Bioinformatics Genomics

Types of PCR

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Common types of PCR are;

Amplified fragment length polymorphism (AFLP) PCR

It is a PCR-based technique that uses selective amplification of a section of digested DNA fragments to generate unique fingerprints for genomes of interest.

Allele-specific PCR

Allele-specific polymerase chain reaction (AS-PCR) is a technique based on allele-specific primers, which can be used to analyze single nucleotide polymorphism.


Alu PCR is a rapid and easy DNA fingerprinting technique based on the simultaneous analysis of many genomic loci surrounded by Alu repetitive elements. 

Assembly PCR

Assembly PCR is a method for the assembly of large DNA oligonucleotides from multiple shorter fragments. In PCR, the size of oligonucleotides used is 18 base pairs, while in assembly PCR lengths of up to 50bp are used to ensure correct hybridization.

Asymmetric PCR

Asymmetric PCR is a variation of PCR used to preferentially amplify one strand of the original DNA more than the other. 


Co-amplification at lower denaturation temperature-based polymerase chain reaction (COLD-PCR) is a novel form of PCR that selectively amplifies low-abundance DNA variants from mixtures of wild-type and mutant-containing (or variant-containing) sequences, irrespective of the mutation type or position on the amplicon. 

Colony PCR

Colony PCR is a method in which, where identification of DNA of interest inserted into the plasmid is obtained by designing the inserted DNA specific primers.

Conventional PCR

Conventional PCR is applied in selective DNA isolation, amplification and quantification of DNA, medical and diagnostic approaches, infectious disease diagnosis, forensic studies and research areas.

Digital PCR

Digital PCR (dPCR) is a quantitative PCR technology that provides a sensitive and efficient way for the measurement of the amount of DNA or RNA present in a sample.

Fast cycling PCR

Fast cycling PCR is a PCR-based technology that allows amplification of specific PCR products with significantly reduced cycling time.

High-fidelity PCR

High-fidelity PCR is a modified PCR method that utilizes a DNA polymerase with a low error rate and results in a high degree of accuracy in the replication of the DNA of interest.

Hot start PCRis

Hot start PCRis a novel form of conventional polymerase chain reaction (PCR) that reduces the occurrence of undesired products and formation of primer-dimers due to non-specific DNA amplification at room temperatures. 

In-Situ Polymerase Chain Reaction

In-Situ Polymerase Chain Reaction(In-situ PCR) is an effective method that detects minute quantities of rare nucleic acid sequences in frozen or paraffin-embedded cells or tissue sections for the compartmentalization of those sequences within the cells.

InterSequence-Specific PCR

InterSequence-Specific PCR (or ISSR-PCR) is a method for DNA fingerprinting that uses primers selected from specific segments repeated throughout a genome to produce a unique fingerprint.

Inverse polymerase chain reaction

Inverse polymerase chain reaction (Inverse PCR) is one of the many variants of the polymerase chain reaction that is used to amplify DNA when only one sequence is known.

LATE (Linear-After-The-Exponential) PCR

LATE (Linear-After-The-Exponential) PCR is a modification of Asymmetric PCR which uses a limiting primer with a higher melting temperature than the excess primer which maintains reaction efficiency as the limiting primer concentration decreases mid-reaction.

Long-Range PCR

Long-Range PCR is a method for the amplification of longer DNA lengths that cannot typically be amplified using routine PCR methods or reagents. 

Methylation-specific PCR

Methylation-specific PCR (MSP) is a method for the detection and analysis of DNA methylation patterns in CpG islands.

Multiplex PCR

Multiplex PCR is a common molecular biology technique used for the amplification of multiple targets in a single PCR test run.

Nested PCR

Nested PCR is a useful modification of PCR technology where the specificity of the reaction is enhanced by preventing the non-specific binding with the help of the two sets of primer.

Quantitative PCR (qPCR)

Quantitative PCR (qPCR), also called real-time PCR or quantitative real-time PCR, is a PCR-based technique that couples amplification of a target DNA sequence with quantification of the concentration of that DNA species in the reaction.

Repetitive sequence-based PCR

Repetitive sequence-based PCR (rep-PCR) is a modified PCR technology that uses primers that target non coding repetitive sequences interspersed throughout the bacterial genome. 

Reverse transcription PCR (RT-PCR)

Reverse transcription PCR (RT-PCR) is a modification of conventional PCR, whereby RNA molecules are first converted into complementary DNA (cDNA) molecules that can then be amplified by PCR.

RNase H-dependent PCR

In this, the primers contain a removable amplification block on their 3’ end.

Single specific primer-PCR (SSP-PCR)

The single specific primer-PCR (SSP-PCR) is a PCR-based technology that permits amplification of genes of which only a piece of partial sequence information is available.

Solid-phase PCR (SP-PCR)

It is a unique PCR technique that allows amplification of target nucleic acids on a solid support where one or both primers are immobilized on the surface.

Suicide PCR

Suicide PCR is commonly used studies where avoiding false positives and ensuring the specificity of the amplified fragment is the highest priority.


TAIL PCR is a powerful tool for the recovery of DNA fragments adjacent to known sequences.

Touch Down PCR

It is a modification of PCR in which the initial annealing temperature is higher than the optimal Tm of the primers and is gradually reduced over subsequent cycles until the Tm temperature or “touchdown temperature” is reached.

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