A cause for reduced translation efficiency in E.coli?

Zhonglin Chai Zhonglin.Chai at baker.edu.au
Mon Aug 26 18:14:34 EST 2002

MFOLD developed by Dr. Zuker would do the job for you. The website is 

You will find out that most of mRNA molecules are almost entirely
hybridized with themselves although some small loops are always

Zhonglin Chai, PhD

Molecular Hypertension Laboratory
Baker Heart Research Institute
Commercial Rd, MELBOURNE, VIC 3004

Post Address:
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Central Melbourne 

Telephone: +61 3, 8532 1231
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email: zhonglin.chai at baker.edu.au

>>> Trond Erik Vee Aune
<trondaun at chembio.REMOVETHISBEFOREREPLYING.ntnu.no> 08/26/02 06:57pm

Is there a possibility that lowered translation efficiency can be
by hybridization of the RNA to itself? If, for instance, a part of the

gene hybridizes with a part of the 5' UTR (untranslated region) in such

a way that ribosome binding is hindered? (I assume that hybridizations

that does not partly overlap the ribosome binding site would not affect

translation since the ribosome would be able to break up the binding)

It could be that a single RNA molecule folds over and hybridizes with 
itself, or, in cases with good transcription, that two different (but 
still from the same transcript) RNA molecules binds to each other.

I know the fact that transcription and translation in E.coli is coupled

  diminishes this possibility, but I think that the ribosome binding 
site with its surrounding regions partly would be free for such 
interactions, especially with other RNA molecules.

I also know that this would probably not be a problem with native
transcripts, but in cases with homologues expression, where the gene
the untranslated region come from different sources, I think this may 
contribute to lowered translation when all other possibilities are 

Do you know of any programs that can analyze RNA sequences looking for

hybridization possibilities?

Trond Erik Vee Aune


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