Difference between Forward and Reverse Primer

Primers are stretches of nucleic acids (either DNA or RNA) that help in DNA replication. DNA polymerases bind with the primer to add nitrogenous bases to the growing strand. DNA replication in eukaryotes assembles a RNA primer, while in-vitro laboratory methods and techniques like polymerase chain reaction (PCR) use DNA primers.

Forward and Reverse primers are used in the process of polymerase chain reaction. They bind to the DNA strand and direct them toward elongation and amplification.

Forward Primer

Forward Primer is a DNA stretch that attaches to the antisense strand (-) of the DNA that runs in 3’ to 5’ direction. The primers anneal to the DNA strand and bring about amplification. The forward primer is complementary to the strand they bind to. The antisense strand usually serves the strand for synthesis of mRNA, therefore they are called coding strands.

Reverse Primer

Reverse Primers are DNA stretches that bind to the sense strand (+) of the DNA that runs in the 5’ to 3’ direction. They amplify the strand they bind to.

Forward vs Reverse Primer

Forward Primer

Reverse Primer

Description

Primers that bind to the antisense strand of the DNA are referred to as forward primers.

Primers that bind to the sense strand of the DNA are referred to as reverse primers.

Strand Annealing

It binds to the template strand of the DNA to synthesise coding strands.

It binds to the non-template strands of DNA to synthesise noncoding strands.

Properties of a Primer

A primer has to be specifically designed according to the strands it has to amplify in the PCR technique. There are numerous tools available now, such as GenScript, Primer-BLAST that can be used to design primers. Following are some of the properties that have to be kept in mind while designing a primer:

  • 18 to 24 base pairs in length.
  • It should be specific to the DNA region that is to be amplified.
  • The melting temperature for both the primers should be in a similar range.
  • Highly repeated sequences should be avoided as it can lead to formation of loops in the primer.
  • The primers designed should be different from each other, otherwise they can anneal to form dimers.

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Frequently Asked Questions

What happens if you only use a forward primer?

If you use only a forward primer, only the template strand will be synthesised but it will not have a complementary strand to bind to, hence no amplification will occur.

Does PCR use DNA or RNA primers?

PCR uses DNA primers. RNA primers are used in replication in vivo.

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