enrich the clone libraries by avoiding sequencing of known, abundant sequence types, instead focusing on novel, rare ones. The protocol is based on gridding the PCR products from clone libraries on membranes and hybridisation of species-specific probes. Clones that do not giv...
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PMID: 18708098
PDF is available here.
PDF is available here.
Zhonghua Yixue Zazhi (88)36 2008
Abstract
Molecular cytogenetic aberrations were found in 79 of the 106 CLL patients (74.5%) and 35 patients (33.0%) showed more than two kinds of abnormalities. The most frequent abnormality detected was del (13q14) in 48 cases (45.3%), followed by trisomy of chromosome 12 in 27 patients (25.5%), IgH translo...
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PMID: 19080644
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)13 2008
Abstract
We characterize this effect on exon and gene expression estimates derived from the Affymetrix Exon Array. We conducted an association analysis between expression levels of probes, exons and transcripts and the genotypes of neighboring SNPs in 57 CEU HapMap individuals. We quantified the dependence o...
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PMID: 18596082
PDF is available here.
PDF is available here.
Abstract
We describe the use of laser capture microdissection microscopy (LCMM) combined with multiplex quantitative real-time reverse transcriptase PCR (qRT-PCR) to isolate and quantify RNA transcripts from small groups of cells at spatially resolved sites within biofilms. The approach was first tested and...
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PMID: 18487401
PDF is available here.
PDF is available here.
Abstract
We described a novel denaturing high-performance liquid chromatography (DHPLC) approach useful for initial detection and identification of crustacean parasites. Because this approach utilizes general primers targeted to conserved regions of the 18S rRNA gene, a priori genetic sequence information on...
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PMID: 18502913
PDF is available here.
PDF is available here.
Abstract
We describe a molecular methodology involving inducible tethering that can be used to position genes at the inner nuclear membrane (INM)-lamina compartment. The consequences of such directed re-positioning on gene activity or other DNA transactions can then be analyzed. This approach can be generali...
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PMID: 18602999
PDF is available here.
PDF is available here.
Abstract
Many countries have introduced mandatory labeling requirements on foods derived from genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (PCR) based upon the TaqMan probe chemistry has become the method mostly used to support these regulations; moreover, event-spe...
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PMID: 18494480
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)11 2008
Abstract
We describe snap-to-it probes, a novel probe technology to enhance the hybridization specificity of natural and unnatural nucleic acid oligomers using a simple and readily introduced structural motif. Snap-to-it probes were prepared from peptide nucleic acid (PNA) oligomers by modifying each terminu...
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PMID: 18448470
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)8 2008
Abstract
The interactions of archetypical nucleic acid ligands with the HIV-1 polypurine tract (PPT) RNA:DNA hybrid, as well as analogous DNA:DNA, RNA:RNA and swapped hybrid substrates, were used to probe structural features of the PPT that contribute to its specific recognition and processing by reverse tra...
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PMID: 18400780
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (112)15 2008
Abstract
Twenty-bases long NH2-modified DNA and PNA probes specific to a pathogen (Mycobacterium tuberculosis) were covalently immobilized onto a polyaniline (PANI)/Au electrode to detect nucleic acid hybridization with complementary, one-base mismatch and noncomplementary targets within 30 s using Methylene...
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PMID: 18335925
PDF is available here.
PDF is available here.
Abstract
We developed the simple, rapid (1 h), and accurate PNA FISH(Flow) method for the identification of Candida albicans. The method exploits unique in solution in situ hybridization conditions under which the cells are simultaneously fixed and hybridized. This method facilitates the accurate identificat...
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PMID: 18287325
PDF is available here.
PDF is available here.
Chemical Society Reviews (37)4 2008
Abstract
Molecular beacons (MBs) have been used as viable fluorescent probes in nucleic acid analysis. Many researchers around the world continue to modify the MBs to suit their needs. As a result, a number of nucleic acid probing systems with close resemblance to the MBs are being reported from time to time...
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PMID: 18362974
PDF is available here.
PDF is available here.
Molecular Biotechnology (38)3 2008
Abstract
The use of fluorescent nucleic acid hybridization probes that generate a fluorescence signal only when they bind to their target enables real-time monitoring of nucleic acid amplification assays. Real-time nucleic acid amplification assays markedly improves the ability to obtain qualitative and quan...
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PMID: 17985254
PDF is available here.
PDF is available here.
Acta Biochimica Polonica (55)4 2008
Abstract
We observed the hybridization stability trend affected by mismatches: G:T approximately G:G > G:A > A:A approximately T:T > A:C approximately T:C > C:C. The experimental data show that mismatches at the center of the oligonucleotide probes have a more profound destabilizing effect on the hybridizati...
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PMID: 19039337
PDF is available here.
PDF is available here.
Abstract
Abstract
In recent years, fluorescently labeled oligonucleotides have become a widely used tool in diagnostics, DNA sequencing, and nanotechnology. The recently developed (phenylethynyl)pyrenes are attractive dyes for nucleic acid labeling, with the advantages of long-wave emission relative to the parent pyr...
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PMID: 18979465
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
We designed, validated and used Synechocystis genome-wide oligonucleotide (70-mer) microarray (representing 96.7% of all chromosomal ORFs annotated at the time of the beginning of this project) to study transcriptional activity of the cyanobacterial genome in response to sulfur (S) starvation. The m...
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PMID: 18644144
PDF is available here.
PDF is available here.
BMC Genomics (9 Suppl 1)suppl 1 2008
Abstract
Since finding unique probes is often not easy, we make use of non-unique probes. Minimizing the number of non-unique probes will result in a smaller DNA microarry design which leads to a smaller chip and considerable reduction of cost. While minimizing the probe set, the decoding ability should not...
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PMID: 18366612
PDF is available here.
PDF is available here.
Abstract
Abstract
We investigated a 2.5-h peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) assay with five Candida species-specific probes to identify Candida colonies and compared it to standard 2-h to 5-day phenotypic identification methods. Suspensions were made and slides were prepared and read...
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PMID: 17804657
PDF is available here.
PDF is available here.
FEMS Yeast Research (7)6 2007
Abstract
Sequencing of the complete 26S rRNA genes of all Dekkera/Brettanomyces species colonizing different beverages revealed the potential for a specific primer and probe design to support diagnostic PCR approaches and FISH. By analysis of the complete 26S rRNA genes of all five currently known Dekkera/Br...
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PMID: 17596183
PDF is available here.
PDF is available here.
Abstract
We have designed a chip-based assay, using microarray technology, for determining the relative binding affinities of duplex and triplex DNA binders. This assay combines the high discrimination capabilities afforded by DNA-modified Au nanoparticles with the high-throughput capabilities of DNA microarr...
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PMID: 17614366
PDF is available here.
PDF is available here.
Journal of Medical Microbiology (56)Pt 7 2007
Abstract
This study evaluated a novel peptide nucleic acid (PNA) probe targeting a region of the 23S rRNA gene of Klebsiella pneumoniae by fluorescence in situ hybridization (FISH). Analytical performance was determined using 39 reference strains and other well-characterized strains of Klebsiella spp. and En...
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PMID: 17577055
PDF is available here.
PDF is available here.
Abstract
We report herein the light-directed synthesis of peptide nucleic acids (PNAs) microarray using PNA monomers protected by photolabile protecting groups and a maskless technique that uses a digital micromirror array system to form virtual masks. An ultraviolet image from the virtual mask was cast onto...
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PMID: 17236754
PDF is available here.
PDF is available here.
Analyst (Cambridge UK) (132)6 2007
Abstract
To allow the ultrasensitive localization and the quantitative detection of parvovirus B19 nucleic acids in single infected cells at various times post-infection, a peptide nucleic acid (PNA)-based in situ hybridisation (ISH) assay with chemiluminescent detection has been developed. The assay is base...
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PMID: 17525808
PDF is available here.
PDF is available here.
Abstract
PCR products obtained by selective amplification of transgenic DNA derived from food samples containing Roundup Ready soybean or Bt-176 maize have been analyzed by anion-exchange HPLC. Peptide nucleic acids (PNAs), oligonucleotide analogues known to bind to complementary single-stranded DNA with hig...
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PMID: 17326652
PDF is available here.
PDF is available here.
Biologicals (35)2 2007
Abstract
We established a method to quantify the percentage of variant strain Type II contained in freeze-dried BCG product with real-time PCR. With this method we examined the master seed lot Tokyo 172, two secondary seed lots, Tokyo 172-1 and Tokyo 172-2, which were produced from Tokyo 172, and four commer...
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PMID: 17074509
PDF is available here.
PDF is available here.
Abstract
We describe the design, synthesis, and properties of DNA-like molecules in which the base pairs are expanded by benzo homologation. The resulting size-expanded genetic helices are called xDNA ("expanded DNA") and yDNA ("wide DNA"). The large component bases are fluorescent, and they display high sta...
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PMID: 17309194
PDF is available here.
PDF is available here.
Abstract
DNA sensing at a single nucleotide resolution is achieved using a hairpin-shaped, unmodified (unlabeled) RNA probe or the precursor double-stranded DNA (dsDNA) in a prokaryotic cell-free translation medium. The molecular-beacon-like probe consists of a loop region that is complementary to the target...
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PMID: 17546001
PDF is available here.
PDF is available here.
Abstract
A fluorescence-based microarray technique that does not require target DNA labeling is detailed. This 'label-free' approach utilizes a cationic, water-soluble conjugated polymer PFBT (poly[9,9'-bis(6''-(N,N,N-trimethylammonium)hexyl)fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide]), and neutr...
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PMID: 17853870
PDF is available here.
PDF is available here.
Abstract
The work present PCR (Polymerase Chain Reaction) with the real time analysis of the increase of product allowing quick detection, duplication and identification of even slight amounts of nucleic acids. Essential methods used in molecular diagnostics, based on marked probes and fluorescence phenomeno...
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PMID: 18595479
PDF is available here.
PDF is available here.
BMC Genomics (8)1 2007
Abstract
Disagreement was observed between gene expression profiles acquired after a second round of amplification compared to a single round. Thirty percent of the differentially expressed genes identified after one round of amplification were not detected after two rounds. These inconsistent genes have a s...
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PMID: 17697374
PDF is available here.
PDF is available here.
Genome Biology (8)8 2007
Abstract
A novel normalization method based on the GC content of probes is developed for two-color tiling arrays. The proposed method, together with robust estimates of the model parameters, is shown to perform superbly on published data sets. A robust algorithm for detecting peak regions is also formulated...
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PMID: 17727723
PDF is available here.
PDF is available here.
Genetic Testing (11)4 2007
Abstract
We evaluated the usefulness of a methylation-specific multiplex ligation-dependent probe amplification (MLPA) kit consisting of 43 probes to detect copy number changes and methylation status in the region. We used the MLPA kit to genotype 82 subjects with chromosome 15 abnormalities (62 PWS, 10 AS a...
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PMID: 18294067
PDF is available here.
PDF is available here.
Abstract
In situ hybridization allows the detection of specific gene transcripts in tissues, cells or, chromosomes. In the cardiovascular field, this powerful and rapid methodology provides precious insights into the complex gene organization and expression within an heterogeneous cell population. This techn...
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PMID: 17568124
PDF is available here.
PDF is available here.
Abstract
This paper describes the synthesis and properties of a novel molecular beacon (MB) containing a benzene-phosphate backbone at the stem moieties. Fluorescent intensity of MBs was found to be stabilized by introducing a benzene-phosphate backbone at stem moieties.
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PMID: 18029702
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)Database issue 2007
Abstract
RNA interference (RNAi) has emerged as a powerful tool to generate loss-of-function phenotypes in a variety of organisms. Combined with the sequence information of almost completely annotated genomes, RNAi technologies have opened new avenues to conduct systematic genetic screens for every annotated...
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PMID: 17135194
PDF is available here.
PDF is available here.
Abstract
We describe a mechanism-based probe, azido-E-64, that can be used for both imaging and proteomics. Azido-E-64 covalently modifies active Cathepsin (Cat) B in living cells, an abundant cysteine protease involved in microbial infections, apoptosis, and cancer. Furthermore, azido-E-64 contains an azide...
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PMID: 17184136
PDF is available here.
PDF is available here.
Journal of Peptide Science (12)12 2006
Abstract
We report the synthesis and the characterization of a new chiral nucleoaminoacid, in which a diaminobutyric moiety is connected to the DNA nucleobase by an amidic bond, and its oligomerization to give the corresponding nucleo-gamma-peptide. The ability of this synthetic polymer to bind complementary...
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PMID: 17131297
PDF is available here.
PDF is available here.
Abstract
Our results confirm that ICE are the most frequent type of unstable chromosomal aberration induced by BLM in mammalian cells. Moreover, the present study shows that an increase in the chromosome number does not necessarily result in an increase in the frequency of BLM-induced ICE. The results also s...
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PMID: 16948055
PDF is available here.
PDF is available here.
Molecular Carcinogenesis (45)10 2006
Abstract
We used array-based comparative genomic hybridization (array-CGH) to screen genomewide alterations in eight pairs of microdissected tissue samples from primary and metastatic OSCC. In addition, 25 primary and metastatic OSCC tissue pairs were examined with immunohistochemistry for protein expression...
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PMID: 16676365
PDF is available here.
PDF is available here.
Abstract
We established a 3-h fluorescence in situ hybridization (FISH) procedure for specific visualization of members of the Mycobacterium tuberculosis complex, M. leprae, M. avium, and M. kansasii. Probe specificity was tested against a panel of 25 Mycobacterium spp. and 10 gram-positive organisms. After...
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PMID: 17021106
PDF is available here.
PDF is available here.
Abstract
The ability of fluorescence resonance energy transfer, molecular-beacon, and TaqMan probes to detect single nucleotide polymorphism (SNP) in the presence of a wild-type allele was evaluated using drug resistance-conferring SNPs in mixed Mycobacterium tuberculosis DNA. It was found that both the abso...
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PMID: 17021120
PDF is available here.
PDF is available here.
Abstract
We have been exploring the suitability of RNA aptamers for this purpose. Using the Escherichia coli heme biosynthetic pathway as a simple model of a negative feedback regulated process, we show that heme-binding RNA aptamers, developed in vitro and expressed intracellularly, induce a heme-dependent...
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PMID: 17168539
PDF is available here.
PDF is available here.
Analytical Biochemistry (355)2 2006
Abstract
We developed the approach to detect single-nucleotide mutation with peptide nucleic acid (PNA) probes and time-resolved fluorometry using a fluorescence lanthanide chelate label, {2,2',2'',2'''-{4'-{[(4,6-dichloro-1,3,5-triazin-2-yl)amino]biphenyl-4-yl}-2,2': 6',2''-terpyridine-6,6''-diyl}bis(methyl...
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PMID: 16842732
PDF is available here.
PDF is available here.
Abstract
In the controls (wild type), the reaction of VIC-labeled MGB probe was positive and the channel of FAM reaction was negative, the DNA sequence was 100% matched to previously published data. In 20 LHON patients and their maternal relatives, 12 cases showed mutations in DNA sequence analysis, all of t...
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PMID: 17081446
PDF is available here.
PDF is available here.
Biochemistry (Washington) (45)30 2006
Abstract
We have studied the excited-state properties of the bases at the CIS and TDB3LYP level in hydrogen-bonded and base-stacked complexes. The results reveal that the first excited state (the fluorescent state) of a hydrogen-bonded complex containing 2-aminopurine and thymine is just the first excited st...
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PMID: 16866360
PDF is available here.
PDF is available here.
Nucleic Acids Research (34)Web Server issue 2006
Abstract
We also offer population-specific substitution of SNP alleles in genomic sequence according to SNP frequencies in HapMap Phase II data. The input to SNPmasker can be defined in chromosomal coordinates or inserted as a sequence. The sequences masked by our web server are most useful as a preliminary...
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PMID: 16845091
PDF is available here.
PDF is available here.
Current Genetics (50)1 2006
Abstract
We are attempting to identify regions of functional importance by searching for strongly conserved domains in RegA orthologs. Here we report the cloning and characterization of regA from the most closely related known taxon, V. carteri f. kawasakiensis. Given the closeness of the relationship betwee...
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PMID: 16622701
PDF is available here.
PDF is available here.
Abstract
8-(Pyren-1-yl)-2'-deoxyguanosine (Py-G) was incorporated synthetically as an optical probe into oligonucleotides. The Py-G group in DNA does not discriminate between any of the four natural nucleosides as a counterbase and exhibits altered optical properties in single strands versus double strands....
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PMID: 16621544
PDF is available here.
PDF is available here.
Abstract
Abstract
We conducted an investigation on the diagnostic potential of Leptospira genes encoding putative transcriptional regulators. While PCR primers derived from transcriptional regulator gene la1137 recognized all 24 pathogenic Leptospira strains representing seven species, those from la1937, la3231, la38...
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PMID: 16604124
PDF is available here.
PDF is available here.
Abstract
The microbial community inhabiting in the rumen is characterized by its high population density, wide diversity and interactive complexity. However, until recently our knowledge of rumen microbiology was primarily based on classical culture based techniques (isolation, enumeration and nutritional ch...
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PMID: 16579489
PDF is available here.
PDF is available here.
Abstract
We studied the WMP2 line using spectral karyotyping (SKY) combined with new established mouse specific multicolor banding (mcb) probes for the chromosomes X, 3, 4, 6 and 18. SKY revealed that the WMP2 cell line developed further four derivative chromosomes. After application of mcb five previously u...
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PMID: 16391817
PDF is available here.
PDF is available here.
BMC Genomics (7)1 2006
Abstract
This study evaluated the relative performance of CSH compared to SSH, and proposes methods to ensure that CSH closely reflects the biological process analyzed by SSH....
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PMID: 16677401
PDF is available here.
PDF is available here.