TY - JOUR. T1 - The effect of nucleobase-specific fluorescence quenching on in situ hybridization with rRNA-targeted oligonucleotide probes. AU - Behrens, Sebastian. AU - Fuchs, Bernhard M.. AU - Amann, Rudolf. PY - 2004/9. Y1 - 2004/9. N2 - Oligonucleotide probes labeled with fluorescent dyes are used in a variety of in situ applications to detect specific DNA or RNA molecules. It has been described that probe fluorescence might be quenched upon hybridization in a sequence specific way. Here, a set of 17 oligonuleotides labeled with 6-carboxyfluorescein was used to examine the relevance of nucleotide specific quenching for fluorescence in situ hybridization (FISH) to whole fixed bacterial cells. Probes quenched upon hybridization to a guanine-rich region of purified RNA in solution were not quenched upon FISH. Among other factors the high protein concentration within cells may prevent quenching of probe fluorescence in situ.. AB - Oligonucleotide probes labeled with fluorescent dyes are used in ...
Thank you for sharing this Applied and Environmental Microbiology article.. NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.. ...
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.
We use cookies to ensure that we give you the best experience on our website. If you click Continue well assume that you are happy to receive all cookies and you wont see this message again. Click Find out more for information on how to change your cookie settings ...
Oligonucleotide quantification methods and units can vary between manufacturers. Be sure you accurately measure and dilute your DNA and RNA oligos.
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
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING. . ...
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 ...
হিস্টিরিয়া একটি নিউরোসিস রোগ। এ রোগটি শারীরিক সমস্যা বা মানসিক সমস্যা নিয়ে প্রকাশ পেতে পারে।যাদের হিস্টিরিয়া রয়েছে তারা সাধারণত কোনো না কোনো ফোবিয়ায় আক্রান্ত, অনিয়মতান্ত্রিক জীবন-যাপন ও মানসিক অবসাদগ্রস্ত থাকেন।
Sequence analysis of domains 3 and 4 of 23S rRNA from Pseudomonas fluorescens Ag1 was carried out to allow the design of a strain-specific rRNA oligonucleotide probe targeting this strain. The specificity of the probe, Ps-Ag1, was assessed by dot blot analysis and whole-cell hybridization, and it was found to be specific for P. fluorescens Ag1. The correlation between the ribosomal content of P. fluorescens Ag1 and growth rate was determined during balanced growth conditions with generation times ranging from 1.2 to 31.8 h. Hybridization of the rRNA-targeting probes combined with charged coupled device-enhanced microscopy was used to determine the rRNA content. The total RNA content per cell was determined by staining with acridine orange and charged coupled device-enhanced microscopy. After 2 h under carbon starvation conditions, the rRNA content per cell decreased to 45% of the content of an exponentially growing cell. After 1 day of carbon starvation, the rRNA content had decreased to 20%. ...
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
In this study an approach that combines the specificity of fluorescent oligonucleotide probes with the sensitivity of PCR was used. E. coli and B. vulgatus were used for evaluation of the 5′ nuclease PCR assay as a tool to identify and quantify intestinal bacteria. Both bacteria are prominent normal gut bacteria that play an important role in the maintenance of a healthy gut microflora.. Conventional PCR has several disadvantages. These include the sensitivity of the assay to inhibition by substances present in the sample to be analyzed, the limitation of a small sample input, and the possibility of nonspecific binding of the primers or the probe. Finally, the PCR assay is very susceptible to contamination. The 5′ nuclease PCR assay (real-time PCR) solves several of these problems. In real-time PCR two primers and one probe are used, and a fluorescent signal can be generated only when all three are bound to the DNA at the correct primer and probe locations, which greatly reduces the risk of ...
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.
Imaging products of gene expression in live cells will provide unique insights into the biology of cells. Molecular beacons make attractive probes for imaging mRNA in live cells as they can report the presence of an RNA target by turning on the fluorescence of a quenched fluorophore. However, when oligonucleotide probes are introduced into cells, they are rapidly sequestered in the nucleus, making the detection of cytoplasmic mRNAs difficult. We have shown that if a molecular beacon is linked to a tRNA, it stays in the cytoplasm and permits detection of cytoplasmic mRNAs. Here we describe two methods of linking molecular beacons to tRNA and show how the joint molecules can be used for imaging an mRNA that is normally present in the cytoplasm in live cultured cells. This protocol should take a total of 4 d to complete.
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.
Taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. A frequently applied technology, fluorescence in situ hybridization (FISH), besides single cell identification, allows the localization and functional studies of the microbial community composition. Careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridization experiments. The PROBE Design tools of the ARB software package take into consideration several criteria such as number, position and quality of diagnostic sequence differences while designing oligonucleotide probes. Additionally, new visualization tools were developed to enable the user to easily examine further sequence associated criteria such as higher order structure, conservation, G+C content, transition-transversion profiles and in situ target accessibility patterns. The different types of sequence
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…
John Sousa is the author of this article in the Journal of Visualized Experiments: Rapid In Situ Hybridization using Oligonucleotide Probes on Paraformaldehyde-prefixed Brain of Rats with Serotonin Syndrome
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. ...
OligoProber are specific oligonucleotide probes for hybridization to its cognate species. These are specially designed 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 5OH 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 ...
Molecular Beacons 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 ...
a- Biosensing: DNA probe/target recognition detected by field effect. DNA is naturally charged (phosphate ions) → negative charge Qext at the surface of the semi conductor. ...
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.
Latest issue of IDTs DECODED newsletter offers informative oligonucleotide selection guide Integrated DNA Technologies (IDT), the world leader in oligonucleotide synthesis, provides a guide to choosing the right oligonucleotide modification in this quarters edition of the companys DECODED newsletter. As IDT offers hundreds of useful modifications for oligonucleotides, choosing the appropriate one for your work can be confusing. The article provides insightful information to help when choosing the right modification, including a detailed list of the modification categories...
This unit provides protocols for the amplification and labeling of mRNA (and the necessary controls) for hybridization to oligonucleotide arrays
Inside PlexPCR® Technology. PlexZyme® technology offers high performance and reliable qPCR detection.. During PlexPCR®, primers amplify target nucleic acid sequences and produce amplicons, which serve as a template for PlexZyme® formation. Once the partzymes have assembled into PlexZyme® enzymes, universal probes bind and enzymatic cleavage of the probes between fluorophore and quencher dye pairs generates fluorescence. Changes in fluorescence allow detection and/or quantification of the target nucleic acid in real time ...
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 ...
Locate Beacon App for iOS. Finds any nearby beacon with real-time distance estimates. Displays identifiers of each beacon discovered. Provides alerts when beacons are around. Allows you to calibrate beacons.
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...
Global Oligonucleotide Market Professional Survey Report Forecast 2017-2021 Published by spinvestconsulting at researchbeam.com [Report Price $3400] 108 Pages
Information about Beacons Pharmaceuticals products database; lists of Beacons Pharmaceuticals pharmaceutical drugs and health care production from Drugs-about.com
110 cheap monthly parking spots available in Beacon Hill starting from $53.10 right now through Spacer, book online now before theyre gone
Beacon Hill Staffing Group of Chicago, IL has earned the 2021 Best of Staffing award for providing remarkable service to their clients! Beacon Hill Staffing Group has 97 verified ratings from their clients earning them 4.8 out of 5 stars!
Beacon 2000 Lamps from Invitrogen,Quartz-Halogen, 100 W, High Intensity,biological,biology supply,biology supplies,biology product