Molecular Biology/primer

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Expert: Umashankar - 9/23/2006


Question
Dear umashanker.
I desined this primer: gtcaaaataaaaa, for randomly amplification of AT rich phytoplasma genom through a crude extract of phytoplasma and plant genomic material. but I hve not ever obtained any bands even by increasing  Mgcl2 in PCR.I think it is because of primer quality.
what do you think about this problem.
thnaks for coopration in advance.
sincerely:
siampou

Answer
Dear majid,

I guess that the primer what you have designed might have
less affinity, because the one of termini' regions contains least gc clamp. (termini gc content is often attributed to good anchoring of primers).

Moreover we have to see both the primers forward and reverse

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Umashankar

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I have got good experience in the field of Bioinformatics,My expertise includes sequence analysis,Molecular modeling, Molecular Dynamics genomics,Proteomics,Metabalomics,Nanoinformatics, and genetics,My areas of Specialization are:- Codon Usage and Bioinformatics software automation

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5 years

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M.Phil in Genetics M.Sc in Zoology PG Diploma in Bioinformatics S-star certification in Bionformatics (S-star alliance -National university of Singapore) Pursuing Ph.D., at School of Genomics, Dept. of Zoology, Loyola College, Chennai,India.

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