Oligonucleotide probes are effective tools for the research of nucleic acids. This project discusses about Oligonucleotide Probes, Multiplex Genetic Analyses, Multiplex nucleic acid analyses, Genetic variation, Different Types of nucleic acid analyses, multiplex oligonucleotide design,
Accuracy of genotyping of single-nucleotide polymorphisms by PCR-ELISA allele-specific oligonucleotide hybridization typing and by amplification refractory mutation ...
APC coding exons 1-15 and well into the 5 and 3 ends of all the introns and untranslated regions are analyzed by sequencing. Gross deletion/duplication analysis determines gene copy number for coding exons 1-15. Additionally, all promoter 1B gross deletions as well as single nucleotide substitutions within the promoter 1B YY1 binding motif are analyzed and reported. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of unknown or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction. Genomic deoxyribonucleic acid (gDNA) is isolated from the patients specimen using standardized methodology and quantified. Sequence enrichment of the targeted coding exons and adjacent intronic nucleotides is carried out by a bait-capture methodology, using long biotinylated oligonucleotide probes followed by polymerase chain reaction (PCR) and next generation sequencing (NGS). Sanger sequencing is performed for any regions ...
NF2 coding exons and well into the 5 and 3 ends of all the introns and untranslated regions are analyzed by sequencing. Gross deletion/duplication analysis determines gene copy number for coding exons. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of unknown or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction. Genomic deoxyribonucleic acid (gDNA) is isolated from the patients specimen using standardized methodology and quantified. Sequence enrichment of the targeted coding exons and adjacent intronic nucleotides is carried out by a bait-capture methodology, using long biotinylated oligonucleotide probes followed by polymerase chain reaction (PCR) and next generation sequencing (NGS). Sanger sequencing is performed for any regions missing or with insufficient read depth coverage for reliable heterozygous variant detection. Reportable small insertions and deletions, potentially homozygous variants, ...
Fluorescence in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes was used to examine the abundance and distribution of planktonic microorganisms within the Cape Fear River estuary in southeastern NC. This black water riverine s ...
Biological sample target classification, detection and selection methods are described, together with related arrays and oligonucleotide probes.
The SPRi-Biochips™ are suitable for a range of surface chemistries and are not restricted to a single probe/target regime. The biochips are easily adapted for specific processes.
Results of molecular beacon end-point assays using the E8/E9 and E9/E10 probes on a representative genomic DNA panel. There is no difficulty in distinguishing a
The GA4GH (Global Alliance for Genomics and & Health) Beacon Projectis a project to encourage international sites to share genetic data in the simplest of all technical contexts. The service is designed merely to accept a query of the form "Do you have any genomes with an A at position 100,735 on chromosome 3" (or similar data) and responds with one of "Yes" or "No.". The Beacon Network lists all the known beacons.. For programmatic access to the COSMIC beacon, the minimal URL for the request is ...
16S rRNA from seven different Vibrio anguillarum strains was partially sequenced and compared. From this sequence information we could design a 25-base-long oligonucleotide and use it as a specific probe for identification of V. anguillarum. This was determined by RNA-DNA colony hybridization and slot-blot hybridization. Strong, specific hybridization to the probe was observed for all V. anguillarum strains tested. Furthermore, no cross-hybridization could be seen against five other bacterial species. The detection limit was 5 x 10(3) bacteria per ml. It was even possible to detect V. anguillarum, by slot-blot hybridization, directly in a homogenized kidney from a fish that had died of vibriosis. The partial sequence information revealed small but significant differences between strains of the same species. These sequence differences are sufficiently significant to allow serotyping on the RNA level. Comparing strains of different serotypes revealed a 10-base and an 11-base difference in V. ...
BACKGROUND: Long oligonucleotide microarrays are potentially more cost- and management-efficient than cDNA microarrays, but there is little information on the relative performance of these two probe types. The feasibility of using unmodified oligonucleotides to accurately measure changes in gene expression is also unclear.. RESULTS: Unmodified sense and antisense 70-mer oligonucleotides representing 75 known rat genes and 10 Arabidopsis control genes were synthesized, printed and UV cross-linked onto glass slides. Printed alongside were PCR-amplified cDNA clones corresponding to the same genes, enabling us to compare the two probe types simultaneously. Our study was designed to evaluate the mRNA profiles of heart and brain, along with Arabidopsis cRNA spiked into the labeling reaction at different relative copy number. Hybridization signal intensity did not correlate with probe type but depended on the extent of UV irradiation. To determine the effect of oligonucleotide concentration on ...
Molecular beacons are oligonucleotide probes that can report the presence of specific nucleic acids in homogenous solutions (Tyagi S, Kramer FR. Molecular beacons: probes that fluoresce upon hybridization, Nature Biotechnology 1996; 14: 303-308.) They are useful in situations where it is either not possible or desirable to isolate the probe-target hybrids from an excess of the hybridization probes, such as in real time monitoring of polymerase chain reactions in sealed tubes or in detection of RNAs within living cells. Molecular beacons are hairpin shaped molecules with an internally quenched fluorophore whose fluorescence is restored when they bind to a target nucleic acid (Figure 1). They are designed in such a way that the loop portion of the molecule is a probe sequence complementary to a target nucleic acid molecule. The stem is formed by the annealing of complementary arm sequences on the ends of the probe sequence. A fluorescent moiety is attached to the end of one arm and a quenching ...
Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from |50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the diversity of the transcriptome and previously studied cotton genes, transcription factors, and genes with homology to Arabidopsis. A small portion of the oligonucleotides target unidentified protein coding sequences, thereby providing an element of gene discovery. Because many oligonucleotides were based on ESTs from
The invention relates to methods for simultaneously or sequentially detecting multiple nucleic acid analytes in a single medium utilizing oligonucleotide hybridization probes coupled to different chemiluminescent labeling reagents. The methods may be used in a heterogeneous, homogeneous or non-homogeneous assay system. The invention also relates to specific combinations of chemiluminescent labeling reagents suitable, when coupled to an oligonucleotide probe, for use together in methods for the detection of multiple nucleic acid analytes. The invention also concerns kits useful in these methods.
This invention pertains to methods, kits and compositions suitable for the detection, identification and/or quantitation of nucleic acids which are electrostatically immobilized to matrices using non-nucleotide probes which sequence specifically hybridize to one or more target sequences of the nucleic acid but do not otherwise substantially interact with the matrix. Once the nucleic acid is immobilized, the detectable non-nucleotide probe/target sequence complex, formed before or after the immobilization of the nucleic acid, can be detected, identified or quantitated under a wide range of assay conditions as a means to detect, identify or quantitate the target sequence in the sample. Because it is reversibly bound, the non-nucleotide probe/target sequence can optionally be removed from the matrix for detecting, identifying or quantitating the target sequence in the sample. Because the non-nucleotide probe/target sequence is protected against degradation, it is another advantage of this invention that
A synthetic oligonucleotide hybridization probe comprising at least one sequence at least 12 nucleotides long, the probe forms duplexes in which at least 80% of the nucleotides are base paired with any nucleotide sequence that is either substantially of the form (Xl...Xi)n in which X is any nucleotide; i which designates the number of nucleotides in the sequence is at least 2 and n is at least 2, or substantially of the form [(Xl...Xi)mY]w in which X is any nucleotide, Y is any group of 1 or more nucleotides and is different from (Xl...Xi), m is at least 1, w is 2, and i is at least 2, the number of nucleotides in said probe being less than 3i when i is greater than 3.
AIMS: To assess whether a reduction in intensity of signal observed using an alkaline phosphatase labelled oligodeoxynucleotide probe could be explained on the basis of procedural steps rather than reduced sensitivity. METHOD: Signal intensity was assessed on in situ hybridisation for pro-opiomelanocortin (POMC) mRNA in rat pituitary and for somatostatin mRNA in human pancreas and in northern blot analysis for POMC mRNA in the presence and absence of formamide. The direct effects of formamide on the alkaline phosphatase detection step were assessed using histochemical enzyme detection in rat kidney. RESULTS: All signals were reduced in systems containing formamide. CONCLUSIONS: In the absence of formamide clear, strong signals for specific mRNAs can be obtained by in situ hybridisation and northern blot analysis using oligodeoxynucleotide probes directly labelled with alkaline phosphatase. Formamide seems to inhibit the activity of alkaline phosphatase.
TY - JOUR. T1 - A new usage of functionalized oligodeoxynucleotide probe for site-specific modification of a guanine base within RNA. AU - Onizuka, Kazumitsu. AU - Taniguchi, Yosuke. AU - Sasaki, Shigeki. PY - 2010/1/29. Y1 - 2010/1/29. N2 - Site-specific modification of RNA is of great significance to investigate RNA structure, function and dynamics. Recently, we reported a new method for sequence-and cytosine-selective chemical modification of RNA based on the functional group transfer reaction of the 1-phenyl-2-methylydene-1,3-diketone unit of the 6-thioguanosine base incorporated in the oligodeoxynucleotide probe. In this study, we describe that the functionality transfer rate is greatly enhanced and the selectivity is shifted to the guanine base when the reaction is performed under alkaline conditions. Detailed investigation indicated that the 2-amino group of the enolate form of rG is the reactant of the functionality transfer reaction. As a potential application of this efficient ...
is also predominant in West Central and East African countries where other subtypes cocirculate.. We developed and validated a relatively simple oligonucleotide probe hybridization ...
SINGLE-USE TEST MODULE FOR DETECTION OF HYBRIDIZATION OF TARGETS WITH OLIGONUCLEOTIDE PROBES - diagram, schematic, and image 93 ...
Label-free optical bifunctional oligonucleotide probe for homogeneous amplification detection of disease markers Kejun Feng, Li-Ping Qiu, Yifeng Yang, Zai-Sheng Wu, Guo-Li Shen and Ru-Qin Yu Biosensors and Bioelectronics Article in Press, Corrected Proof doi:10.1016/j.bios.2011.07.068Oligonucleotide-based detection schemes that avoid chemical modification possess significant advantages, including simplified design, intrinsic affinity for targets, low cost and ease to…
ChiRP-Seq (Chromatin Isolation by RNA purification) is a high-throughput sequencing method to discover regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest). Recent studies have shown that a significant proportion of some genomes (including mouse and human genomes) synthesize RNA that apparently do not code for proteins. The function of most of these non-coding RNA still has to be ascertained. Various genomic methods are being developed to map the functional association of these novel RNA to distinct regions of the genome to gain a better understanding of their function. ChiRP-Seq is one of these new methods which uses the massively parallel sequencing capability of 2nd generation sequencers to catalog the binding sites of these novel RNA molecules on a genome. Overview of ChiRP-Seq method: Tens of oligonucleotide probes are designed to be complementary to the RNA of interest. These oligos are labeled with biotin. Cells are ...
OligoProber are specific oligonucleotide probes for hybridization to its cognate species. These are specially suited for use in conjunction with Gene Link RT-PCRmers as the complementary target sequence is in the amplified sequence. The OligoProber can also be used for all northern blots. OligoProber are available for use as hybridization probes with either 5 OH for 32P labeling or with 3 biotin or digoxigenin for non-radioactive detection. The OligoProber is supplied as a lyophilized powder in aliquots of 2 nmoles. The 2 nmoles of probe when dissolved in 100uL sterile water or TE will give a solution of 20 uMolar i.e. 20 pmoles/uL. ...
LONDON - In the past year, the value of the worlds oligonucleotide pool exceeded USD 1.29 billion. It is expected to go beyond USD 2.32 billion, registering an 8.5% CAGR over 2017-2022. Robust growth is attributed to such factors as increasing Big PharmaCos investments in oligonucleotide drug development, constantly widening application area of oligonucleotides and also rising involvement of CMOs in therapeutic oligonucleotides manufacturing, amid others.. Still, there are certain barriers to the further growth in the oligonucleotide pool market, for instance, inaccuracy issues associated with specific oligonucleotides and complexity in the manufacturing technology.. At present, North America captures the major share of the global oligonucleotide pool market; as of 2016, the regions share was slightly over 42%.. Some of the prominent global market players include Creative Biogene, CustomArray, Agilent Technologies, TriLink BioTechnologies, MYcroarray, Integrated DNA Technologies, Twist ...
... are hybridization probes that are used in a real time PCR assay for quantification of the target DNA. Molecular Beacons are single stranded and bind to the target when the target sequence is complementary
I am a graduate student in Microbiology using extracted _S. cerevisae_ DNA as part of a series of standard controls in dot-blot hybridizations, and have one (seemingly trivial) question. One of the oligo probes which I am using is described as Universal, and it does indeed bind to yeast genomic DNA (as well as mitochondrial, I assume). In the literature the probes specificity is for the 16S rRNA coding region (E. coli numbering). I am assuming that this particular sequence is identical to a similar region in the 18S rRNA region of yeast...(?) In any case, does anyone know how many binding sites in a single yeast genome (approximately) would bind this probe assuming that it binds rRNA? ...or perhaps where I could discover this information? Thanks in advance. David Singleton University of Georgia - Microbiology dsingle at uga.cc.uga.edu ...
The invention discloses and claims a signal amplification method for detecting a target nucleic acid analyte having a homopolymeric region and a target sequence. The method comprises (a) contacting an analyte under hybridizing conditions with a multiplicity of reporter probes, each probe including a signal region and an oligonucleotide sequence which is complementary to, and capable of forming a stable hybrid with the analyte homopolymeric region, whereby the hybridization of multiple reporter probes to the homopolymeric region provides for signal amplification; and (b) forming an analyte:capture probe hybrid by contacting the analyte target sequence with a capture probe under hybridizing conditions.
This unit provides protocols for the amplification and labeling of mRNA (and the necessary controls) for hybridization to oligonucleotide arrays
The Negative RNA is composed of oligonucleotide Probes; It is supplied as stable ready-to-use reagents labelled with biotin. It does not contain any sequences of human or viral origin. Therefore, the negative control probes should not yield any ...
Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes: 1471-2350-6-36.fm ral ss BioMed CentBMC Medical
Free Download ORMA (Oligonucleotide Retrieving for Molecular Applications) by Marco Severgnini - ORMA (Oligonucleotide Retrieving for Molecular Applications) is a series of integrated scripts in Matlab, which performs an accurate search of all the positions able to specifically discriminate...
... Published by spinvestconsulting at researchbeam.com [Report Price $3400] 108 Pages
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Epidemiological studies have shown an inverse relationship between risk of CVD and intake of whole grain (WG)-rich food. Regular consumption of breakfast cereals can provide not only an increase in dietary WG but also improvements to cardiovascular health. Various mechanisms have been proposed, including prebiotic modulation of the colonic microbiota. In the present study, the prebiotic activity of a maize-derived WG cereal (WGM) was evaluated in a double-blind, placebo-controlled human feeding study (n 32). For a period of 21 d, healthy men and women, mean age 32 (sd 8) years and BMI 23·3 (sd 0·58) kg/m2, consumed either 48 g/d WG cereal (WGM) or 48 g placebo cereal (non-whole grain (NWG)) in a crossover fashion. Faecal samples were collected at five points during the study on days 0, 21, 42, 63 and 84 (representing at baseline, after both treatments and both wash-out periods). Faecal bacteriology was assessed using fluorescence in situ hybridisation with 16S rRNA oligonucleotide probes ...
Use of an oligonucleotide probe to detect Vibrio parahaemolyticus in artificially contaminated oysters.: A 26-mer oligonucleotide specific to Vibrio parahaemoly
The present invention provides methods to detect biomolecules on a microarray using a scanning electron microscope. In one embodiment of the invention, errors in oligonucleotide synthesis during manufacturing of microarrays are detected by monitoring synthesis of control probes on the chips. In another embodiment, misalignment of features on the chip is determined. In yet another embodiment, the size, shape and edge definition of features on the chip is determined. In further embodiments, methods are provided for analyzing interactions between an oligonucleotide target and an oligonucleotide probe on a microarray and methods for testing conditions in a microarray manufacturing process.
Southwestern blotting, based along the lines of Southern blotting (which was created by Edwin Southern) and first described by B. Bowen, J. Steinberg and colleagues in 1980, is a lab technique which involves identifying and characterizing DNA-binding proteins (proteins that bind to DNA) by their ability to bind to specific oligonucleotide probes. The proteins are separated by gel electrophoresis and are subsequently transferred to nitrocellulose membranes similar to other types of blotting. The name southwestern blotting is based on the fact that this technique detects DNA-binding proteins, since DNA detection is by Southern blotting and protein detection is by western blotting. However, since the first southwestern blottings, many more have been proposed and discovered. The former protocols were hampered by the need for large amounts of proteins and their susceptibility to degradation while being isolated. "Southwestern blot mapping" is performed for rapid characterization of both DNA-binding ...
... ,These extended-length microarrays are custom designed to meet your needs. Two probe density format configurations are available: 8,455 features per array (2 arrays/1 x 3 glass slide) or 22,575 features per array (1 array/slide).,biological,biology supply,biology supplies,biology product
We have used oligonucleotide arrays to study the changes in mRNA expression after stimulation of the human HT1080 cell line with different IFNs. The effectiveness of this approach was evident by the ability to successfully identify and quantify the mRNA levels for many known ISGs. Previous Northern blot analyses of HT1080 cells showed that while IFN-α induced 6-16 mRNA levels by more than 20-fold, there was no detectable induction by IFN-γ; also, 9-27 mRNA levels were induced by both IFN-α and IFN-γ, although the level of 9-27 induction by IFN-α was 3-fold higher than by IFN-γ (5). These characteristics were replicated with remarkable similarity by the oligonucleotide arrays: 6-16 was absent in untreated cells and induced at least 20- and 21-fold by IFN-α or IFN-β, respectively, but not by IFN-γ; 9-27 was induced 23- and 22-fold by IFN-α or IFN-β and 8-fold by IFN-γ (Fig. 1 and Table 2). The consistency between our data and previous studies regarding IFN-specific inducibility further ...
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Methods of detecting, probing, mapping and directed sequencing of target nucleic acids are provided using a guide RNA and a Cas9 protein. Methods for detecting the binding of the guide RNA/Cas9 complex to a target nucleic acid where the guide RNA includes a 3 tail sequence that can hybridize to a probe are provided. Methods for detecting the binding of the guide RNA/Cas9 complex to a target nucleic acid where the complex is physically detected are provided.
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A set of broad-range PCR primers for the 16S rRNA gene in bacteria were tested, along with three series of oligonucleotide probes… Expand ...
Hogan KJ Burmester JK Caldwell MD Hogan QH Coursin DB Green DN Selzer RM Broderick TP Rusy DA Poroli M Lutz AL Sanders AM Oldenburg MC Koelbl JA de Arruda-Indig M Halsey JL Day SP Domanico MJ Perioperative genomic profiles using structure-specific oligonucleotide probes. Clin Med Res . 2009 Sep;7(3):69-84 ...
KNect365s TIDES: Oligonucleotide and Peptide Therapeutics is the worlds largest meeting to accelerate oligonucleotide and peptide products from early discovery to late-stage development & commercialization.
Customer Care and Technical Services are available via phone and email at the numbers and addresses listed below. Use the Chat now button to reach us by web chat.. We service customers through direct sales and a network of distributors. Our staff includes experts in molecular biology, oligonucleotide design, sequencing, mutagenesis, PCR, and related research applications. We are available for consultation before or after an order is placed. ...
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