Is it possible for ribosomes to recognize mRNA and initiate translation without the shine-dalgarno sequence and initiation codon? In the Nirenberg -Matthei experiment with poly U mRNA and E.coli cell free systems that helped in cracking the genetic code, there is no mention about these requirements. My doubt is that how was it possible to initiate translation in a poly U mRNA (or any other synthetic mRNAs) without the recognition and initiation signals?
Ribosomes initiate translation by utilizing a complementary rRNA sequence within the 3' end of their 16S rRNA. Even if the exact shine-delgarno sequence isn't available, the ribosome may still be able to bind to sites that are similar enough to initate translation; however, the translation efficiency will not be all that high, and you may end up with truncated products. I have witnessed this first-hand in CFPS where our ribosomal binding sites were not optimized and our laboratory ended up with all sorts of truncated products that we visualized on western blot. We then optimized our RBS and it improved our translational efficiency >300 fold. There is a de novo dna website that shows you how to improve your translational efficiencies.
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