Team:Illinois/Protocols

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== '''Protocols''' ==
== '''Protocols''' ==
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This page describes protocols or includes links to protocols used in our project.  Recipes used are also listed in a separate section.  Protocols are organized by category.
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This page describes protocols or includes links to protocols used in our project.  Recipes used are also listed in a separate section.  Protocols are organized by category. They were collected from Open Wet Ware, our advisors, and labs around the University of Illinois campus.
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== '''Standard''' ==
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== '''Standard''' ==
*[http://www.biochem.northwestern.edu/morimoto/research/Protocols/I.%20Prokaryotes/A.%20Bacteriology.pdf Bacterial Culture Basics (media/plate preparation, growth, streaking, and storage)]
*[http://www.biochem.northwestern.edu/morimoto/research/Protocols/I.%20Prokaryotes/A.%20Bacteriology.pdf Bacterial Culture Basics (media/plate preparation, growth, streaking, and storage)]
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*[http://www.methodbook.net/dna/agarogel.html Agarose Gel Electrophoresis Protocol]
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*[[Preparing Cryo stocks]]
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*[http://www.5prime.com/media/29661/perfectprep%20spin%20mini%20kit%20manual_5prime_1048299_072007.pdf Miniprep Protocol (PerfectPrep Spin Mini Kit)]
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*[http://www.stanford.edu/~teruel1/Protocols/pdf/Transformation%20Protocol%20Using%20Heat%20Shock.pdf Transformation by Heat Shock Protocol]
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== '''sRNA Characterization''' ==
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*[http://www.methodbook.net/dna/agarogel.html Agarose Gel Electrophoresis Protocol]
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'''Taken from:''' [http://www.springerlink.com.proxy2.library.uiuc.edu/content/h752r3415261357p/ A Green Fluorescent Protein (GFP)-Based Plasmid System to Study Post-Transcriptional Control of Gene Expression In Vivo]: Johannes H. Urban and Jörg Vogel, 2009
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*[http://www.sigmaaldrich.com/life-science/custom-oligos/custom-dna/learning-center/annealing-oligos.html Annealing Oligonucleotides Protocol]
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This protocol is used to characterize an E. coli small RNA and its ability to downregulate a reporter gene (GFP). The small RNA is cloned out of the E. coli chromosome and inserted into a high-copy number plasmid (pJU-334).  The sRNA's target sequence is also cloned out of the E. coli chromosome and inserted into a low-copy number plasmid (pXG-10).  Both plasmids are then transformed into E. coli Top10F' cells.  Successful sRNA repression is indicated by a decreased level of fluorescence in the cells.
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*[http://www1.qiagen.com/Products/DnaCleanup/GelPcrSiCleanupSystems/QIAquickPCRPurificationKit.aspx?r=1745#Tabs=t2 PCR Cleanup Protocol (QIAquick PCR Purification Kit)] -- Click on "QIAquick Spin Handbook - English (PDF)" under the "Handbooks" header
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'''Procedure:'''
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*[http://www.5prime.com/media/29661/perfectprep%20spin%20mini%20kit%20manual_5prime_1048299_072007.pdf Miniprep Protocol (PerfectPrep Spin Mini Kit)]
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''sRNA Expression Plasmid''
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*[http://www.promega.com/tbs/tb374/tb374.pdf Miniprep Protocol (PureYield Plasmid Miniprep System)]
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1. 50&mu;L PCR reaction (plasmid backbone)
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*[[BioBrick information]]
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*1&mu;L (10-50 ng) pJU-334 template
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*0.4&mu;L oligonucleotide pLlacOB
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*0.4&mu;L oligonucleotide JVO-2164
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*10&mu;L Phusion buffer
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*1&mu;L dNTP mix
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*0.3&mu;L DNA polymerase
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Run for 30s @ 98&deg;C, then 30 cycles of the following:10s @ 98&deg;C, 30s @ 58&deg;C, 2 min 20s @ 72&deg;C.  Incubate for 5 min @ 72&deg;C, then analyze 5&mu;L of the reaction in 0.8% agarose gel, looking for a ~3.1kbp fragment.
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2. Mix in 1.5&mu;L of DpnI with remaining 45&mu;L of reaction, incubate for 3 hr at 37&deg;C.
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3. Purify reaction with NucleoSpin Extract II DNA purification kit, elute DNA in 30&mu;L water.
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== '''sRNA Characterization''' ==
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4. 30&mu;L digestion reaction (plasmid backbone)
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'''Taken from:''' [http://www.springerlink.com.proxy2.library.uiuc.edu/content/h752r3415261357p/ A Green Fluorescent Protein (GFP)-Based Plasmid System to Study Post-Transcriptional Control of Gene Expression In Vivo]: Johannes H. Urban and Jörg Vogel, 2009
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*25&mu;L eluted DNA
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*3&mu;L 10x Tango buffer
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*2&mu;L XbaI
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Digest for 6 hr (or overnight) at 37&deg;C, then add 1&mu;L shrimp alkaline phosphatase (SAP) and incubate for 1 hr at 37&deg;C.
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5. Purify the ~2.2kbp fragment in 0.8% agarose gel (there should also be a ~0.9kbp fragment), elute DNA in 25&mu;L water using NucleoSpin Extract II DNA purification kit.
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This protocol is used to characterize an E. coli small RNA and its ability to downregulate a reporter gene (GFP).  The small RNA is cloned out of the E. coli chromosome and inserted into a high-copy number plasmid (pJU-334).  The sRNA's target sequence is also cloned out of the E. coli chromosome and inserted into a low-copy number plasmid (pXG-10).  Both plasmids are then transformed into E. coli Top10F' cells.  Successful sRNA repression is indicated by a decreased level of fluorescence in the cells.
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6. 25&mu;L PCR reaction (sRNA gene of interest)
 
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*1&mu;L (10-50 ng) chromosomal E. coli K12 template DNA
 
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*0.2&mu;L of each primer (Note: The sense primer pairs with the sRNA gene starting at the +1 transcriptional start nucleotide and is 5'-phosphorylated for blunt-end ligation.  The antisense primer pairs ~40nt down from the terminator and has an XbaI site and five additional nucleotides.)
 
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*2.5&mu;L 10x Pfu buffer
 
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*0.5&mu;L dNTP mix
 
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*0.4&mu;L Pfu DNA polymerase
 
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*20.2&mu;L water
 
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Run for 5 min @ 95&deg;C, then 30 cycles of the following: 45s @ 95&deg;C, 45s @ 56&deg;C, 30s @ 72&deg;C. Incubate for 5 min @ 72&deg;C, then analyze 5&mu;L of the reaction in 3% agarose gel.
 
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7. Purify reaction with NucleoSpin Extract II DNA purification kit, elute DNA in 15&mu;L water.
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'''[[sRNA characterization procedure]]'''
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8. 10&mu;L digestion reaction (sRNA gene of interest)
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*8&mu;L eluted DNA
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*1&mu;L 10x Tango buffer
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*1&mu;L XbaI
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== '''Recipes''' ==
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Digest for 3 hr at 37&deg;C.
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9. Purify the proper fragment in 3% agarose gel, elute DNA in 15&mu;L water using NucleoSpin Extract II DNA purification kit.
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[[LB Broth]]
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10. 5&mu;L small-scale ligation reaction
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[[LB Plates]]
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*~12ng digested plasmid backbone
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*~5ng digested sRNA gene
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*0.5&mu;L 10x T4 DNA Ligase Reaction Buffer
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*0.5&mu;L T4 DNA ligase
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Incubate 1 hr at room temperature. Include control ligation where DNA insert is replaced by water.
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11. Transform 2&mu;L of reaction into E. coli Top10F' cells. Expect 50-200 colonies.
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[[EDTA]]
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''Target-GFP Fusion Cloning''
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1. Inoculate single colony of E. coli Top10 cells containing pXG-10 plasmid into 4mL LB containing 20&mu;g/mL chloramphenicol, grow overnight at 37&deg;C with agitation.
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2. Dilute culture in 400mL fresh LB medium, incubate overnight.
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3. Isolate pXG-10 plasmid using the NucleoBond PC100 plasmid purification kit. Use double volumes of washing buffer in each step mentioned in the manufacturer's protocol. Resuspend DNA in 80&mu;L water.
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4. 60&mu;L digestion reaction (pXG-10)
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*4&mu;g pXG-10 plasmid
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*40&mu;L NheI
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*20&mu;L BfrBI
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*1x Tango buffer
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Digest for 7 hr (or overnight) at 37&deg;C, then add 20&mu;L shrimp alkaline phosphatase (SAP) and incubate for 3 hr at 37&deg;C..
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5. Load reaction on 1% agarose gel and excise the 4.1kbp band. Purify using NucleoSpin Extract II DNA purification kit and elute in 50&mu;L water.
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6. 25&mu;L PCR reaction (sRNA target sequence)
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*1&mu;L (10-50 ng) chromosomal E. coli K12 template DNA
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*0.2&mu;L of each primer
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*2.5&mu;L 10x Pfu buffer
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*0.5&mu;L dNTP mix
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*0.4&mu;L Pfu DNA polymerase
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*20.2&mu;L water
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Run for 5 min @ 95&deg;C, then 30 cycles of the following: 45s @ 95&deg;C, 45s @ 58&deg;C, 45s @ 72&deg;C. Incubate for 5 min @ 72&deg;C, then analyze 5&mu;L of the reaction in 3% agarose gel.
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7. Purify reaction with NucleoSpin Extract II DNA purification kit, elute DNA in 15&mu;L water.
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8. 15&mu;L digestion reaction (sRNA target sequence)
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*12&mu;L eluted DNA
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*7.5U NheI
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*7.5U BfrBI
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*1x Tango buffer
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Digest for 3 hr at 37&deg;C.
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9. Purify the proper fragment in 3% agarose gel, elute DNA in 15&mu;L water using NucleoSpin Extract II DNA purification kit.
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10. 5&mu;L small-scale ligation reaction
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*~12ng digested pXG-10
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*~5ng digested sRNA target sequence
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*0.5&mu;L 10x T4 DNA Ligase Reaction Buffer
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*0.5&mu;L T4 DNA ligase
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Incubate 1 hr at room temperature. Include control ligation where DNA insert is replaced by water.
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11. Transform 2&mu;L of reaction into E. coli Top10 cells. Expect 50-200 colonies.
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== '''Recipes''' ==
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*LB Growth Media
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[[TAE Buffer]]
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**1L dH<sub>2</sub>0
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**10g NaCl
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**5g yeast extract
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**10g Bacto-tryptone
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*Agarose Gel
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[[TBE Buffer]]
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**50mL 0.5x TBE buffer
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**Agarose (To determine number of grams to use, multiply volume (50mL) by percentage of gel.  For example, use 1.5g of agarose in a 3% agarose gel.)
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**2.5&mu;L ethidium bromide
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[[Agarose Gels]]
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Questions about our Wiki page?  Please email Dave Korenchan at [mailto:korench1@illinois.edu korench1@illinois.edu].
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{{IllinoisBottomNav}}

Latest revision as of 15:50, 10 August 2009

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Protocols

This page describes protocols or includes links to protocols used in our project. Recipes used are also listed in a separate section. Protocols are organized by category. They were collected from Open Wet Ware, our advisors, and labs around the University of Illinois campus.

Standard

  • [http://www.biochem.northwestern.edu/morimoto/research/Protocols/I.%20Prokaryotes/A.%20Bacteriology.pdf Bacterial Culture Basics (media/plate preparation, growth, streaking, and storage)]
  • [http://www.stanford.edu/~teruel1/Protocols/pdf/Transformation%20Protocol%20Using%20Heat%20Shock.pdf Transformation by Heat Shock Protocol]
  • [http://www.methodbook.net/dna/agarogel.html Agarose Gel Electrophoresis Protocol]
  • [http://www.sigmaaldrich.com/life-science/custom-oligos/custom-dna/learning-center/annealing-oligos.html Annealing Oligonucleotides Protocol]
  • [http://www1.qiagen.com/Products/DnaCleanup/GelPcrSiCleanupSystems/QIAquickPCRPurificationKit.aspx?r=1745#Tabs=t2 PCR Cleanup Protocol (QIAquick PCR Purification Kit)] -- Click on "QIAquick Spin Handbook - English (PDF)" under the "Handbooks" header
  • [http://www.5prime.com/media/29661/perfectprep%20spin%20mini%20kit%20manual_5prime_1048299_072007.pdf Miniprep Protocol (PerfectPrep Spin Mini Kit)]
  • [http://www.promega.com/tbs/tb374/tb374.pdf Miniprep Protocol (PureYield Plasmid Miniprep System)]

sRNA Characterization

Taken from: [http://www.springerlink.com.proxy2.library.uiuc.edu/content/h752r3415261357p/ A Green Fluorescent Protein (GFP)-Based Plasmid System to Study Post-Transcriptional Control of Gene Expression In Vivo]: Johannes H. Urban and Jörg Vogel, 2009

This protocol is used to characterize an E. coli small RNA and its ability to downregulate a reporter gene (GFP). The small RNA is cloned out of the E. coli chromosome and inserted into a high-copy number plasmid (pJU-334). The sRNA's target sequence is also cloned out of the E. coli chromosome and inserted into a low-copy number plasmid (pXG-10). Both plasmids are then transformed into E. coli Top10F' cells. Successful sRNA repression is indicated by a decreased level of fluorescence in the cells.


sRNA characterization procedure

Questions about our Wiki page? Please email us at illinoisiGEM@gmail.com.

Retrieved from "http://2009.igem.org/Team:Illinois/Protocols"