Primer- Definition, Types, Primer Design Online Tools, Uses


A primer is a short strand of nucleic acid, either RNA or DNA, that provides a starting point for DNA synthesis . It is bound to the template DNA and has a free 3`-OH end that can be extended by DNA polymerase . Primers are needed for DNA replication in living organisms and for polymerase chain reaction (PCR) in the laboratory .

In living organisms, primers are short strands of RNA that are synthesized by an enzyme called primase, which is a type of RNA polymerase. The primer serves to prime and lay a foundation for DNA synthesis by providing a 3`-OH end for DNA polymerase to attach new DNA nucleotides to an existing strand of nucleotides. The primers are removed before DNA replication is complete, and the gaps in the sequence are filled in with DNA by DNA polymerases.

In the laboratory, scientists can design and synthesize DNA primers with specific sequences that bind to sequences in a single-stranded DNA molecule. These DNA primers are commonly used to perform PCR to copy pieces of DNA or for DNA sequencing. PCR is a technique that uses repeated cycles of heating and cooling to amplify a specific region of DNA using a pair of primers that flank the target sequence. DNA sequencing is a technique that determines the order of nucleotides in a DNA molecule using primers that initiate the synthesis of complementary strands.

Primers are essential tools for molecular biology and biotechnology, as they enable the manipulation and analysis of DNA. Primers can be used for various purposes, such as cloning, gene expression, mutation detection, genotyping, gene editing, and more. Primers can also be modified with labels, such as fluorescent dyes or biotin, to facilitate detection or purification of the amplified or sequenced DNA.

Primers must be designed carefully to ensure specificity, efficiency, and accuracy of the desired reaction. Some factors that affect primer design include length, melting temperature, GC content, secondary structure, complementarity, and cross-hybridization. Various online tools are available to assist with primer design, such as Primer3, PrimerQuest, PerlPrimer, Oligo Primer Analysis Software, GenScript Real-Time PCR Primer Design, and AutoPrime.