Silent Mutagenesis: Program wanted

Gary Rudnick rudnick at biomed.med.yale.edu
Thu Apr 14 13:14:50 EST 1994


In article <2oh6qm$cca at news.duke.edu> mjtino at acpub.duke.edu (Michael J. Tino) writes:
>From: mjtino at acpub.duke.edu (Michael J. Tino)
>Subject: Silent Mutagenesis: Program wanted
>Date: 13 Apr 1994 16:32:22 GMT

>My lab is in search of a program which will help us design restriction sites
>within our genes of interest without changing the protein sequence.  So far,
>we have found an IBM-compatible program, but none for the Macintosh (and
>all of the department's computers are Macs).  Does anyone out there know of
>one?  I'd greatly appreciate it if you could e-mail responses directly to
>me, or better yet, to my advisor, Dr. Jo Rae Wright, at her e-mail
>address:  jo_rae_wright at cellbio.duke edu

>Thanks in advance,
>Michael Tino
>Department of Cell Biology
>Duke University
>Durham, NC 27705

I've done this sort of thing with MacVector, but it takes a lot of time.  You 
can translate the DNA to protein, and then backtranslate to an ambiguous DNA 
sequence.  If you ask for enzymes that will digest the ambiguous sequence, you 
get a lot of sites, including the silent ones.  The problem is that you get a 
lot of sites that aren't really possible without changing the amino acid 
sequence.  The reason for this is complicated, but it is due, at least in 
part, to amino acids like serine where for one base in the 2nd position there 
are 4 possibilities in the 3rd and only 2 possibilities with another base in 
the 2nd position.  Anyway, if you have the energy to sort through, you can 
find all the silent sites.  The other possibility is to use the VAX GCG 
package, if you have access to it.  There is a silent option to the map 
program, but it was broken when I tried to use it.  Perhaps it's been fixed.
I hope this helps.
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