|MadSci Network: Biochemistry|
In the case of prokaryotes, transcription (the formation of mRNA) and translation (protein synthesis from mRNA) are coupled temporally; they can occur at the same time. So, ribosomes (the machinery for protein synthesis) are interacting with the mRNA immediately after transcription begins. The presence of these ribosomes likely prevents annealing or self interaction of mRNA with antisense mRNA.
In Eukaryotes, transcription and translation occur in separate compartments, and the mRNA is processed (it is structurally altered to have a cap at one end and a poly-A tail at the other end), which enhances mRNA stability, and prevents degradation. Then, enzymes transport the processed message (mRNA) across the nuclear envelope to allow protein synthesis. It is likely that in the case of both prokaryotic and eukaryotic mRNA, interaction with enzymes for processing or translation simply sterically prevent annealing with complementary mRNAs (the enzymes are basically just in the way). If these mRNAs are just free floating, they tend to get degraded quickly, perhaps before being able to interact with each other.
Studies have shown that when mRNA does anneal to form double stranded (ds) RNA; it is selectively degraded by an "RNA interference machinery" dedicated to destroying dsRNA as well as their matching RNA's. This effectively knocks down or decreases the amount of that particular mRNA in the cell, leading to decreased synthesis of that protein or peptide.
If you would like to read more about this machinery, see the reference below.
Hammond SM. Dicing and slicing The core machinery of the RNA interference pathway. FEBS Lett. 2005 Oct 31;579(26):5822-9. Epub 2005 Sep 27.
Hope I have helped.
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