Biomolecular Breadboards:Protocols

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{{Template:Biomolecular Breadboards for Prototyping and Debugging Synthetic Biocircuits}}
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{{Template:Biomolecular Breadboards}}
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[[Biomolecular Breadboards for Prototyping and Debugging Synthetic Biocircuits:Protocols:Crude Extract Prep|''E. Coli'' Crude Extract Preparation, 3X]]
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=== Cell-free circuit breadboard ===
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The following protocols are available for the cell-free circuit breadboard:
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* [[Biomolecular Breadboards:Protocols:Reaction Preparation|Reaction Preparation]] - Cell-free expression of circuits from linear or plasmid DNA
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** [[Biomolecular Breadboards:Protocols:Crude Extract Prep|''E. Coli'' Crude Extract Preparation, 3X]]  
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** [[Biomolecular Breadboards:Protocols:Amino Acids Prep|Amino Acid Preparation]]
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** [[Biomolecular Breadboards:Protocols:3-PGA Buffer Prep|3-PGA Buffer Preparation, 14X]]
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* [[Media: TXTL_v2_3.xlsx | TXTL template, v2.3]] - TXTL spreadsheet for designing experiments
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[[Biomolecular Breadboards for Prototyping and Debugging Synthetic Biocircuits:Protocols:Amino Acid Prep|Amino Acid Preparation]]
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We are the in the process of publishing a paper in the ''Journal of Visualized Experiments'' ([http://www.jove.com JoVE]) that describes this protocol in much more detail.  The JoVE paper will be an open access paper.  If you would like a preprint, contact [[Biomolecular Breadboards:More Info|Richard Murray]].
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=== Cost estimate ===
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The cell-free circuit breadboard costs approximately 2.64 cents per uL, or 31.7 cents per 12 uL reaction. The cost distribution is shown in the table below.
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{| border="1" cellpadding="5" style="width: 800px"
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! scope="col" | Component
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! scope="col" | Material price per
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μL of reaction
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! scope="col" | Labor price per
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μL of reaction
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! scope="col" | Total price per
 +
μL of reaction
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! scope="col" | Total price per
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12 μL reaction
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|-
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| style="width: 150px;" | ''E. coli'' crude extract || style="text-align:center; width: 100px;" | 0.45 cents || style="text-align:center; width: 100px;" | 0.62 cents || style="text-align:center; width: 100px;" | 1.07 cents || style="text-align:center; width: 100px;" | 12.84 cents
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|-
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| Amino acids ||  style="text-align:center" | 0.21 cents || style="text-align:center" | 0.03 cents || style="text-align:center" | 0.24 cents || style="text-align:center" | 2.93 cents
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|-
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| 3-PGA ||  style="text-align:center" | 0.39 cents || style="text-align:center" | 0.94 cents || style="text-align:center" | 1.33 cents || style="text-align:center" | 15.96 cents
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|-
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| '''Total price''' ||  style="text-align:center" | 1.05 cents ||  style="text-align:center" | 1.6 cents || style="text-align:center" | '''2.64 cents''' || style="text-align:center" | '''31.7 cents'''
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|}
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For a more detailed cost estimate, please see [[Biomolecular Breadboards:Protocols:cost_estimate|Breadboard Cost Estimate]].
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=== Design Cycle Time Analysis ===
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{| border = "1" cellpadding="5" style="width: 800px"
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|-
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! rowspan=2 width=250px | Circuit
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! colspan=4 | Assembly time
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|-
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! ''In vitro'' testing <br>(linear DNA)
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! ''In vitro'' testing <br>(multiple plasmids)
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! ''In vitro'' testing <br>(single plasmid)
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! ''In vivo'' testing <br>(single plasmid)
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|-
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| Negatively autoregulated gene
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| style="text-align:center" | 6.5 hours
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| style="text-align:center" | N/A
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| style="text-align:center" | 3 days
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| style="text-align:center" | 3 days*
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|-
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| Bistable switch
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| style="width: 200px; text-align:center" | 6.5 hours*
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| style="width: 200px; text-align:center" | 3 days
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| style="width: 200px; text-align:center" | 5 days*
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| style="width: 200px; text-align:center"  | 5+ days*
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|}
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<nowiki>* Estimated time based on similar constructions. All other times are measured.</nowiki>
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For a more detailed description, please see [[Biomolecular Breadboards:Protocols:Cycle Time Measurements|Breadboard Cycle Time Measurements]].

Revision as of 12:04, 11 May 2013

Home Protocols DNA parts Preliminary Data Models More Info

Cell-free circuit breadboard

The following protocols are available for the cell-free circuit breadboard:

We are the in the process of publishing a paper in the Journal of Visualized Experiments (JoVE) that describes this protocol in much more detail. The JoVE paper will be an open access paper. If you would like a preprint, contact Richard Murray.

Cost estimate

The cell-free circuit breadboard costs approximately 2.64 cents per uL, or 31.7 cents per 12 uL reaction. The cost distribution is shown in the table below.

Component Material price per

μL of reaction

Labor price per

μL of reaction

Total price per

μL of reaction

Total price per

12 μL reaction

E. coli crude extract 0.45 cents 0.62 cents 1.07 cents 12.84 cents
Amino acids 0.21 cents 0.03 cents 0.24 cents 2.93 cents
3-PGA 0.39 cents 0.94 cents 1.33 cents 15.96 cents
Total price 1.05 cents 1.6 cents 2.64 cents 31.7 cents

For a more detailed cost estimate, please see Breadboard Cost Estimate.

Design Cycle Time Analysis

Circuit Assembly time
In vitro testing
(linear DNA)
In vitro testing
(multiple plasmids)
In vitro testing
(single plasmid)
In vivo testing
(single plasmid)
Negatively autoregulated gene 6.5 hours N/A 3 days 3 days*
Bistable switch 6.5 hours* 3 days 5 days* 5+ days*

* Estimated time based on similar constructions. All other times are measured.

For a more detailed description, please see Breadboard Cycle Time Measurements.

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