Team:Johns Hopkins-BAG/A New Standard

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Revision as of 12:59, 21 September 2009

Someething

tRNA genes have been as a documented source of genome instability in Saccharomyces cerevisiae v. 1.0. As a measure to combat genome instability, as well as examine the effects of a more rigidly constrained genome, the tRNA genes for Sc 2.0 are being relocated to a specialized chromosome, the tRNA array. This entirely synthetic chromosome thus far only consists of the tRNA genes from chromosomes III and IX of S. cerevisiae. The tRNA array of chromosomes III and IX of S. cerevisiae 2.0 consists of 17 tRNA genes; each gene consists of the coding region of the tRNA From S. cerevisiae and the upstream and downstream flanking regions from a close relative of S. cerevisiae, Ashbya gossypii. Use of the fusion tRNA genes was required to avoid incorporating the repetitive sequences often found upstream of tRNAs in S. cerevisiae, as another aspect of our redesign philosophy for Sc 2.0 is to minimize nonessential repetitive DNA. Each of the genes is a representation of the same gene found on chromosome III and IX with all duplicates removed. Between each tRNA gene is a rox recombination site that will allow for subsequent induced recombination within and limited to the tRNA chromosome, when the Dre recombinase is expressed at the whim of the investigator, so that the importance of order and relative copy numbers of tRNA genes on the tRNA array chromosome can be examined. Also it will be possible to detect deletions and more complex rearrangements of genes using this system and their phenotypic effect.

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-==Building Blocks: A revolution==
+==Someething==
-The Johns Hopkins team presents the work of a Build-a-Genome course that fabricates synthetic yeast genome Sc2.0 and provides students tools to meld seamless arrays of DNA into redesigned synthetic chromosomes. Our team is part of a larger effort to develop new technologies and standards for synthetic genomic construction allowing for the production of longer more complicated DNA sequences without certain constraints of current Biobrick standards. By using overlap assembly PCR, followed by Uracil Specific Excision Reaction (USER), and finally, multiple rounds of homologous recombination we create pieces of chromosomes and finally full chromosomes, efficiently and cheaply. We will present improved methodology for building block synthesis, the software created to aid in our synthesis, and applications of the yeast genome redesign, focusing on the implications the Build-a-Genome course has on future genomic technologies that rely on and teach students.
+tRNA genes have been as a documented source of genome instability in Saccharomyces cerevisiae v. 1.0. As a measure to combat genome instability, as well as examine the effects of a more rigidly constrained genome, the tRNA genes for Sc 2.0 are being relocated to a specialized chromosome, the tRNA array. This entirely synthetic chromosome thus far only consists of the tRNA genes from chromosomes III and IX of S. cerevisiae. The tRNA array of chromosomes III and IX of S. cerevisiae 2.0 consists of 17 tRNA genes; each gene consists of the coding region of the tRNA From S. cerevisiae and the upstream and downstream flanking regions from a close relative of S. cerevisiae, Ashbya gossypii. Use of the fusion tRNA genes was required to avoid incorporating the repetitive sequences often found upstream of tRNAs in S. cerevisiae, as another aspect of our redesign philosophy for Sc 2.0 is to minimize nonessential repetitive DNA.  Each of the genes is a representation of the same gene found on chromosome III and IX with all duplicates removed. Between each tRNA gene is a rox recombination site that will allow for subsequent induced recombination within and limited to the tRNA chromosome, when the Dre recombinase is expressed at the whim of the investigator, so that the importance of order and relative copy numbers of tRNA genes on the tRNA array chromosome can be examined. Also it will be possible to detect deletions and more complex rearrangements of genes using this system and their phenotypic effect.
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