What I normally do is get the protein primary sequence from the PDB and I order the right sequence of the DNA from the company. Any suggestion/tutorial?
The DNA sequence you use could vary depending on what you intend to use it for. For example, if you want to use it as an expression vector, you should design the sequence to have optimum codon usage for the cell type it is to be expressed in. If you want to use the sequence to form a double-stranded DNA with as high a melting temperature as possible, you would try to make it as GC-rich as possible.
Since there is generally more than one codon for any given amino acid, the process of going back from AA sequence to a nucleic acid sequence can lead to a lot of different results - https://en.wikipedia.org/wiki/Codon_degeneracy
But, at least in theory, you can look at the "conversion table" and then work from there.
The DNA sequence you use could vary depending on what you intend to use it for. For example, if you want to use it as an expression vector, you should design the sequence to have optimum codon usage for the cell type it is to be expressed in. If you want to use the sequence to form a double-stranded DNA with as high a melting temperature as possible, you would try to make it as GC-rich as possible.
If the purpose of the gene is to produce recombinant protein then you should use an optimize sequence of the gene. This includes using the knowledge of codon preference of the host strain in which you would like to express and purify your protein of interest.
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