primer design with RE sites - (Feb/25/2008 )
Hi,
i designed some primer with RE site included the sequence of primer is as follows
AAA AAA CCG GAA TTC GGT CAT GCA ATC in this sequence GAATTC is the RE recognition site. this sequence is correct or not.
please have a look on this and send your suggestions to me.
Thank you very much.
SVRREDDY.
i designed some primer with RE site included the sequence of primer is as follows
AAA AAA CCG GAA TTC GGT CAT GCA ATC in this sequence GAATTC is the RE recognition site. this sequence is correct or not.
please have a look on this and send your suggestions to me.
Thank you very much.
SVRREDDY.
hi! which is hte specific sequence and which is the added?.. You have to consider that the restriccion enzymes needs around 3 nucleotides more (depending on the enzyme) to cut efficiently. This is appart from the target sequence .
You can check this on manuals (promega, new england biolabs) etc. Depending how much nucleotides the enzyme needs is the efficiency of the cut.
Good luck!
hi! which is hte specific sequence and which is the added?.. You have to consider that the restriccion enzymes needs around 3 nucleotides more (depending on the enzyme) to cut efficiently. This is appart from the target sequence .
You can check this on manuals (promega, new england biolabs) etc. Depending how much nucleotides the enzyme needs is the efficiency of the cut.
Good luck!
Hi marielita,
AAA AAA CCG is the sequence added by me to before enzyme recognition sequence based NEB catolog is CCG, and AAA AAA is the i added based on the suggestions from this forum,
GAA TTC is the enzyme sequence,
GGT CAT GCA ATC this is the sequence of actual primer.(of course i added just letters to confirm my designing primer with restriction sites)
so please have look once again and send your suggestion to me
i am so thankfull to your suggestions.
SVRREDDY.
i designed some primer with RE site included the sequence of primer is as follows
in this sequence GAATTC is the RE recognition site. this sequence is correct or not.
please have a look on this and send your suggestions to me.
Thank you very much.
SVRREDDY.
Your template binding sequence is only 12 bp long. This is too short. The sequence should be 18-22 bp typically.
I second this. Although not due to shortness per se, but rather the Tm will be ridiculously low.