The Lazy Scientist

The Lazy Scientist is a translation tool aimed to assist synthetic biologists. The app has a number of functions including DNA to amino acid translation, back translation, reverse, complement and reverse complement. The app also contains a genetic codon lookup table allowing all corresponding codons for an amino acid to be looked up. The app is available for free in both the iPhone App Store and the Android Market.

The Gene Cutter & The Gene Slicer

The Gene Cutter (iPhone app) and The Gene Slicer (Android app) are gene cutting tools aimed to assist synthetic biologists. The apps have two functions to help restriction mapping of nucleotide sequences. The apps are able to search a sequence for a specific enzyme and can also return a list of enzymes not present in the sequence. The app is available for free in both the iPhone App Store and the Android Market.

Gene Synthesis

Many synthetic biologyprojects involve the heterologous expression of foreign genes in a host such asE. coli/S. cerevisiae etc. For successful and efficient translation, thecodon usage of the newly introduced gene must be optimised to match the tRNApool of the host organism. However, if one simply picked the most common codonfor each amino acid, the rate of translation would be extremely fast across theentire gene. This may lead to subtle characteristics of translation being lost.For example, it has been suggested that in certain regions of the gene, thesource organism may ‘choose’ a short run of rare codons, in order to slow downtranslation in that region. This slowing of the emerging polypeptide from theribosome has been suggested to facilitate the correct folding of theheterologous protein and/or allow time for the insertion of essentialco-factors. [19] These regions of "slow" translation, mayoccur in loops between different domains of the protein. It may be thereforeimportant for certain genes, to maintain this pattern of fast to slow translationin the target organism. “Gene Synthesiser” is ajava application that makes this possible by enabling codon usage patternmatching. The application analyses the patterns of codon usage of the gene thatone wants to express, in its native organism and generates new synthetic DNA sequence,optimised for the codon usage of the new target organism, yet matching anypatterns of rare to common codons. Gene Synthesiser utilises codon usagedata for over 35000 organisms. [20].

Instructions:

Enter the DNA sequence ofthe gene in its native organism and select the original organism from the dropdown box. Then select the new host you wish to express this gene in from thesecond drop down box. Gene Synthesiser will generate a new synthetic DNA sequence,optimised for the codon usage of the new target organism, yet closely matching anypatterns of rare to common codons from the original gene.

To try the Gene Synthesiser for yourself click HERE