restriction sites and gene synthesis

Fri Jan 26 10:14:47 EST 1996

Martin Stone writes:

>I am trying to design the sequences of oligonucleotides to use for
>synthesis and expression of a gene. Can somebody please help me with the
>following two issues.
>(1) Does anybody have any suggestions about a codon usage table available
>in gcg that has worked well for gene expression in E. coli? I want to
>optimize the sequence of my DNA to get maximum expression levels.

FETCH the file ECOHIGH.COD  Synthesized genes designed according to this 
codon table usually work well.

>(2) Is there any way in gcg of getting a list of restriction sites that
>could potentially be introduced into a DNA sequence without changing the
>amino acid sequence of the protein encoded by the DNA.

Try MAP -SILent on a sequence file containing precisely the reading frame.
It will look for restriction sites with one-base mismatches which do not 
alter the translation.  See GENHELP MAP OPTIONAL_PARAMETERS.

Hope this helps.

                                       Paul H. Roy
                                       Departement de biochimie,FSG
                                       Universite Laval
                                       Quebec, QC  G1K 7P4

                                       Internet: 2020000 at SAPHIR.ULAVAL.CA
                                             or: PROY at RSVS.ULAVAL.CA
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