Search a DNA sequence to match either a DNA query, or a protein translation, or an annotation.Īutomatically annotate common features, or manually annotate coding sequences and other features.ĭesign and annotate primers for PCR, sequencing, or mutagenesis. If you want to design primers for other applications where efficiency and specificity of the primers can be taken into account, you shouldn't use SnapGene, use CLC Main Workbench or Primer-Blast instead.SnapGene Viewer allows molecular biologists to create, browse, and share richly annotated DNA sequence files up to 1Gb in length.Ĭreate a DNA sequence file by either entering a sequence, or importing a record from GenBank, or opening an annotated sequence stored in one of many common file formats.īrowse or print a DNA sequence and its annotations using customizable Map, Sequence, Enzymes, Features, Primers, and History views. If you are happy with the sequence of the primer click Add primer to template. Select to make a primer for the Bottom strand: To transform the selection into a primer expand Primers in the top menu and select Add primer. Select a sequence that starts after the stop codon of Rab5 with the correct Tm: Try to do the exercise without peeking at the solution. So the only requirements of the reverse primer are its location (directly after the stop codon) and its Tm (60-62☌).
This means we can use the existing BamH1 site right downstream of the rab5 gene. If you are happy with the sequence of the primer click Add primer to template (green).įor cloning Rab5 into the vector later on, we will use a BamHI restriction site. To do this click at the 5’ end of the primer and type a random sequence of 6 nt (red):
To shield the site we will some random nucleotides to the 5' end of the primer. The sequence of the site is now added to the 5' end of the primer (blue). Select BspE1' in the site box (red) and click the Insert button (green): To add the restriction site select the Insertions tab:
As you elongate your selection, SnapGene automatically displays the length and Tm of the selection: Go back to the Sequence view of mRFP1-Rab5 and select a sequence that starts with the ATG start codon of Rab5. The only thing that is still variable in this case is the length of the primer, which will be determined by the Tm that we wish. We want primers with a Tm in the range of 60-62☌. The forward primer should also contain a BspE1 restriction site to fuse the gene to AcGFP1. For this, our choice of primers is restricted: the forward primer needs to start with the Rab5 start codon so its location is fixed. For cloning this is often the case.įor instance, we want to make primers to clone the Rab5 gene from plasmid mRFP1-Rab5 as a fusion to the AcGFP1 gene in plasmid pAcGFP1-C1. Only when you have no flexibility in your choice of primers, I would use SnapGene to design them.
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