Judging/Variance/Johns Hopkins-BAG

From 2009.igem.org

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(New page: Dear iGEM Team, <br> I am writing to you on behalf of the JHU BAG iGEM team to request a variance from the BioBrick standard of biological parts and assembly of biological parts. Our iGEM ...)
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===Request===
Dear iGEM Team, <br>
Dear iGEM Team, <br>
I am writing to you on behalf of the JHU BAG iGEM team to request a variance from the BioBrick standard of biological parts and assembly of biological parts. Our iGEM team has focused on developing new technologies and standards for synthetic genome construction. Our method for assembling genomic pieces depends on a new standard we refer to as the “Building Block”.  The workflow of our system is as follows:
I am writing to you on behalf of the JHU BAG iGEM team to request a variance from the BioBrick standard of biological parts and assembly of biological parts. Our iGEM team has focused on developing new technologies and standards for synthetic genome construction. Our method for assembling genomic pieces depends on a new standard we refer to as the “Building Block”.  The workflow of our system is as follows:
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James DiCarlo, <br>
James DiCarlo, <br>
JHU - BAG Team
JHU - BAG Team
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===Judges' Response===
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Hi James,
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Thanks for your email.
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Quick question.
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Please clarify if you are only requesting a variance from one of the ~6 existing BioBrick physical assembly standards, and if so please confirm that what you are proposing is different.
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You can find the existing BioBrick technical standards online here:  http://openwetware.org/wiki/The_BioBricks_Foundation:RFC
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BBF RFC #29 may be a good place to start.
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Alternatively, is your team proposing a new physical assembly standard as part of its iGEM 2009 entry?  For example, such a contribution would satisfy option 3 of the iGEM gold medal requirements. See: http://2009.igem.org/Judging/Judging_Criteria
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If you are proposing a new physical assembly standard then you should format your new assembly standard following the standard BBF RFC template.  Please see BBF RFC #0 in this case.
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All best!
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Drew

Revision as of 16:25, 11 September 2009

Request

Dear iGEM Team,
I am writing to you on behalf of the JHU BAG iGEM team to request a variance from the BioBrick standard of biological parts and assembly of biological parts. Our iGEM team has focused on developing new technologies and standards for synthetic genome construction. Our method for assembling genomic pieces depends on a new standard we refer to as the “Building Block”. The workflow of our system is as follows:

  1. Optimized protocols to create “Building Blocks” (BBs) by Overlap Extension/Assembly PCR from oligomers.
  2. USER (uracil specific excision reaction) protocol to join BBs into smaller chunks
  3. Homologous recombination in vivo to assemble smaller chunks to larger chunks, and using a second round of homologous recombination to assemble larger chunks into chromosome arms and full chromosomes

The purpose of our team is to develop and optimize techniques for large DNA construction as well as further the effort of the construction a synthetic Saccharomyces cerevisiae. Our team also has designed several novel computer programs for high throughput analysis of trace files and other sequence information. We fully understand the uniqueness of our team and we will be emphasizing that our central goals are somewhat distinct from those of most iGEM Teams (we are building a complex chassis, not stringing together parts into devices). All our methods will be described on our wiki from this perspective.

We hope that our team can provide new tools, both wet and dry, to broaden the perspective of iGEM and provide a generic toolset for the synthetic Biology community.

Advantages of our Building Block Standard:

  • Unlike BioBricks - No scars; seamless construction. Scars are not consistent with our genome redesign strategy because our knowledge of the rules of genome structure and function is insufficient.
  • DNA sequence requirements at joints are extremely flexible and can be found in any sequence; consensus of joining sites is A {Nx} T where x= 3,5,7,9 or 11
  • Much larger DNA pieces such as whole chromosomes may be assembled, with no constraints on restriction enzyme site positions.
  • Building blocks that are assembled can more easily contain more parts (gene, promoter, rbs, etc.), and systems of parts of very different sizes


Disadvantages:

  • Lack of standard Biobrick assembly standard


Difference from BioBricks:

  • Building blocks used for genome assembly, may contain more than one part or may containing partial pieces of parts. This can be viewed as an advantage or a disadvantage, depending on perspective.


Respectfully submitted,
James DiCarlo,
JHU - BAG Team

Judges' Response

Hi James,

Thanks for your email.

Quick question.

Please clarify if you are only requesting a variance from one of the ~6 existing BioBrick physical assembly standards, and if so please confirm that what you are proposing is different.

You can find the existing BioBrick technical standards online here: http://openwetware.org/wiki/The_BioBricks_Foundation:RFC

BBF RFC #29 may be a good place to start.

Alternatively, is your team proposing a new physical assembly standard as part of its iGEM 2009 entry? For example, such a contribution would satisfy option 3 of the iGEM gold medal requirements. See: http://2009.igem.org/Judging/Judging_Criteria

If you are proposing a new physical assembly standard then you should format your new assembly standard following the standard BBF RFC template. Please see BBF RFC #0 in this case.

All best! Drew