6 Applications of Primer Synthesis in Biotechnological Processes

May 30, 2024

Primer synthesis plays a fundamental role in various processes aimed at manipulating, amplifying, sequencing, and analysing DNA or RNA molecules. Primers are essential in techniques like Polymerase Chain Reaction (PCR), DNA sequencing, site-directed mutagenesis, cloning, and gene expression analysis. 

What is a Primer?

A primer is a short, single-stranded DNA sequence, typically around 18 to 25 nucleotides in length. It serves as a starting point for DNA synthesis. In various biotechnological applications, primers are designed to anneal to specific target sequences within DNA or RNA molecules. This initiates processes such as DNA amplification, sequencing, mutagenesis, cloning, and gene expression analysis. 

Let’s delve deeper into the significance of primer synthesis in biotechnology.

Polymerase Chain Reaction (PCR)

Primers are indispensable components of PCR, a widely-used technique for amplifying specific DNA sequences. Custom-designed primers complementary to the target DNA region are synthesised. During PCR, these primers anneal to the DNA template precisely, marking the starting and ending points for DNA amplification. Primer synthesis ensures the availability of tailored primers, facilitating the precise amplification of desired DNA fragments.

Reverse Transcription (RT)-PCR

In RT-PCR, primers help to initiate the synthesis of complementary DNA (cDNA) from RNA templates by reverse transcriptase enzyme. This technique allows for the detection and quantification of gene expression levels by amplifying RNA transcripts.

In Situ Hybridization (ISH)

In ISH techniques, researchers use primers labelled with fluorescent or other detection tags to visualise specific nucleic acid sequences within cells or tissues. ISH is a common method for conducting gene expression analysis, chromosome mapping, and studying the cellular localisation of nucleic acids.

Site-Directed Mutagenesis

Primers are instrumental in introducing specific mutations into target DNA sequences. Mutagenic primers are designed with desired mutations incorporated into their sequences. Primer synthesis ensures the generation of custom-designed primers containing the desired mutations, enabling precise modification of DNA sequences for functional studies or engineering purposes.


Primers play a crucial role in cloning procedures by amplifying DNA fragments for subsequent insertion into vectors. Designed with sequences complementary to the ends of the DNA fragment of interest, primers facilitate the amplification of DNA fragments suitable for cloning. Primer synthesis ensures the availability of primers tailored to the cloning strategy, enabling efficient amplification of DNA fragments for subsequent cloning steps.

Gene Expression Analysis

In techniques such as RT-PCR and qPCR, primers are essential for amplifying and quantifying specific RNA or DNA sequences corresponding to target genes. Gene-specific primers amplify cDNA synthesized from RNA samples. Primer synthesis ensures the availability of optimized primers for gene expression analysis, facilitating accurate quantification of gene expression levels. Additionally, oligos/primers with modifications, such as probes and quenchers, play a crucial role in probe-based qPCR and RT-qPCR, enhancing the sensitivity and specificity of the assays.

Primer Synthesis at Bio Basic Asia Pacific

Primer Synthesis at Bio Basic Asia Pacific

Bio Basic Asia Pacific has been synthesizing oligonucleotides (non-modified oligo & modified oligo) applications for over 15 years. Custom-designed primers tailored to specific applications ensure the efficiency and accuracy of these techniques, making primer synthesis an indispensable component of modern biotechnology. At Bio Basic Asia Pacific, we offer access to over 100 free universal primers to enhance sequencing reactions. If you are looking for custom or universal primers and synthesis services, head to our website or contact us at sg@biobasic-asia.com. Our comprehensive oligonucleotide synthesis service includes the production of high-quality primers, ensuring optimal performance for your research needs.