In Situ PCR, Procedure, Applications, Limitations

In-situ PCR is a modern category of Polymerase Chain Reaction that utilizes the in situ hybridization with blend of cellular localization & extreme sensitivity of PCR.

Through particular gene segment amplification within tissue or intact cell and copy numbers that are incrementing to extents measurable by immunohistochemistry and ISH.

This is a useful technique to detect viral DNA including HIV, HBV, and CMV with chromosomal translocation, intra suspension viral RNA, cytocentrifuge preparation, and DNA rearrangements.

It is a type of histological process that utilizes PCR benefits to find mRNA & DNA in tissue matrix directly. It may also merges the in-situ hybridization and Polymerase Chain Reaction together which is conventionally used to target localization mRNA and DNA in cell organelles, tissue matrix, or whole cell.

The ex-situ reaction happens outside the original spot while In situ reaction happens in the dedicated place of it.

Typical in-situ reaction is a type hybridization utilized in DNA microarray and fish.

In situ PCR

What is In situ in PCR?

In Situ is a Latin word which means in the original position. The word scientifically means that in situ reaction takes place in the it original position. The paraffin implanted tissues specimen so the reaction happens straight on paraffin implanted tissue, after certain purification steps.

In in this reaction category, the instance if specimen is a cell layer, the biochemical reaction may happens on the cell surface.

In-Situ PCR?

It is tri step process that includes

  • Tissue preparation to be amplify
  • DNA amplification
  • Proteolytic dissolution

The tissue is affix upon silane coated slide. Silane is utilizes to affix tissue upon slide which means it aids in cell sticking.

Post tissue cleansing and fixing, the ennzyme names proteolytic dissolute cell’s protein section. Typical agents in this dissolution that aids are proteinase K, pepsin, and trypsin.

Chymotrypsin, trypsin, and pepsin are continuously liked in the in-situ Polymerase Chain Reaction absorption due to its more limited life expectancy.

After the dissolution completed, a particular master-matrix is put into cell top together with the primers and various other additives of PCR.

Post enveloping it, the slide is straightforwardly positioned for intensification/amplification in thermocycler.

The fact is this Polymerase Chain Reaction procedure is a kind of very touchy and drawn-out. The yield of the response relies upon how we set up the intensification example.

in situ pcr protocol

The beginning stuff or tissue for the in-situ are cell culture, paraffin-implanted tissues, a cell suspension or a flimsy cell layer.

Place the sample for 10-12 hours overnight along with formalin (10% formalin) added in it.

Use phosphate buffer saline to wash twice the tissue/sample in order to get contaminations removed.

Wash the cell sample with by two round PBS of centrifugation of about 2500 rpm.

Then prepare with saline the slide covering, salive helps in cell fixation.

Now set thin paraffin implanted tissue layer to slide.

Paraffin can stop intensification, so it is compulsory for the tissue to be treated with xylene ethanol.

Set the slide on fresh solution of xylene fo about 9 minites and set in beneath ethanol (100% ethanol) for about 12 minutes.

Let the slide to be air dry to eliminate ethanol excess.

the observe, if the tissue is attached to slide, it is ready to be utilized for PCR.

In-situ PCR Procedure

This PCR type begins with tissue fixation.

The fixation aids in tissue structural hierarchy to be maintained along with tissue morphology prevention. This also will protect DNA integrity.

The slide sample in the next step will be allowed to process proteolytic dissolution.

2ml of proteolytic protein can be utilized for the assimilation taken after by alcohol washing.

Now the sample have to be amplified in the next step.

We have to get ready master-blend for in-situ Polymerase Chain Reaction succession. for the purpose, one of the primer categories are chosen from the below:

  • Arbitrary octa/hexa nucleo-primers.
  • Primers that are flourescently marked.
  • Oligo primers.

This strategy is typically applied to DNA quantification in the sample, also, it is the best known PCR variant available.

Utilize flourescent marked oligo primers for real time PCR process.

Once apparatus settled, the slide have to be coverslip into thermocycler.

in-situ Polymerase Chain Reaction procedure

In situ Hybrdization

Hybridization phenomena occurs straight at the exact place on tissue, on slide surface with aid of RNA or DNA is known as insitu hybridization.

Utilization of flourescent marked probes in flourescent in-situ hybridization (FISH) is a best hybridization instance.

Tissue specimen in FISH is attached over slide and permeabilized with chemical process aid.

Short RNA or DNA probes that are fluorescent marked are applied to the hybridization site with the iterated chemical treatment process.

This technique is highly useful in figuring chromosomal aberrations along with the capability to find many ither molecular abnormalities.

In-Situ PCR Applications:

By taking in consideration the in-situ Polymerase Chain Reaction, a sole DNA copy in the sample can be amplified.

visualizing & restricting amplicon inside the cell is conceivable by in-situ.

The low DNA duplicates can be distinguished with high affectability using this Polymerase Chain Reaction category.R

It is broadly utilized in embryogenesis and organogenesis investigation, likewise, it is utilized in irresistible illness determination like HIV.

In real-time insitu, DNA measurement is additionally a conceivable thing .

In Situ PCR Limitations

There is low reaction precision in this procedure.

High non particular binding possibilities during the operation.

Because of few duplicates multiplexing is not a feasible thing.


This slide Polymerase Chain Reaction type is an excellent strategy for nucleic acid detection for extremely low duplicates. Within the RT-Insitu Polymerase Chain Reaction, the target of interest is mRNA from which cDNA is created and expression level of gene is specifically measured on slide surface.

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