I have a list of plasmid sequences but I don't have primers. I thought that I could use the ORF sequence for the design, however, the primers are not specific. Can anyone tell me how to design a specific primer for the plasmid? Thank you
The question is too vague. Do you know the vector backbones? the selection marker? Do you have any other information?
Honestly, if you are given vectors of unknown backbone and no sequence, just do whole plasmid nanopore sequencing (no need for primers). You'll get the sequence of the entire vector and then you can start designing primers for downstream experiments. An example company is: https://www.plasmidsaurus.com/index/
Designing specific primers for a plasmid requires identifying unique regions within the plasmid sequence to ensure specificity. Here's a general approach to designing specific primers for a plasmid:
Remember that the success of primer design and PCR amplification depends on the complexity and uniqueness of the plasmid sequence. If the plasmid has repetitive or highly conserved regions, designing specific primers may be challenging. In such cases, alternative approaches such as restriction enzyme digestion or amplification using universal primers may be considered..
Many plasmids come with standard primer sites, such as M13F, M13R, SP7 and so forth. If you know the plasmid names you can search for maps and look for these universal primer sites. Or, you can get the primer sequences and search your plasmid sequences.
- Badges
- Science topic
- Similar topics
- Physical Sciences
- Materials Science
- Plating