IGEM:IMPERIAL/2007/Projects/Reporters: Difference between revisions
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==Useful Reporters== | ==Useful Reporters== | ||
===Bioluminescence=== | ===Bioluminescence=== | ||
'''Advantages''': | '''Advantages''': | ||
*More sensitive than other spectroscopy reporters, since there is often neglectable background bioluminescence. | *More sensitive than other spectroscopy reporters, since there is often neglectable background bioluminescence (not naturally found in cells). | ||
*Relatively fast response | *Relatively fast response | ||
'''Disadvantages''': | '''Disadvantages''': | ||
Line 130: | Line 126: | ||
**Enzyme reaction can be stopped during assay | **Enzyme reaction can be stopped during assay | ||
*Disadvantages: | *Disadvantages: | ||
**Requires cells to be killed to release enzymes | **Must use lacZ<sup>-</sup> strain of ''E. coli'' to prevent cross-talking | ||
**Requires cells to be killed to release enzymes for Miller's assay | |||
====β-D-Glucuronidase==== | |||
*Gene name: ''gus'' | |||
*'''Description''': Acts similarly to β-galactosidase, can hydrolyze 5-bromo-4-chloro-3-indolyl glucuronide (X-Gluc) into a coloured compound, which absorbs at ??? nm. Alternatively, 4-Methylumbelliferyl-β-D-glucuronide (MUG) can be hydrolyzed into a fluorescent compound, which absorbs at 390 nm and emits at 480 nm. | |||
*Enzyme: [http://www.expasy.org/enzyme/3.2.1.31 EC 3.2.1.31] | |||
*Reaction: A beta-D-glucuronoside + H<sub>2</sub>O <=> D-glucuronate + an alcohol | |||
*Response Time: ??? (possibly within minutes) | |||
*Steady State Time: ??? | |||
*Concentration sensitivity: ??? | |||
*Advantages: | |||
** | |||
*Disadvantages: | |||
**β-glucuronidase naturally in ''E. coli'' might interfere with expression of recombinant gene | |||
===Other Possible Reporters=== | ===Other Possible Reporters=== |
Revision as of 10:28, 29 July 2007
Useful Reporters
Bioluminescence
Advantages:
- More sensitive than other spectroscopy reporters, since there is often neglectable background bioluminescence (not naturally found in cells).
- Relatively fast response
Disadvantages:
- Generally metabolically stressing, since key metabolic compounds are required in the generation of light.
- Usually requires the addition of substrates to be oxidized, which can limit the luminescence signal.
Firefly luciferase
- Gene name: lucff
- Gene sequence: 1781 bp, GenBank
- Description: Oxidizes luciferin with the help of oxygen, releases light as a product of oxidation.
- Enzyme: EC 1.13.12.7
- Reaction: Photinus luciferin + O2 + ATP <=> oxidized Photinus luciferin + CO2 + AMP + diphosphate + light
- Response Time: ~30 minutes
- Steady State Time: 4 hours
- Concentration sensitivity: Moderate
- Advantages:
- Fast response
- Can be initiated by addition of luciferin
- Disadvantages:
- Metabolic stress, ATP is consumed
- Substrate limiting
Bacterial luciferase
- Gene name: luxCDABE
- Description: 5 subunit protein which oxidizes FMN with the help of oxygen to generate FMN and H2 complex. This complex breaks down to form light.
- Enzyme: EC 1.14.14.3
- Reaction: RCHO + reduced FMN + O2 <=> RCOOH + FMN + H2O + light
- Response Time: ~30 minutes
- Steady State Time: 8 hours
- Concentration sensitivity: Moderate
- Advantages:
- Fast response
- Can be initiated by addition of substrate
- Disadvantages:
- Five subunits required
- Metabolic stress, FMN is consumed
- Substrate limiting
Questions: What substrate does this need?
Renilla luciferase
- Gene name: luci
- Part: BBa_J52008
- Description: Requires renilla luciferin, which is oxidized by oxygen to genrate light. The only luciferase part in the registry.
- Enzyme: EC 1.13.12.5
- Reaction: Renilla luciferin + O2 <=> oxidized Renilla luciferin + CO2 + light
- Response Time: ???
- Steady State Time: ???
- Concentration sensitivity: Moderate
- Advantages:
- Disadvantages:
- Substrate limiting
Fluorescence Reporters
Advantages:
- They are highly stable, and can be active even in dead cells
- Does not require additional substrates, only light excitation
- Can be fused with other proteins
Disadvantages:
- Slow folding time, resulting in generally slow response
Green Fluorescent Protein
- Gene name: gfp
- Gene sequence: 5170 bp, GenBank
- Part: BBa_E0040
- Description: protein which can be exicited under 488 nm, releasing emission at 509 nm that is detected as a green light.
- Response Time: ~1 hour
- Steady State Time: 8 hours
- Concentration sensitivity: High
- Advantages
- GFP can be fused with other proteins
- Highly stable, can be visible in dead cells
- Disadvantages
- Requires UV excitation
- Slow folding
Red Fluorescent Protein
- Gene name: rfp
- Part: BBa_E1010
- Description: Fluorescent protein which can be excited under 584 nm, releasing emission at 607 nm that is detected as a red light.
- Response Time: ~8 hours
- Steady State Time: 12++ hours
- Concentration sensitivity: Moderate (due to long folding hours)
- Advantages:
- Visible under normal light
- Disadvantages:
- Very slow folding
Enzymic Reporters
Advantages:
- Usually colourmetric and does not require sophisicated equipment
Disadvantages:
- Requires killing of the cell to release enzymes
- Substrate specific
Alkaline Phosphatase
- Gene name: ppb
- Part: BBa_J61032
- Description: Enzyme which functions optimally in alkaline environments (periplasm), breaks down para-nitrophenol phosphate to form compound which absorbs at 405 nm. Sometimes known as SEAP (secreted akaline phosphatase).
- Enzyme: EC 3.1.3.1
- Reaction: Phosphate monoester + H2O <=> an alcohol + phosphate
- Response Time: ??? (possibly within minutes)
- Steady State Time: ???
- Concentration sensitivity: High
- Advantages:
- High concentration sensitivity
- Disadvantages:
- Enzymatic reaction is slow
β-D-Galactosidase
- Gene name: lacZ
- Part: BBa_E0033 Note: This part is special and works only when both fragments of lacZ are present.
- Description: β-galactosidase cleaves a synthetic lactose homologue, o-nitrophenyl-β-D-galactoside (ONPG) to give a yellow compound, o-nitrophenol, which has a peak absorbance at 420 nm. Using Miller's equation, the amount of β-galactosidase can be determined.
Alternatively, 5-bromo-4-chloro-3-indolyl- beta-D-galactopyranoside (X-gal) or variants (such as S-gal) can be also be cleaved into a coloured compound absorbing at 420 nm. - Enzyme: EC 3.2.1.23
- Reaction: o-nitrophenyl-β-D-galactoside + H2O <=> galactose + o-nitrophenol
- Response Time: Within minutes
- Steady State Time: 2-3 hours
- Concentration sensitivity: Very high (with Miller)
- Advantages:
- Visible under white light, good for selection purposes
- Very high concentration sensitivity
- Enzyme reaction can be stopped during assay
- Disadvantages:
- Must use lacZ- strain of E. coli to prevent cross-talking
- Requires cells to be killed to release enzymes for Miller's assay
β-D-Glucuronidase
- Gene name: gus
- Description: Acts similarly to β-galactosidase, can hydrolyze 5-bromo-4-chloro-3-indolyl glucuronide (X-Gluc) into a coloured compound, which absorbs at ??? nm. Alternatively, 4-Methylumbelliferyl-β-D-glucuronide (MUG) can be hydrolyzed into a fluorescent compound, which absorbs at 390 nm and emits at 480 nm.
- Enzyme: EC 3.2.1.31
- Reaction: A beta-D-glucuronoside + H2O <=> D-glucuronate + an alcohol
- Response Time: ??? (possibly within minutes)
- Steady State Time: ???
- Concentration sensitivity: ???
- Advantages:
- Disadvantages:
- β-glucuronidase naturally in E. coli might interfere with expression of recombinant gene
Other Possible Reporters
- Chloramphenicol Acetyltransferase (CAT)
- Human Growth Hormone (hGH)
Detecting Reporters
- Spectrometric Assays
- Enzyme Activity Assays
- Immunology Assays