How we can Design Primer? Primer Blast. Primer Specificity. forward and reverse primer, GC and Tm?
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Primers are used to amplify
Primers are used to amplify ORF in PCR. Primers are of basically two types forward primer and reverse primer. primers start from 5 prime and ends at 3 prime. The primer design is an important step to get an optimal PCR. If you pick up primers without design, the amplification may not work or give you "strange" results, for example if the primer can hybridize at another position in the genome. Short primers are mainly used for amplifying a small, simple fragment of DNA. On the other hand, a long primer is used to amplify a eukaryotic genomic DNA sample. However, a primer should not be too long or too short. to design a primer some points are very important so that we can design a specified primer.
GC content
formula for GC content is
GC=(G+C/TOTAL nucleotide) 100
TM which is melting temperature can be find out by below formula:
Tm= 2(A+T)+ 4 (G+C)
After designing primer it can be checked by primer Blast that i had explained in one of my videos of Easy to understand playlist Bioinformatic tools. Link for Primer BLAST is given below:
How to blast Primers? How to check GC...
by PRIMER BLAST we can check primers specificity
GC content
formula for GC content is
GC=(G+C/TOTAL nucleotide) 100
TM which is melting temperature can be find out by below formula:
Tm= 2(A+T)+ 4 (G+C)
After designing primer it can be checked by primer Blast that i had explained in one of my videos of Easy to understand playlist Bioinformatic tools. Link for Primer BLAST is given below:
How to blast Primers? How to check GC...
by PRIMER BLAST we can check primers specificity
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