Team:Toronto/Notebook-w01-tue
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Week 1: May 17, 2016
Tuesday, 5/17/2016
Introductory presentation on plasmid design (was held at 10 A.M. at Gerstein rm 2000)
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It was decided that team members are to download and play around with various plasmid design software in order to help determine the appropriate one for this particular project. These include: Benchling, ApE and an iGem-compatible software (Molecula Maxima Cytostudio), DNA 2.0, Geneious (free trial).
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The content of the presentation were recorded and distributed.
Research
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Each individual analysed his or her assigned plasmid design software.
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We also did some research as to the actual size of the del cluster. The potential of using BACs (Bacterial Artificial Chromosomes) was researched.
Findings:
Size of the del Cluster
The del cluster is about 58kbp in size, with the delH gene making up 18.5kbp and delE, delF and delG adding up to 20kbp. The large size of the del cluster may pose a number of problems. These include:
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possible issues with using regular plasmids as vectors;
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high cost of synthesis and high error rate if publicly available sequence data is used; and/or
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challenges in extracting the del cluster from D. acidovorans.
Our preliminary research seems to point us in the direction of using BACs as a possible solution for handling the large insert size. Advantages and disadvantages of using BACs were canvassed.
