Name: ish probes for dna and rna detection
Uploaded: 2021-04-07T12:12:00.000Z
Duration: 2 min 31 s
Channel: JoVE

K12 Standards

Tennessee Academic Standards

High School

Biology

links-among-engineering-technology-science-and-society

Links Among Engineering, Technology, Science, and Society

BIO1.ETS2.1

In-situ Hybridization

In situ hybridization is a technique used to locate DNA or RNA in cultured cells or in chemically preserved tissue sections.
RNA in situ hybridization is used to monitor where a gene is being expressed by detecting and quantifying the specific mRNA transcripts.
The target mRNAs are detected by single-stranded, complementary RNA probes that are created by in vitro transcription of a DNA template or synthesized by a chemical reaction.
The probes are labeled with radioactive isotopes, fluorophores, or other reporter molecules, such as biotin or digoxigenin, that can be bound and detected by a labeled antibody.
RNA in situ hybridization has four main steps: tissue fixation, permeabilization, hybridization, and detection.
To begin, fresh tissue is harvested and chemically treated to stop any biochemical reactions within the tissue and preserve its structural integrity. This preservation technique is called tissue fixation.
Next, proteins and lipids in the tissue need to be removed for the probe to access and bind the target RNA.
To degrade the proteins and permeabilize the cell membrane, the sample is treated with 0.2 molar hydrochloric acid and enzymes such as proteinases, while detergents are used to break down the lipids.
The target RNA is then hybridized with the probes at a temperature just below the melting point of the RNA-probe hybrid. This helps the probes to anneal with the complementary mRNAs. Unbound and loosely bound probes are removed by performing several washes.
The method for detecting the hybridized probes depends on the type of label. Radioactive probes are exposed to photographic films, while fluorescent probes are visible under fluorescent microscopes.
For other labels, antibodies against the reporter molecule are tagged with a fluorescent or colorimetric dye.
Detection of hybridized probes reveals the distribution of specific mRNAs indicating where the genes of interest are expressed.

in-situ hybridization

In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled probe. The technique was first used in 1969 for the investigation of nucleic acids. It is currently an essential tool in scientific research and clinical settings, especially for diagnostic purposes.
<h4>Types of probes and labels </h4>
A probe is a complementary strand of DNA or RNA that binds to corresponding nucleotide sequences in a cell. Many different&#160; probes, such as single-stranded DNA probes, double-stranded DNA probes, antisense RNA probes or riboprobes, and synthetic oligodeoxynucleotide probes, are used in in situ hybridization. The choice of probe depends on several&#160; factors, including their sensitivity, specificity, stability, and ease of penetration into the tissue sample.
These probes can be labeled with radioisotopes, fluorescent dyes, or other antigen molecules for detection purposes. The 3H, 35S, and 32P are widely used radiolabeled probes, while non-radioactive labels include biotin, digoxigenin, and fluorescein. These labels can be attached to the probe DNA molecule via end-labeling, nick-translation, or random primer synthesis methods. Detection methods, such as autoradiography, fluorescence microscopy, or immunohistochemistry, are used for target visualization based on the label attached to the hybridized probe.&#160;
<h4>Advantages and disadvantages of in situ hybridization</h4>
One of the major advantages of in situ hybridization is that it can even be applied to frozen tissues to enable maximum use of tissues that are difficult to obtain. In addition, it can be combined with other techniques, such as immunohistochemistry, to detect protein and active mRNA in the sample. However, while working with samples that have low DNA and RNA copies, it may be difficult to identify targets using in situ hybridization.

In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled ...

Education

JoVE Core

Molecular Biology

Unit 2

Analyzing Gene Expression and Function

KEY TERMS AND CONCEPTS

ish probes for dna and rna detection

In situ hybridization (ISH) uses labeled probes to detect and localize specific DNA or RNA molecules in cells, tissues, or tissue sections. The probe is a complementary strand of DNA or RNA that binds to a matching nucleotide sequence in the sample. Since its first use in 1969 for nucleic acid studies, ISH has become an important tool in research and in clinical diagnosis.

Several probe types can be used in ISH. These include single-stranded DNA probes, double-stranded DNA probes, antisense RNA probes, also called riboprobes, and synthetic oligodeoxynucleotide probes. The best choice depends on sensitivity, specificity, stability, and how easily the probe can enter the tissue sample.

Probes can also carry different labels for detection. Common labels include radioisotopes, fluorescent dyes, and other antigen molecules. Widely used radiolabeled probes include 3H, 35S, and 32P. Non-radioactive labels include biotin, digoxigenin, and fluorescein.

These labels are attached to the DNA probe by end-labeling, nick-translation, or random primer synthesis. After the probe binds to its target, the signal can be seen with autoradiography, fluorescence microscopy, or immunohistochemistry, depending on the label. ISH can even be used on frozen tissues, which helps when tissue samples are hard to obtain. It can also be combined with techniques such as immunohistochemistry to detect protein and active mRNA in the same sample. However, targets with low DNA or RNA copy number can be difficult to find with this method.

ISH Probes for DNA and RNA Detection

in vitro mutagenesis

In Vitro Mutagenesis for Gene Analysis

In vitro mutagenesis is a lab method used to change DNA and study gene function. It helps scientists test how specific DNA changes affect a gene’s activity and the traits it controls. A common approach is to make a known change in a DNA sequence and then examine the result. This can be done by deleting, inserting, or altering selected bases in a gene. The method is useful for linking a DNA change to a biological effect. Researchers use in vitro mutagenesis in molecular biology, genetics, and...

genetic screens

Using Genetic Screens to Find Disease Genes

Genetic screens are tools used to find genes and mutations linked to specific traits. They are also used to identify people or groups at risk for genetic diseases. That can support early intervention, targeted therapy, and reproductive choices. Forward genetic screens, also called classical screens, start with random DNA changes in an organism. Researchers may use radiation, mutagens, or added bases to create mutations that lead to visible phenotype changes. The mutant is then inbred so...

test cross

Test Cross in Genetic Inheritance

A test cross is a genetics tool used to determine the genotype of an organism with a dominant trait. It helps reveal whether the dominant individual is homozygous or heterozygous by crossing it with a recessive individual. The outcome of the cross shows the hidden genotype. If any offspring show the recessive trait, the dominant parent must carry one recessive allele. If all offspring show the dominant trait, the dominant parent is likely homozygous dominant. Test crosses are common in basic...

complementation tests

Using Crosses to Group Mutations

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single nucleotide polymorphisms-snps

SNPs as Genetic Markers and Variants

Single nucleotide polymorphisms, or SNPs, are small DNA changes at one specific genomic position. They are the most common type of sequence variation in the human genome. A point mutation counts as an SNP when it appears in more than 1% of the population.

bacterial transformation

Bacterial Transformation in the Lab

Bacterial transformation is a lab method used to move new DNA into bacteria. Scientists use it to change how bacteria behave or to help them carry a gene of interest. In high school biology, this process is often shown with plasmids, which are small circular DNA molecules. During transformation, bacteria take up DNA from their surroundings. The new DNA can then be used by the cell, depending on the experiment. This technique is an important part of genetic engineering and is widely used in...

transgenic organisms

Making Transgenic Organisms

Transgenic organisms are living things with DNA added from another organism. A transgene is the inserted gene. Scientists use this method to change an organism’s traits and to study how genes work. To make a transgenic organism, researchers first identify the gene they want to add. They then place that gene into the target organism’s DNA. Once the gene is integrated, the organism can pass it to new cells as it grows. This approach is useful in biology because it helps scientists analyze gene...

reproductive cloning

Cloning an Organism by Reproduction

Reproductive cloning creates a new organism that is genetically the same as the donor. It is different from cloning genes or cells because the goal is to make a whole living individual. This process usually relies on somatic cell nuclear transfer. In this method, the nucleus from a body cell is placed into an egg cell that has had its own nucleus removed. The egg can then develop into an embryo with DNA from the donor cell. Reproductive cloning is used to produce a copy of an organism, such...

crispr

CRISPR Gene Editing Basics

CRISPR is a gene editing tool that helps scientists make targeted changes to DNA. It uses a guide system to find a chosen sequence and a cutting protein to act at that spot. This method is based on a natural defense system found in bacteria. In high school biology, it is often studied as a way to see how genes can be edited with precision. CRISPR is widely used in molecular biology research. It helps scientists explore how genes function and how DNA changes can affect living things.

experimental rnai

RNAi for Gene Silencing and Discovery

RNA interference (RNAi) is a gene-silencing process used to reduce gene expression. It can block transcription or trigger RNA degradation. Scientists first discovered this mechanism in plants in 1998 through Andrew Fire and Craig Mello. RNAi has since been found in many eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. Researchers use it as a practical tool to study gene function. It can show what a gene does without permanently changing the organism’s DNA. <br...

reporter genes

Reporter Genes in Cells and Plasmids

Reporter genes are protein-coding genes used to track gene activity in cells. They are often tagged to a gene of interest so scientists can see whether that gene is present or active. When the tagged genes are expressed together, reporter genes can produce visible signals such as fluorescence or luminescence. These signals help show the presence or absence of a gene of interest in an organism. They can also reveal the pattern of gene expression or the location of a DNA segment or protein...

In situ hybridization (ISH) uses labeled probes to detect and localize specific DNA or RNA molecules in cells, tissues, or tissue sections. The probe is a complementary strand of DNA or RNA that binds to a matching nucleotide sequence in the sample. Since its first use in 1969 for nucleic acid studies, ISH has become an important tool in research and in clinical diagnosis. Several probe types can be used in ISH. These include single-stranded DNA probes, double-stranded DNA probes, antisense...

chromatin immunoprecipitation- chip

ChIP Methods for DNA-Protein Binding

Chromatin immunoprecipitation, or ChIP, is an antibody-based method for finding where proteins bind to DNA. It is used to identify DNA sites bound by transcription factors or histone proteins. ChIP also helps show which histone changes are present, including acetylation, phosphorylation, and methylation. ChIP is commonly divided into two forms: X-ChIP and N-ChIP. X-ChIP first cross-links proteins to DNA inside the cell, then breaks the DNA into pieces by sonication. The protein-DNA complexes...

synthetic biology

Synthetic Biology in Crops and Cells

Synthetic biology combines engineering, molecular biology, cell biology, and systems biology to redesign living systems. Scientists use it to remodel organisms from nature or to build new synthetic organisms. These tools can support protein or enzyme production, bioremediation, the production of useful macromolecules, and the addition of helpful traits to crops. One well-known example is golden rice. This genetically modified rice plant makes grains rich in β-carotene, which is a precursor of...

ribosome profiling

Ribosome Profiling for Translation Snapshot

Ribosome profiling is a deep sequencing method that gives a snapshot of active translation in a cell. It sequences the mRNAs protected by ribosomes. This shows which messages are being read to make proteins at a specific moment. The method has several uses in biology. It can track translation in a living organ or tissue type. It also helps measure new protein synthesis levels. Researchers use it to find translated open reading frames, which are stretches of RNA that can make protein. It can...

transgenic plants

Transgenic Plants for Better Crops

Transgenic plants are crops that have been changed with recombinant DNA technology, also called transgenesis. This method adds a foreign gene or removes a harmful one from an organism. The result is a genetically modified organism. The first transgenic plant was a tobacco plant made in 1983, and it was resistant to tobacco mosaic virus. Since then, transgenic plants have been developed for many uses in agriculture, horticulture, and ornamental plants. Some are designed to resist pests or...

gene therapy

Gene Therapy for Disease Treatment

Gene therapy is a treatment approach that changes gene activity to help address disease. It focuses on the genetic cause of a problem rather than only easing symptoms. In this way, it is used in disease intervention. One common strategy is to replace a faulty gene with a normal copy. Another strategy is to inactivate a gene that is causing harm. Gene therapy can also introduce a new gene to help cells work more normally.

epistasis analysis

Gene Interaction Maps in Epistasis

Gene interaction maps in epistasis show how different genes work together to shape a phenotype. In epistasis, the interaction of genes or alleles at different locations affects the final trait. This often happens when one gene masks or interferes with the expression of another gene. Epistasis is common when genes are part of the same biochemical pathway. In that case, the expression of one gene can depend on a gene product made earlier in the pathway. Genes that mask or inhibit other genes in...

genome-wide association studies-gwas

Using SNP Patterns to Link Disease Risk

Genome-wide association studies, or GWAS, look for common SNPs, or single nucleotide polymorphisms, that may be linked to disease. Researchers compare how often a SNP appears in people with a disease and in people without it. When a SNP is seen more often in the disease group, it is considered associated with that disease. GWAS uses chi-square analysis to test the chance that an allele is linked to the disease. This approach does not require scientists to first find the target gene behind the...

key terms and concepts

Learn how in situ hybridization uses labeled DNA and RNA probes to find specific sequences in cells and tissues, with common labels and detection methods.

ISH Probes for DNA and RNA Detection | JoVE K12

molecular biology

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Obtain, evaluate, and communicate information on how molecular biotechnology may be used in a variety of fields.
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BIO1.ETS2.3

ISH Probes for DNA and RNA Detection

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