Hybridization and mirna oligonucleotide probes. Medical search. Frequent questions

Regulatory noncoding microRNAs (miRNAs) play a critical role in the regulation of gene expression [ 5 ] and are potential candidates for studying their role in the progression of PCa to androgen-independent stage. (biomedcentral.com)
MicroRNAs (miRNAs), a recently identified class of endogenous, small (~22 nt), non-protein coding, single-stranded RNA molecules, negatively regulate protein-coding genes by base-pair matching with the 3' UTRs of mRNAs. (biomedcentral.com)
Here, we describe a microfluidic-based method which enables the detection of microRNAs or miRNAs in single intact cells by flow-FISH using locked nucleic acid (LNA)-containing probes. (nih.gov)
MicroRNAs (miRNAs or miRs) play an active role in the regulation of gene expression by modifying mRNA stability and translation, usually through specific albeit partial complementary binding to the 3′ untranslated region. (nature.com)
Detections of small non-coding RNAs such as microRNAs and short oligonucleotide therapeutics such as ASO and siRNA require a robust, highly specific and sensitive assay with minimal time and effort, , delivering data for easy interpretation. (acdbio.com)
MicroRNAs (miRNAs) are 21-24 nt long non-coding RNAs that regulate gene expression at the post-transcriptional level. (researchsquare.com)
MicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in many developmental and cellular processes. (biomedcentral.com)
MicroRNAs (miRNAs) are an abundant class of small (approximately 22 nt) endogenous non-coding RNAs that direct post-transcriptional regulation of gene expression. (biomedcentral.com)
MicroRNAs (miRNAs) are associated with cytogenetics and molecular subtypes of acute myelogeneous leukemia (AML), but their impact on AML pathogenesis is poorly understood. (ashpublications.org)
The best characterized of these small RNAs are small interfering RNAs (siRNAs) and microRNAs (miRNAs). (moam.info)

In situ hybridization (ISH) is a type of hybridization that uses a labeled complementary DNA, RNA or modified nucleic acids strand (i.e., probe) to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ) or if the tissue is small enough (e.g., plant seeds, Drosophila embryos), in the entire tissue (whole mount ISH), in cells, and in circulating tumor cells (CTCs). (wikipedia.org)
In situ hybridization is used to reveal the location of specific nucleic acid sequences on chromosomes or in tissues, a crucial step for understanding the organization, regulation, and function of genes. (wikipedia.org)
The key techniques currently in use include in situ hybridization to mRNA with oligonucleotide and RNA probes (both radio-labeled and hapten-labeled), analysis with light and electron microscopes, whole mount in situ hybridization, double detection of RNAs and RNA plus protein, and fluorescent in situ hybridization to detect chromosomal sequences. (wikipedia.org)
RNA ISH (RNA in situ hybridization) is used to measure and localize RNAs (mRNAs, lncRNAs, and miRNAs) within tissue sections, cells, whole mounts, and circulating tumor cells (CTCs). (wikipedia.org)
In situ hybridization was invented by American biologists Mary-Lou Pardue and Joseph G. Gall. (wikipedia.org)
In situ hybridization is a powerful technique for identifying specific mRNA species within individual cells in tissue sections, providing insights into physiological processes and disease pathogenesis. (wikipedia.org)
However, in situ hybridization requires that many steps be taken with precise optimization for each tissue examined and for each probe used. (wikipedia.org)
In addition, in-situ hybridization on tissue sections require that tissue slices be very thin, usually 3 µm to 7 µm in thickness. (wikipedia.org)
Common methods of preparing tissue sections for in-situ hybridization processing include cutting specimens with a cryostat or a Compresstome tissue slicer. (wikipedia.org)
An alternative technology, branched DNA assay, can be used for RNA (mRNA, lncRNA, and miRNA ) in situ hybridization assays with single molecule sensitivity without the use of radioactivity. (wikipedia.org)
Paraffin-embedded glioma specimens were used for MiRNA locked nucleic acid (LNA) in situ hybridization and immunohistochemistry, and frozen glioma specimen were used for Real-time PCR. (biomedcentral.com)
Flow cytometry in combination with fluorescent in situ hybridization (flow-FISH) is a powerful technique that can be utilized to rapidly detect nucleic acids at single-cell resolution without the need for homogenization or nucleic acid extraction. (nih.gov)
The expression of circSHKBP1 was evaluated using quantitative real-time PCR and RNA in situ hybridization, and the molecular mechanism of circSHKBP1 was demonstrated by western blot, RNA pulldown, RNA immunoprecipitation, luciferase assays and rescue experiments. (biomedcentral.com)
The miRNAscope™ Assay is a highly sensitive and specific in situ hybridization assay that allows for the visualization of ASO, miRNA, siRNA and other nucleic acid targets between 17-50 nucleotides expression in intact tissues or cultured cells with single-cell resolution, preserving spatial and morphological context. (acdbio.com)
Luciferase reporter assays and fluorescence in situ hybridization were used to confirm the target regulation between miR-486-6p and HAT1. (researchsquare.com)
Whole mount in situ hybridisation (Wmish) of wild type Xenopus laevis embryos at different developmental stages. (xenbase.org)

A typical target-specific probe will contain 40 oligonucleotides, resulting in 20 oligo pairs that bind side-by-side on the target for detection of mRNA and lncRNA, and 2 oligos or a single pair for miRNA detection. (wikipedia.org)
miRNAs control gene expression by binding to the complementary sites in the 3' untranslated regions (3' UTRs) of target mRNAs and triggering either translational inhibition or mRNA degradation by a molecular mechanism which is a subject of intense investigation [ 6 - 9 ]. (biomedcentral.com)
It is likely that the intronic miRNAs are processed from the same primary transcript as the precursor mRNAs and thus, their expression levels are regulated by the expression of the host mRNA [ 39 ]. (biomedcentral.com)
MiRNAs post-transcriptionally silence target genes by binding to the 3′ untranslated region (3'UTR) of messenger RNA (mRNA) [ 10 ]. (biomedcentral.com)
DNA microarrays take advantage of the major feature of the DNA double helix, the sequence complementarity of the two-paired strands, by using DNA capture probes which are the complement of the expressed target sequence (mRNA, cRNA or cDNA made from the mRNA). (ddw-online.com)
The MO removed the poly(A) tail and blocked zebrafish cdk9 (zcdk9) mRNA translation, showing functional mimicry between miRNA and MO. (echinobase.org)
A) Target sequence within the zcdk9 mRNA 3′-UTR and MO hybridization positions. (echinobase.org)
A) Terminal sequence of the zcdk9 mRNA 3′-UTR and hybridization positions of antisense MOs . (echinobase.org)
RNA-like oligonucleotides that are complementary to a portion of a target mRNA molecule. (genomicglossaries.com)
More specifically, antisense oligonucleotides that are useful as reagents for target validation , or as drugs, are engineered molecules that differ from natural RNA but that have a base sequence that is recognized as being complementary to a very specific mRNA sequence. (genomicglossaries.com)
Generally, both miRNAs and siRNAs with perfect base-pairing to mRNA target that mRNA for degradation, whereas imperfect base-pairing to mRNA targets predominantly leads to translational repression (10, 75). (moam.info)

ViewRNA assays) can be used to visualize up to four targets in one assay, and it uses patented probe design and bDNA signal amplification to generate sensitive and specific signals. (wikipedia.org)
With their expertise and through clear communication, we developed several assays to detect both RNA and short oligonucleotides in tissue. (acdbio.com)
Majority of the assays identify specific sequence through hybridization of an immobilized probe to the target analyte after the latter has been modified with a covalently linked optical probe. (nanomaterialpowder.com)

A simple carbon nanodot-based electrogenerated chemiluminescence biosensor is described for sensitive and selective detection of microRNA-21 (miRNA-21), a biomarker of several pathologies including cardiovascular diseases (CVDs). (uam.es)
These results paved the way for the development of a sensitive ECL biosensor for the detection of miRNA-21. (uam.es)
The biosensor shows a linear response to miRNA-21 concentration up to 100.0 pM with a detection limit of 0.721 fM. (uam.es)
Enzyme-free hybridization chain reaction (HCR) technology is often used as a signal amplification tool for the detection of different targets. (bvsalud.org)
In this web page, recent advances in nucleic acid detection using exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probe technologies are introduced to you. (ne.jp)
In ECHO probes, a hybridization-dependent fluorescent nucleotide regulated by the H-aggregation of thiazole orange organic dyes (D 514 ) is incorporated into specific sequence contexts and serves as fluorescent detection readout for target nucleic acids. (ne.jp)
Multicolor detection and auxiliary functional modules have been built into ECHO probes to accommodate a broad range of biological applications. (ne.jp)
using functionalized Au NPs for biosensing, namely, sensing of DNA and oligonucleotides, SPR biosensor with functionalized Au NPs, cell detection and labeling with functionalized Au NPs, protein detection, detecting heavy metal ions, sensing of glucose, and sensing of other biological-related molecules with functionalized gold nanoparticles, respectively. (nanomaterialpowder.com)
Detection of DNA, aptamers, and oligonucleotide has received great attention in the past few years because it has important applications in medical research and diagnosis and food and drug industry monitoring. (nanomaterialpowder.com)

1 , 2 Most miRNAs are predicted to regulate several hundred mRNAs, and many mRNAs are regulated by multiple miRNAs. (nature.com)
Metazoan miRNAs guide the miRISC to partially complementary sites in the 3' UTRs of target mRNAs to promote their translational repression or deadenylation and degradation. (biomedcentral.com)
Chemically modified antimiR oligonucleotides sequester the mature miRNA in competition with cellular target mRNAs leading to functional inhibition of the miRNA and derepression of the direct targets. (biomedcentral.com)

In this review, we focus on the use of antisense oligonucleotides (antimiRs) in miRNA inhibition for loss-of-function studies. (biomedcentral.com)
Pharmaceutical biology antisense, antisense DNA, antisense oligonucleotides. (genomicglossaries.com)

Even though it has its own biases, small RNA sequencing appears to be the best method available for several reasons, it does not rely on probe design and hybridization, you can discriminate amongst members of the same microRNA family and you can detect, quantitate and discover in the same experiment (Linsen et al ref). (blogspot.com)

A large number of miRNAs are encoded in organized intronic clusters within many protein coding genes. (biomedcentral.com)
Here we have examined the expression of mature miRNAs of miR 17-92, miR 106b-25 and miR 23b-24 clusters along with their host genes C13orf25, MCM7 and AMPO respectively in PCa cell lines. (biomedcentral.com)
The expression profiling of miRNAs and host genes was performed in androgen-sensitive MDA PCa 2b and LNCaP as well as in androgen-refractory PC-3 and DU 145 cell culture models of PCa. (biomedcentral.com)
We found significant expression variations between host genes and their resident miRNAs. (biomedcentral.com)
The expressions of C13orf25 and miR 17-92 cluster as well as MCM7 and miR 106b-25 cluster did not reveal statistically significant correlation, thus suggesting that host genes and resident miRNAs may be expressed independent of each other. (biomedcentral.com)
Gene expression modulating miRNAs are encoded in diverse genomic locations including intergenic regions, introns of protein-coding genes and introns/exons of noncoding RNA genes [ 36 ]. (biomedcentral.com)
4 , 5 , 6 The idea, however, that miRNAs may play an important role in some human disease/disorders is gaining momentum, and as these molecules have the ability to silence many genes simultaneously, dysregulation of even a single miRNA can have a significant polygenic effect. (nature.com)
miRNAs are either expressed from independent transcriptional units or derive from introns of protein-coding genes or exons or introns of long ncRNAs. (biomedcentral.com)
miRNA genes are transcribed by RNA polymerase II into long primary miRNA transcripts, termed pri-miRNAs that are usually several kilobases long and possess a 5' CAP and a poly(A) tail. (biomedcentral.com)

The probe hybridizes to the target sequence at elevated temperature, and then the excess probe is washed away (after prior hydrolysis using RNase in the case of unhybridized, excess RNA probe). (wikipedia.org)
probe sequence. (genelink.com)
Synthetic oligonucleotides with covalently-attached CDPI3 have enhanced DNA affinity and have improved the hybridization properties of sequence-specific DNA probes. (genelink.com)
This was developed by immobilization of a thiolated oligonucleotide, fully complementary to the miRNA-21 sequence, on the disposable gold electrode. (uam.es)
However, even this newly designed fluorescent probe exhibits a sequence-dependent change in the ratio of the fluorescence intensities for double- and single-stranded states. (ne.jp)
87(5): 1663-1667] Specifically, the investigators started by priming whole cerebellar RNA with a synthetic oligonucleotide containing a T7 RNA polymerase promoter sequence. (genomicglossaries.com)
Here we employ the probe sequence derived from the Hepatitis C virus to identify the optimal hybridization and thiol-Au NP tagging conditions. (springeropen.com)

Moreover, there is now ample evidence that perturbations in the levels of individual or entire families of miRNAs are strongly associated with the pathogenesis of a wide range of human diseases. (biomedcentral.com)

Aberrant miRNA expression in smokers compared to non-smokers and COPD compared to normal was analyzed using microarray datasets and reverse-transcriptase quantitative polymerase chain reaction (qPCR). (researchsquare.com)
In a typical polymerase chain reaction, the probes are initially subjected to flash heating at elevated temperatures to obtain efficient annealing. (springeropen.com)

Then, the probe that was labeled with either radio-, fluorescent- or antigen-labeled bases (e.g., digoxigenin) is localized and quantified in the tissue using either autoradiography, fluorescence microscopy, or immunohistochemistry, respectively. (wikipedia.org)

Because hybridization capture focuses on specific genomic regions of interest, it is a cost-effective and sequencing effort-saving approach. (idtdna.com)
This set of tracks shows the genomic positions of probes and targets from a full suite of in-solution-capture target enrichment exome kits for Next Generation Sequencing (NGS) applications. (ucsc.edu)

Subsequent signal amplification is predicated on specific hybridization of adjacent probes (individual oligonucleotides [oligos] that bind side by side on RNA targets). (wikipedia.org)
Signal amplification is achieved via a series of sequential hybridization steps. (wikipedia.org)
The probe self-dimer must be thermodynamically unstable because it contains many mismatched base pairs, but this plausible self-dimeric structure may inhibit fluorescence quenching because the formation of a 'primer dimer' in PCR experiments significantly decreases amplification efficiency. (ne.jp)
Before performing hybridization capture, DNA samples are converted into sequencing libraries -a process that involves random shearing of DNA and ligation of sequencing adaptors to the ends of the resulting fragments (PCR amplification may or may not be required). (idtdna.com)

Existing methods for measuring transcript levels in single cells include RT-qPCR (1), single molecule counting using digital PCR (2) or hybridization probes (3, 4), and next generation sequencing (5). (justia.com)

No. 63/298,867, filed Jan. 12, 2022, entitled "CASCADE OLIGONUCLEOTIDE DISPLACEMENT PROBES," the entire contents of which are incorporated herein by reference. (justia.com)

ECHO probes have a fluorescence-labeled nucleotide in which two molecules of thiazole orange or its derivatives are linked covalently. (ne.jp)
The clear change in fluorescence intensity depending on hybridization is useful for visible gene analysis. (ne.jp)

ISH can also use two or more probes, labeled with radioactivity or the other non-radioactive labels, to simultaneously detect two or more transcripts. (wikipedia.org)

These findings indicate that TIMP3 is a critical target of miR-221 and miR-222 and that these two miRNAs could be critical therapeutic targets and survival predictors in glioma. (biomedcentral.com)
Indeed, disease-associated miRNAs represent a new class of targets for the development of miRNA-based therapeutic modalities, which may yield patient benefits unobtainable by other therapeutic approaches. (biomedcentral.com)
The identified variants become the targets for a customized tumor-specific xGen MRD Hybridization Panel that can be designed, synthesized, and shipped within 5 business days from when the order is placed. (idtdna.com)

MiRNAs are dysregulated in tumors and function as oncogenic miRNAs or as tumor suppressor miRNAs [ 4 ]. (biomedcentral.com)
Growing evidence has indicated important roles for miRNAs in tumor invasion. (biomedcentral.com)
These reversible modifications are deemed to contribute to tumor suppressor gene inactivation by way of DNA methylation, histone modifications or miRNA expression. (hdacassay.com)

I particularly like the experiments performed in the Silence paper using a degenerate 21-mer RNA oligonucleotide. (blogspot.com)

They act as co-reactant agents in the anodic electrochemiluminescence (ECL) of [Ru(bpy)3]2+, producing different signals for the probe (single-stranded DNA) and the hybridized target (double-stranded DNA). (uam.es)
Pre-miRNAs are exported to the cytoplasm by Exportin-5 and processed further by Dicer, to ~22 nt double-stranded miRNA duplexes that are loaded into an Argonaute protein in the miRISC and rapidly unwound. (biomedcentral.com)

So if you were a crazy scientist who wanted to know all the miRNAs being expressed in the salivary glands of flies, would it be better to use NGS on the miRNA prep from the gland to do it, rather then use in a microarray of miRNAs (if there is such a thing? (blogspot.com)
The use of advanced bioinformatics, ultra-pure oligonucleotides, superior surface chemistry and advanced microarray cleanroom manufacturing facilities guarantees that Pathways™ Microarrays outperform the highest industry standards. (arrayit.com)

The aim of this study is to investigate the key regulatory miRNA-486-5p and underlying molecular mechanisms in chronic obstructive pulmonary disease (COPD) progression. (researchsquare.com)
Research advances have demonstrated the crucial regulatory roles of miRNAs in many diseases, including COPD [ 13 , 14 ]. (researchsquare.com)

The xGen MRD solution offers a complete sample preparation workflow including custom MRD hybridization capture panels delivered quickly and affordably. (idtdna.com)
Learn more about the design algorithm in this white paper The xGen™ Off-Target Quality Control (QC) Method increases accessible probe design space for hybridization capture when compared to the repeat annotation based QC method . (idtdna.com)

For hybridization histochemistry, sample cells and tissues are usually treated to fix the target transcripts in place and to increase access of the probe. (wikipedia.org)

Short CDPI3-oligonucleotides hybridize with single-stranded DNA to give more stable DNA duplexes than unmodified ODNs of similar length. (genelink.com)
The miRNA duplexes are loaded into an Argonaute protein in the miRNA-induced silencing complex (miRISC) and rapidly unwound. (biomedcentral.com)

Hybridization capture, also called target enrichment, is one method of targeted next generation sequencing (other methods include the use of amplicons or molecular inversion probes). (idtdna.com)
For sequencing runs that require additional sequencing precision, adapters with unique molecular identifiers (UMIs) can be used with hybridization capture. (idtdna.com)

Target-specific probes hybridize to each target RNA. (wikipedia.org)
Hybridization capture is a targeted next generation sequencing method that uses long, biotinylated oligonucleotide baits (probes) to hybridize to the regions of interest. (idtdna.com)

We report a dual gate/common channel organic transistor architecture designed for quantifying the concentration of one of the strands of miRNA-21 in solution. (unimore.it)
The ratio of quantum yields between after and before addition of the complementary nucleic acid strands showed a strong relationship with the number of possible Watson-Crick base pairs formed within two bases from D 514 in the 'self-dimer' of the probe. (ne.jp)
Gillespie and Spiegelman (1) observed that single stranded DNA binds strongly to nitrocellulose membranes in a manner that minimises the two strands reassociating with each other, but allows the hybridisation to complementary RNA. (ddw-online.com)

Pathways™ Microarrays offer the highest sensitivity and specificity of any product on the market, empowered by long-mer oligonucleotides, proprietary attachment and surface chemistry, and a unique one gene-one spot™ design. (arrayit.com)

While expression profiling studies of miRNAs are common place, little is known about the host gene and their resident miRNAs coordinated expression in PCa cells. (biomedcentral.com)
No significant correlation between the miRNA expression and the intrinsic hormone-responsive property of PCa cells was observed. (biomedcentral.com)
Androgen-sensitive MDA PCa 2b cells exhibited the highest level of expression of most miRNAs studied in this report. (biomedcentral.com)
Our results suggest that miRNA expression profiles may not predict intrinsic hormone-sensitive environment of PCa cells. (biomedcentral.com)
Therefore, the role of miRNAs and their differential signature expression patterns in androgen-dependent and androgen-independent PCa cells requires a closer validation. (biomedcentral.com)
We aimed to evaluate the selected miRNAs expression based on bioinformatic analysis and their changes before and after an ultramar. (researchgate.net)

Impedance spectroscopy and surface plasmon resonance (SPR) performed on the same oligonucleotide pair were correlated to the electronic current transduced by the EGOFET, and confirmed the selectivity of the biorecognition probe covalently bound on the gold surface. (unimore.it)

What is hybridization capture (target enrichment)? (idtdna.com)

Interestingly, we found circRNA-mediated regulation of target miRNAs and an in vivo growth inhibitory effect upon TUSC3 circ104557 transduction. (oncotarget.com)

In this study, an ultrasensitive and label-free method for detecting miRNA-21 was developed using the nanopore ionic current rectification (ICR) technology coupled with HCR technology. (bvsalud.org)
In this section, we will discuss a few examples of using functionalized Au NPs as ultrasensitive tools for sensing DNA, aptamers, and oligonucleotides. (nanomaterialpowder.com)

The recent explosion in miRNA research has accelerated the development of several computational and experimental approaches for probing miRNA functions in cell culture and in vivo . (biomedcentral.com)

The study has revealed the beneficial role of flash heating at 95 °C for efficient hybridization and the presence of citrate buffer for rapid and effective thiol tagging over the Au NPs. (springeropen.com)

The introduction of solid supports for DNA hybridisation/reassociations greatly broadened the range of applications of nucleic acid hybridisations, and provided the basis for solid-based methods being used today. (ddw-online.com)

In majority of these techniques, the efficient hybridization between the thiol-tagged probe and target DNA is crucial. (springeropen.com)

As a positive control for nucleic acid integrity in the tissue sections, we used a probe that hybridizes to a conserved region of the highly expressed PPIB of M. musculus (Cat. (cdc.gov)

The target miRNA-21 was hybridized with the probe on the electrode surface, and the hybridization was detected by the enhancement of the [Ru(bpy)3]2+/DNA ECL signal using CNDs. (uam.es)
Compared to standard complementary probes, the signal we obtained using ACD Bio was evident and specific. (acdbio.com)

We applied specific or control probes and then incubated the slides at 40°C for 2 h. (cdc.gov)

Anatomy9

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