BIOINFORMATICS 101: THE BASICS
PRIMER DESIGN
WHAT IS PRIMER?
A primer is a short single strand of RNA or DNA generally about 18-22 bases that serves as a starting point for DNA synthesis. It is required for DNA replication and amplification in PCR because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA. The polymerase starts replication at the 3′-end of the primer, and copies the opposite strand.
How to design primer?
FIRST STEP
Bring up the chosen sequence and choose the exons of interest
SECOND STEP
Paste the sequence into one of the resources of primer design
THIRD STEP
Change the parameters to suit optimal amplification
FOURTH STEP
Once the desired sequence is obtained, use the net primer
FIFTH STEP
Select gene of interest on the ensemble genome browser
Once a good pair is obtained, blast the sequence to make sure sequence is amplified
FINAL STEP
