Team:Johns Hopkins/Notebook/GROUP 1: Fluorescent Proteins

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== GROUP 1: Fluorescent Proteins ==
== GROUP 1: Fluorescent Proteins ==
 +
 +
 +
  Date: Oct 19, 2008
 +
  Status report by: Tejas
 +
  Part no.: BBa_K110017 -> BBa_K110023
 +
  Part Description: yESapphire , mCherry, venusYFP, and Citrine <br>
 +
  Work on YFP has progressed, though the biobrick system is giving diffiulty in obtaining a useful
 +
  construct. Moreover, the YFP sequence may not fully match the expected sequence. However,
 +
  fluoroescent proteins (yeast optimized) sent us as STABS from MIT are showing promise, and may be
 +
  ready for some use by the Jamboree date if all goes well. Work will continue on venus YFP and
 +
  mCherry (though mCherry unfortunately contains a restriction site). Sapphire must be started over
 +
  sue to technical difficulties getting a clone.
 +
 +
  Date: July 22, 2008
 +
  Status report by: Tejas, Ingrid
 +
  Part no.: BBa_K110017 -> BBa_K110023
 +
  Part Description: yESapphire , mCherry, venusYFP, and Citrine <br>
 +
  Work on yESapphire was gratiously done by James. Primers were designed. Restriction site
 +
  ends have been added through PCR. The product was cloned into JM109. Colonies were picked
 +
  and an inoculation was grown. Miniprep was performed and subsequent DNA was CS PCR'd
 +
  and run on a gel to verify contents.
 +
  <b>([http://www.jhu.edu/iGEM/Group3:ShortTwo-wayStops/2008-7-22.Short%202Way%20Stop,%20Alpha%20Promoters,%20&%20Sapphire%20FP.Allison%20Suarez%20and%20Nate%20Sotuyo%20.html  Short 2Way Stop, Alpha Promoters, & Sapphire FP])</b> BioBrick is currently being sequenced. <br>
 +
  Work on mCherry and venusYFP (BBa_K110018 -> BBa_K110021) is currently being done. Primers were designed.
 +
  Restriction sites have been added through PCR.  ([http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-23.PCR%20Products:%20mCherry%20and%20Venus%20YFP,%20both%20RtL%20and%20LtR.Ingrid,%20Tejas.html PCR Products: mCherry and Venus YFP, both RtL and LtR]) The
 +
  products were cloned into JM109 and plated. 3 colonies per 4 BioBricks (total 12) were picked, grown out,
 +
  mini prepped, and digested for verification on a gel.<br>
 +
  According to the results, (<b>[http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-22.Venus%20YFP%20and%20mCherry%20Miniprep%20check%20via%20digest.Ingrid.html Venus YFP and mCherry Miniprep check via digest]</b>) , only one of the mCherry's
 +
  (BBa_K110019) is the correct product. A second Digest was preformed to check this, meanwhile new colonies
 +
  have been picked on 7.22.2008 and are being grown out for a higher yield of DNA so that it can be sent off
 +
  for sequencing. <b>[http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-23.Re-Digest%20of%20three%20samples%20of%20mCherry%20BBa_K110018.Ingrid%20.html Re-Digest of three samples of mCherry BBa_K110018]<br></b>
 +
  Work on Citrine has not yet begun. Primers have been designed and ordered, but template DNA must be grown out.
 +
  Template DNA will be grown and extracted by James should we later decide that Citrine will be needed.<br> 
 +
  *Note that mCherry and Citrine both have restriction sites within the coding region, and are therefore not
 +
  optimal. Advice/help on this issue would be appreciated.
 +
 +
Another Digest was done [http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-8-19.mCherry%20and%20YFP%20Digest%20Gel.Ingrid%20Spielman.html mCherry and YFP Digest Gel] and weird lines exist.
   Date: July 17 2008
   Date: July 17 2008
Line 16: Line 52:
   Problems to be solved: Had some extra unknown products, with unknown bands in the gel
   Problems to be solved: Had some extra unknown products, with unknown bands in the gel
   Current status of this part: Done with touchdown PCR and gel. Next step is to clone product.
   Current status of this part: Done with touchdown PCR and gel. Next step is to clone product.
-
 
-
  Date: July 17 2008
 
-
  status report by: Ingrid
 
-
  Part no.: BBa_K110019
 
-
  Part Description: mCherry:
 
-
  Part Location (in build a genome lab): In silver fridge by door
 
-
  PCR successful?; Yes
 
-
  [http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-22.PCR%20Products%20of%20mCherry%20and%20vYFP.Ingrid%20&%20Tejas.html PCR Products of mCherry and vYFP]
 
-
  <b>Cloning of PCR product successful: Inconclusive
 
-
  [http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-22.Venus%20YFP%20and%20mCherry%20Miniprep%20check%20via%20digest.Ingrid.html Venus YFP and mCherry Miniprep check via digest]</b>
 
-
  Sequencing of cloned PCR product successful: No
 
-
  Joining of validated part to adjacent part(s) status: Not done
 
-
  Problems to be solved: Need to figure out if gel after digest shows correct products
 
   Date: July 17 2008
   Date: July 17 2008
Line 44: Line 67:
   Current status of this part: Done with touchdown PCR and gel. Next step is to clone product.
   Current status of this part: Done with touchdown PCR and gel. Next step is to clone product.
-
   Date: July 17 2008
+
   Date: July 1 2008
 +
  status report by: Ingrid (work done by James)
 +
  Part no.: BBa_K110017
 +
  Part Description: yESapphire
 +
  Part Location (in build a genome lab): In James and Jasper's PCR product Box,
 +
  Stainless Steel 4 degree
 +
  PCR successful?; Yes
 +
  Cloning of PCR product successful: Y/N
 +
  Sequencing of cloned PCR product successful: Not done
 +
  Joining of validated part to adjacent part(s) status: Not done
 +
  Current status of this part: This part is being Sequenced
 +
 
 +
  Date: August 27 2008
   status report by: Ingrid  
   status report by: Ingrid  
-
   Part no.: BBa_K110021
+
   Part no.: BBa_K110018, 19, 20, 21
-
   Part Description: Venus Enhanced YFP
+
   Part Description: mCherry, YFP
-
   Part Location (in build a genome lab): In silver fridge by door
+
   Part Location (in build a genome lab): In James and Jasper's PCR product Box,
-
   PCR successful?; Yes  
+
  Stainless Steel 4 degree
-
   [http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-22.PCR%20Products%20of%20mCherry%20and%20vYFP.Ingrid%20&%20Tejas.html PCR Products of mCherry and vYFP]
+
   PCR successful?; Yes
-
  <b>Cloning of PCR product successful: Inconclusive
+
   Cloning of PCR product successful: Y/N
-
  [http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-22.Venus%20YFP%20and%20mCherry%20Miniprep%20check%20via%20digest.Ingrid.html Venus YFP and mCherry Miniprep check via digest]</b>
+
   Sequencing of cloned PCR product successful: Successful for YFP LtR and RtL
-
   Sequencing of cloned PCR product successful: No
+
   Joining of validated part to adjacent part(s) status: In progress
-
   Joining of validated part to adjacent part(s) status: Not done
+
   Current status of this part: Ligation into vector
-
  Problems to be solved: Had some extra unknown products, with unknown bands in the gel
+
  Digest of colonies repicked from mCherry and YFP
-
   Current status of this part: Done with touchdown PCR and gel. Next step is to clone product.
+
  [[Image:Igem_8-29-08_-Ingrid_FP_miniprepdigest.jpg|thumb|left|200px]]
 +
  Aug 29, 2008
 +
  Lane 1: 18.1 mCherry LtR
 +
  Lane 2: 18.2 mCherry LtR
 +
  Lane 3: 19.1 mCherry RtL
 +
  Lane 4: 20.1 Venus YFP LtR
 +
  Lane 5: 20.2 Venus YFP LtR
 +
  Lane 6: 21.1 Venus YFP RtL
 +
  Lane 7: 21.2 Venus YFP RtL
 +
  Lane 8: Ladder
 +
  Used digest protocol. Sequences have been made, YFP and mCherry have mutations.
 +
  mCHerry mutations seem deleterious =  discontinued use.
 +
  YFP mutations are not essential and therefore the RtL
 +
  Venus YFP will be ligated into final vector product!

Latest revision as of 03:32, 30 October 2008

GROUP 1: Fluorescent Proteins

 Date: Oct 19, 2008
 Status report by: Tejas
 Part no.: BBa_K110017 -> BBa_K110023
 Part Description: yESapphire , mCherry, venusYFP, and Citrine 
Work on YFP has progressed, though the biobrick system is giving diffiulty in obtaining a useful construct. Moreover, the YFP sequence may not fully match the expected sequence. However, fluoroescent proteins (yeast optimized) sent us as STABS from MIT are showing promise, and may be ready for some use by the Jamboree date if all goes well. Work will continue on venus YFP and mCherry (though mCherry unfortunately contains a restriction site). Sapphire must be started over sue to technical difficulties getting a clone.
 Date: July 22, 2008
 Status report by: Tejas, Ingrid
 Part no.: BBa_K110017 -> BBa_K110023
 Part Description: yESapphire , mCherry, venusYFP, and Citrine 
Work on yESapphire was gratiously done by James. Primers were designed. Restriction site ends have been added through PCR. The product was cloned into JM109. Colonies were picked and an inoculation was grown. Miniprep was performed and subsequent DNA was CS PCR'd and run on a gel to verify contents. ([http://www.jhu.edu/iGEM/Group3:ShortTwo-wayStops/2008-7-22.Short%202Way%20Stop,%20Alpha%20Promoters,%20&%20Sapphire%20FP.Allison%20Suarez%20and%20Nate%20Sotuyo%20.html Short 2Way Stop, Alpha Promoters, & Sapphire FP]) BioBrick is currently being sequenced.
Work on mCherry and venusYFP (BBa_K110018 -> BBa_K110021) is currently being done. Primers were designed. Restriction sites have been added through PCR. ([http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-23.PCR%20Products:%20mCherry%20and%20Venus%20YFP,%20both%20RtL%20and%20LtR.Ingrid,%20Tejas.html PCR Products: mCherry and Venus YFP, both RtL and LtR]) The products were cloned into JM109 and plated. 3 colonies per 4 BioBricks (total 12) were picked, grown out, mini prepped, and digested for verification on a gel.
According to the results, ([http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-22.Venus%20YFP%20and%20mCherry%20Miniprep%20check%20via%20digest.Ingrid.html Venus YFP and mCherry Miniprep check via digest]) , only one of the mCherry's (BBa_K110019) is the correct product. A second Digest was preformed to check this, meanwhile new colonies have been picked on 7.22.2008 and are being grown out for a higher yield of DNA so that it can be sent off for sequencing. [http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-23.Re-Digest%20of%20three%20samples%20of%20mCherry%20BBa_K110018.Ingrid%20.html Re-Digest of three samples of mCherry BBa_K110018]
Work on Citrine has not yet begun. Primers have been designed and ordered, but template DNA must be grown out. Template DNA will be grown and extracted by James should we later decide that Citrine will be needed.
*Note that mCherry and Citrine both have restriction sites within the coding region, and are therefore not optimal. Advice/help on this issue would be appreciated.
Another Digest was done [http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-8-19.mCherry%20and%20YFP%20Digest%20Gel.Ingrid%20Spielman.html mCherry and YFP Digest Gel] and weird lines exist.
 Date: July 17 2008
 status report by: Ingrid 
 Part no.: BBa_K110018 
 Part Description: mCherry: 
 Part Location (in build a genome lab): In silver fridge by door
 PCR successful?; Yes 
 [http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-22.PCR%20Products%20of%20mCherry%20and%20vYFP.Ingrid%20&%20Tejas.html PCR Products of mCherry and vYFP]
 Cloning of PCR product successful: Inconclusive 
 [http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-22.Venus%20YFP%20and%20mCherry%20Miniprep%20check%20via%20digest.Ingrid.html Venus YFP and mCherry Miniprep check via digest]
 Sequencing of cloned PCR product successful: Not done
 Joining of validated part to adjacent part(s) status: Not done
 Problems to be solved: Had some extra unknown products, with unknown bands in the gel
 Current status of this part: Done with touchdown PCR and gel. Next step is to clone product.
 Date: July 17 2008
 status report by: Ingrid 
 Part no.: BBa_K110020 
 Part Description: Venus Enhanced YFP
 Part Location (in build a genome lab): In silver fridge by door
 PCR successful?; Yes 
 [http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-22.PCR%20Products%20of%20mCherry%20and%20vYFP.Ingrid%20&%20Tejas.html PCR Products of mCherry and vYFP]
 Cloning of PCR product successful: inconclusive
 [http://www.jhu.edu/iGEM/Group1:FluorescentProteins/2008-7-22.Venus%20YFP%20and%20mCherry%20Miniprep%20check%20via%20digest.Ingrid.html Venus YFP and mCherry Miniprep check via digest]
 Sequencing of cloned PCR product successful: No
 Joining of validated part to adjacent part(s) status: Not done
 Problems to be solved: Had some extra unknown products, with unknown bands in the gel
 Current status of this part: Done with touchdown PCR and gel. Next step is to clone product.
 Date: July 1 2008
 status report by: Ingrid (work done by James)
 Part no.: BBa_K110017
 Part Description: yESapphire 
 Part Location (in build a genome lab): In James and Jasper's PCR product Box,
 Stainless Steel 4 degree
 PCR successful?; Yes
 Cloning of PCR product successful: Y/N
 Sequencing of cloned PCR product successful: Not done
 Joining of validated part to adjacent part(s) status: Not done
 Current status of this part: This part is being Sequenced
 Date: August 27 2008
 status report by: Ingrid 
 Part no.: BBa_K110018, 19, 20, 21
 Part Description: mCherry, YFP  
 Part Location (in build a genome lab): In James and Jasper's PCR product Box,
 Stainless Steel 4 degree
 PCR successful?; Yes
 Cloning of PCR product successful: Y/N
 Sequencing of cloned PCR product successful: Successful for YFP LtR and RtL
 Joining of validated part to adjacent part(s) status: In progress
 Current status of this part: Ligation into vector
 Digest of colonies repicked from mCherry and YFP
Igem 8-29-08 -Ingrid FP miniprepdigest.jpg
 Aug 29, 2008
 Lane 1: 18.1 mCherry LtR
 Lane 2: 18.2 mCherry LtR
 Lane 3: 19.1 mCherry RtL
 Lane 4: 20.1 Venus YFP LtR
 Lane 5: 20.2 Venus YFP LtR
 Lane 6: 21.1 Venus YFP RtL
 Lane 7: 21.2 Venus YFP RtL
 Lane 8: Ladder
 Used digest protocol. Sequences have been made, YFP and mCherry have mutations. 
 mCHerry mutations seem deleterious =  discontinued use. 
 YFP mutations are not essential and therefore the RtL 
 Venus YFP will be ligated into final vector product!