metalgear21 Posted August 20, 2018 Posted August 20, 2018 Anyone help me with this primer design question? I have searched everywhere on the internet but cant seem to get everything I need. So far I understand that https://imgur.com/a/PfwAhO0 Forward primer is: Restriction enzyme start codon Tag Primer 20 bases from sequence of gene EcoRI Strep tag Primer 20 bases of gene So I got 5' GAATTC ATGGCCTCGTGGTCGCATCCGCAGTTCGAGAAGTCGGGGGTG ATGCGGCTCTGCATCCCGCA 3' Reverse primer is: Restriction enzyme Tag Primer compliment of 20 bases from end of gene Stop codon BamHI Hexa Histidine tag Primer stop codon So I got 3' GGATCC GTGGTGGTGGTGGTGGTG TGCACCAGCCGCACAATGAATAA 5' I know this is not correct. Is the question asking for two sets of primers considering it gives two restriction enzymes? Are the restriction enzyme recognition sites that are given supposed to be in the gene sequence in the question because I cant find them in it? Also which start and stop codon do you use in the gene sequence as there is multiple ones of both? Any help or guidance would be greatly appreciated as this topic is driving me mad
BabcockHall Posted August 21, 2018 Posted August 21, 2018 Do you understand the purpose of the question? In other words, do you know why someone would want to go into the laboratory to do this? Do you know something about PCR mutagenesis?
metalgear21 Posted August 21, 2018 Author Posted August 21, 2018 I understand that primers need to be designed with specific requirements depending on the DNA template that's being amplified. I know what a primer does, it anneals to the single stranded DNA molecules after denaturation to allow polymerase to synthesize a new DNA strand. I dont know much about mutagenesis only that Mutagenesis involves incorporating a mutation into the DNA such as by a mismatching base used on the primer. I just dont fully understand the rules when it comes to designing the primers.
BabcockHall Posted August 21, 2018 Posted August 21, 2018 You have answered a different question from the one I intended to ask. My educated guess is that this assignment presumes that one's purpose is to produce and purify a large quantity of this serotonin receptor. That explains why one would want a start codon, a hexahistidine tag, etc. BTW there is only one true start codon for a gene. As for the problem itself, do you think that one could add restriction sites into a piece of DNA as part of the process of amplifying it via PCR? If so, how? Assuming that one wished to amplify the gene for this receptor, how many primers would you need?
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