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Primers

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

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Primers

Postby nokok » Thu Jan 08, 2009 8:36 am

I found that some paper shown the primers like this " 5'-AGA GAG AGA GAG AGA GYT-3' " and
"5'-AGA GAG AGA GAG AGA GYC-3' "

GYT and GYC is collect or not? and possible be? :shock:

Thank you for your answer
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Re: Primers

Postby blcr11 » Thu Jan 08, 2009 2:07 pm

The "Y" usually means any pyrimidine. So each primer is probably a mixture of two. For the first primer the two possible end sequences would be GTT and GCT; for the second primer they would be GTC and GCC. I don't know if that makes sense. You'll have to put that in the context of what they were trying to do.
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Postby canalon » Thu Jan 08, 2009 6:30 pm

I second blcr11's answer. it is usually used when you have a polymorphism in your target and the PCR is designed to amplify all the possible forms.
For information from the sigma genosys website, here are the possible degeneracies and their codes:
M=A+C_________D=A+G+T
R=A+G_________B=C+G+T
W=A+T________N=A+G+C+T
S=C+G_________I=deoxyinosine (will pair with all 4)
Y= C+T________U=deoxyuridine (will replace T like in RNA)
K=G+T
V=A+C+G
H=A+C+T
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Postby nokok » Fri Jan 09, 2009 12:58 am

Thank you every much " blcr11" and "canalon".
Your 's answers give me understand.
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