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-   -   I need immediate help!! How to PCR primer designing? :help: (http://www.molecularstation.com/forum/pcr-polymerase-chain-reaction-forum/70107-i-need-immediate-help-how-pcr-primer-designing-help.html)

veniesh 08-16-2009 09:07 AM

I need immediate help!! How to PCR primer designing? :help:
 
I need immediate help!!

How to PCR primer designing?

I know primer design based on comparison of sequences of specific gene from GenBank.

Conserved regions were identified by using software Clustal X/W. Than primer A was designed based on the conserved amino acid sequence motif DD(T/I)(I/Y/F)D(A/V)Y(A/G). The sequence of sense primer A was 5’-GA(C/T) GA(C/T) III T(T/A)(T/C) GA(C/T) GCI (C/T)A(C/T) GG-3’.

My question is how to write the sequence of sense primer A from conserved amino acid sequence motif primer A ?? Please give references, concept and web site for further reading… you help I needed.

thanks...:help:

butters 08-20-2009 03:58 PM

Re: I need immediate help!! How to PCR primer designing? :help:
 
Collected from BioEdit version 7.0.0
Degenerate Table
R = A or G
Y = C or T/U
K = G or T/U
S = G or C
M = A or C
W = A or T/U
B = G, C or T/U
V = A, G or C
D = A, G or T/U
H = A, C or T/U
N = A, G, C or T/U
I=A, T, C or G <-- added by me, lolz

5’-GA(C/T) GA(C/T) III T(T/A)(T/C) GA(C/T) GCI (C/T)A(C/T) GG-3’
will be written as
5'-GAYGAYIIITWYGAYGCIYAYGG-3'

ps u have 4x I this primer will definitely be expensive

butters 08-20-2009 04:00 PM

Re: I need immediate help!! How to PCR primer designing? :help:
 
i forgot to mention the method is simple once u understand it.

(C/T) is represented by Y thus just put Y to replace ur (C/T) and same go for other :) cheers


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