In a recent research they found that although silent mutations dont change the amino acids in the polypeptide chain they can harm its function... so then there is something more between the protein and the DNA.... somethin that we definitely dont know...

Can you provide a link to the research or give us a direction for further comment? What do you think the "something more" might be?

Hmmm I kinda doubt this. And I'm an RNA/DNA guy...

 

I can see how there might be some promoter elements present within the coding region, that maybe disrupted and result lower protein expression. But that's not really harming function.

I found that reaseearch result in "nature"....http://www.nature.com

I think you're going to have to be more specific than that.

Can you find a link to a paper? or article at least?

 

(To mean it sounds like you're missinterpreting the recently discovered histone code...)

I think he is referring to effects of the sequence on, say splicing, mRNA transport or translation.

One example that I know of and which is quite intuitively understandable is for instance a silent mutation changes to a rarely used codon (but leading to the same AA). So if the given tRNA is less abundant in the cell, the translation is slowed down apparently leading to a different, less efficient conformation. This has been demonstrated for the MDR1 gene, for instance.

(Kimchi-Safarty, Science 2006).

^^ He's so unspecific that your guess is just as good as anyone elses.

Good point. Actually funny how the focus of one's own work influences the interpretation, though (I am more of an RNA/Protein guy...).