Thank you, everyone, for your replies. I did go ahead and order it as is because expression is a strange beast. One never knows what may happen, I feel. It is around the 600th bp or so.
Yes, it was detected by computational means. I am hesitant to change codon usage at this stage just in case the gene as is works better. I'll give it a shot, and if it doesn't work, I'll take your recommendations and post back about the result. Thanks again, Sangeetha. On Sat, Nov 21, 2009 at 9:12 AM, Artem Evdokimov <[email protected]> wrote: > Dear Sangeetha, > > > > Can I assume that you detected the hairpin by computational means? In > general a single hairpin may not necessarily doom your experiment or reduce > expression – however you could reduce the hairpin stability via silent codon > changes just to be on the safe side. Keep in mind that in some cases the > presence of specific secondary structure of RNA can be important for proper > expression and folding. Alternatively you could try the gene as is and if > you encounter trouble you can always change the nucleotides later. > > > > Cheers, > > > > Artem > ------------------------------ > > *From:* CCP4 bulletin board [mailto:[email protected]] *On Behalf Of > *Sangeetha > Vedula > *Sent:* Friday, November 20, 2009 8:03 PM > *To:* [email protected] > *Subject:* [ccp4bb] hairpin formation in gene > > > > Dear bb-ers, > > > I am trying to have a gene synthesized and found out that it forms an 11-bp > hairpin. Does that complicate expression? Would it be better to try and > disrupt it by altering codon usage to improve expression? > > Thank you in advance, > > Sangeetha. >
