Team:Illinois/3'-Acting sRNAs

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== '''3'-Acting sRNAs Team''' ==
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'''Members:'''
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== '''mRNA Degradation Team''' ==
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Francis Lee
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Lucy McCommas
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Van Ceu
'''Goals:'''
'''Goals:'''
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Our goal is to work with sRNAs that bind to the 3' UTR.  We will study this regulation system using the Vogel protocol.  We want to have two sRNAs controlling one gene, which could be accomplished through using a combination of 5' and 3' acting sRNAs.
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'''Background:'''
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Colony Boil-Streak plate E. Coli K12 on LB agar, incubate overnight at 37C.  Pick healthy colony with sterile glass pasteur pipette and innoculate 100 uL dH20.  Boil for 10 min, centrifugate for 5 min at 14K rpm.  Extract 1 uL of supernatant as template DNA for PCR.
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'''GadY Gene Sequence:'''  (K-12 substr. MG1655: 3662867-3663047)
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ACTGAGAGCA CAAAGTTTCC CGTGCCAACA GGGAGTGTTA TAACGGTTTA TTAGTCTGGA GACGGCAGAC TATCCTCTTC CCGGTCCCCT ATGCCGGGTT TTTTTTATGT CTGAGTAAAA CTCTATAATC TTATTCCTTC
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'''GadX 3' UTR Sequence:''' (K-12 substr. MG1655: 3662641-3662717)
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AGTTTTACTC AGACATAAAA AAAACCCGGC ATAGGGGACC GGGAAGAGGA TAGTCTGCCG TCTCCAGACT AATAAA
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'''GadX 3' UTR Sequence (2):''' (K-12 substr. MG1655: 3662641-3663008)
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AGTTTTACTC AGACATAAAA AAAACCCGGC ATAGGGGACC GGGAAGAGGA TAGTCTGCCG TCTCCAGACT AATAAACCGT TATAACACTC CCTGTTGGCA CGGGAAACTT TGTGCTCTCA GTAAGTTAAA TATAACTTTT ACTGGAAATA AGATCAGCCA TTTTTTTATA AACATAAGCT ATACGCTGTG CGAAAATATA TTCGTGCTGC ATTTACTTAT TATCAATTAA CTGTTATGCA AAACTACTTT GTGGATAAAT TTTGGTCCTA CCAAATCTGG CAGTTTTTGC GCTAAGAAAC AGTCTGGCAT CATTTCATTA GTATACTGAA ATTGAAATAA TCGCAGTATG AAATATAAGG GATAATC
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'''Primers Used:'''
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*Forward/sense gadY (sRNA gene) primer: ACTGAGAGCACAAAGTTTCC
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*Reverse/antisense gadY (sRNA gene) primer: (XbaI)-GTTTTTTCTAGAGAAGGAATAAGATTATAGAG
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*Forward/sense gadX (sRNA target sequence) primer: (SwaI)-GTTTTTATTTAAATAGTTTTACTCAGACATAAAAAAAACC
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*Reverse/antisense gadX (sRNA target sequence) primer: (XbaI)-GTTTTTTCTAGATTTATTAGTCTGGAGACGGCAG
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*Reverse/antisense gadX (sRNA target sequence) primer 2: (XbaI)-GTTTTTTCTAGAGATTATCCCTTATATTTCATAC
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'''PCR Products:'''
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GadY GENE (XbaI restriction site)-152bp
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GadX 3' UTR (SwaI, XbaI restriction sites)-102bp, 393bp :
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== '''July 9''' ==
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We cloned the GadY gene as well as the 3' UTR of gadX.  We used two different primers for gadX because we weren't sure which design would work the best.  Primer 2 goes all the way to the start codon of gadW. 
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We did this with a successful PCR.
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[[Image:IllinoisiGEM_gadY_gel1.jpg]]
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We then purified the PCR product that was not used in the gel.  We also prepared an overnight of dh5&alpha; transformed with pXG-1.
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== '''July 10''' ==
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Today we performed a midiprep to extract the plasmid DNA from dH5&alpha;.
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== '''References''' ==
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[http://jb.asm.org/cgi/content/abstract/186/20/6698 GadY, a Small-RNA Regulator of Acid Response Genes in Escherichia coli] Jason A. Opdyke, Ju-Gyeong Kang, and Gisela Storz
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Latest revision as of 21:06, 19 July 2009

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Contents

3'-Acting sRNAs Team

Members:

Francis Lee

Lucy McCommas

Van Ceu

Goals:

Our goal is to work with sRNAs that bind to the 3' UTR. We will study this regulation system using the Vogel protocol. We want to have two sRNAs controlling one gene, which could be accomplished through using a combination of 5' and 3' acting sRNAs.

Background:

Colony Boil-Streak plate E. Coli K12 on LB agar, incubate overnight at 37C. Pick healthy colony with sterile glass pasteur pipette and innoculate 100 uL dH20. Boil for 10 min, centrifugate for 5 min at 14K rpm. Extract 1 uL of supernatant as template DNA for PCR.

GadY Gene Sequence: (K-12 substr. MG1655: 3662867-3663047)

ACTGAGAGCA CAAAGTTTCC CGTGCCAACA GGGAGTGTTA TAACGGTTTA TTAGTCTGGA GACGGCAGAC TATCCTCTTC CCGGTCCCCT ATGCCGGGTT TTTTTTATGT CTGAGTAAAA CTCTATAATC TTATTCCTTC

GadX 3' UTR Sequence: (K-12 substr. MG1655: 3662641-3662717)

AGTTTTACTC AGACATAAAA AAAACCCGGC ATAGGGGACC GGGAAGAGGA TAGTCTGCCG TCTCCAGACT AATAAA

GadX 3' UTR Sequence (2): (K-12 substr. MG1655: 3662641-3663008)

AGTTTTACTC AGACATAAAA AAAACCCGGC ATAGGGGACC GGGAAGAGGA TAGTCTGCCG TCTCCAGACT AATAAACCGT TATAACACTC CCTGTTGGCA CGGGAAACTT TGTGCTCTCA GTAAGTTAAA TATAACTTTT ACTGGAAATA AGATCAGCCA TTTTTTTATA AACATAAGCT ATACGCTGTG CGAAAATATA TTCGTGCTGC ATTTACTTAT TATCAATTAA CTGTTATGCA AAACTACTTT GTGGATAAAT TTTGGTCCTA CCAAATCTGG CAGTTTTTGC GCTAAGAAAC AGTCTGGCAT CATTTCATTA GTATACTGAA ATTGAAATAA TCGCAGTATG AAATATAAGG GATAATC

Primers Used:

  • Forward/sense gadY (sRNA gene) primer: ACTGAGAGCACAAAGTTTCC
  • Reverse/antisense gadY (sRNA gene) primer: (XbaI)-GTTTTTTCTAGAGAAGGAATAAGATTATAGAG
  • Forward/sense gadX (sRNA target sequence) primer: (SwaI)-GTTTTTATTTAAATAGTTTTACTCAGACATAAAAAAAACC
  • Reverse/antisense gadX (sRNA target sequence) primer: (XbaI)-GTTTTTTCTAGATTTATTAGTCTGGAGACGGCAG
  • Reverse/antisense gadX (sRNA target sequence) primer 2: (XbaI)-GTTTTTTCTAGAGATTATCCCTTATATTTCATAC

PCR Products:

GadY GENE (XbaI restriction site)-152bp

GadX 3' UTR (SwaI, XbaI restriction sites)-102bp, 393bp :

July 9

We cloned the GadY gene as well as the 3' UTR of gadX. We used two different primers for gadX because we weren't sure which design would work the best. Primer 2 goes all the way to the start codon of gadW.

We did this with a successful PCR.

IllinoisiGEM gadY gel1.jpg


We then purified the PCR product that was not used in the gel. We also prepared an overnight of dh5α transformed with pXG-1.

July 10

Today we performed a midiprep to extract the plasmid DNA from dH5α.

References

[http://jb.asm.org/cgi/content/abstract/186/20/6698 GadY, a Small-RNA Regulator of Acid Response Genes in Escherichia coli] Jason A. Opdyke, Ju-Gyeong Kang, and Gisela Storz

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

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