Team:Cornell/Notebook/Nah operon

From 2012.igem.org

(Difference between revisions)
(edited summary)
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===June 10th-16th===
===June 10th-16th===
====June 13th, Wednesday====
====June 13th, Wednesday====
-
*Set up [http://2011.igem.org/Team:Cornell/Protocols PCR] for four fragments of the nah operon as well as the pBMT-1 backbone, using primers designed to mutate cut-sites concurrently with Gibson Assembly. Also set up a PCR for the entire nah operon. Due to length of the fragments, a longer extension time was chosen.
+
*Set up [[PCR]] for four fragments of the nah operon as well as the pBMT-1 backbone, using primers designed to mutate cut-sites concurrently with Gibson Assembly. Also set up a PCR for the entire nah operon. Due to length of the fragments, a longer extension time was chosen.
*If Gibson Assembly fails, but we are able to PCR the entire 10kb nah operon using Phusion polymerase, an alternate method of mutation using Phusion will be pursued.
*If Gibson Assembly fails, but we are able to PCR the entire 10kb nah operon using Phusion polymerase, an alternate method of mutation using Phusion will be pursued.
**''Work done by: Caleb, Claire, Dylan, Spencer, Steven, and Swati''
**''Work done by: Caleb, Claire, Dylan, Spencer, Steven, and Swati''
====June 14th, Thursday====
====June 14th, Thursday====
-
*PCR only amplified nah1, nah3, and nah4 - longer fragments (nah2, the full nah operon, and pBMT-1) were not identified on the PCR product gel. Set up another [http://2011.igem.org/Team:Cornell/Protocols PCR] with shorter extension time.
+
*PCR only amplified nah1, nah3, and nah4 - longer fragments (nah2, the full nah operon, and pBMT-1) were not identified on the PCR product gel. Set up another [[PCR]] with shorter extension time.
====June 15th, Friday====
====June 15th, Friday====
Line 17: Line 17:
===June 17th-23rd===
===June 17th-23rd===
====June 17th, Sunday====
====June 17th, Sunday====
-
*Successful PCR of pBMT-1 [http://2011.igem.org/Team:Cornell/Protocols gel purified].
+
*Successful PCR of pBMT-1 [[Gel Purification | gel purified]].
====June 19th, Tuesday====
====June 19th, Tuesday====
-
*Ran [http://2011.igem.org/Team:Cornell/Protocols Gibson Assembly] of nah operon fragments into pBMT-1 backbone and [http://2011.igem.org/Team:Cornell/Protocols transformed] into DH5a electrocompotent ''E. coli'' cells.  
+
*Ran [[Gibson Assembly]] of nah operon fragments into pBMT-1 backbone and [[Transformation | transformed]] into DH5a electrocompotent ''E. coli'' cells.  
-
*Set up [http://2011.igem.org/Team:Cornell/Protocols PCR] to amplify the Gibson Assembly products.  
+
*Set up [[PCR]] to amplify the Gibson Assembly products.  
**''Work done by: Dylan and Swati''
**''Work done by: Dylan and Swati''
====June 20th, Wednesday====
====June 20th, Wednesday====
-
*Set up a [http://2011.igem.org/Team:Cornell/Protocols digestion] of the PCR of Gibson Assembly products and ran the digested products on a gel to see if Gibson worked.
+
*Set up a [[digestion]] of the PCR of Gibson Assembly products and ran the digested products on a gel to see if Gibson worked.
-
*Three colonies on plates of DH5a transformed with Gibson Assembly product. Made [http://2011.igem.org/Team:Cornell/Protocols liquid cultures] to miniprep and sequence.
+
*Three colonies on plates of DH5a transformed with Gibson Assembly product. Made [[liquid cultures]] to miniprep and sequence.
**''Work done by: Dylan and Swati''
**''Work done by: Dylan and Swati''
====June 22nd, Friday====
====June 22nd, Friday====
-
*[http://2011.igem.org/Team:Cornell/Protocols Miniprepped] directly transformed Gibson Assembly product for sequencing using the the Gibson nah1F and nah4R primers (each w/ 20 bp overhangs).
+
*[[Miniprep | Miniprepped]] directly transformed Gibson Assembly product for sequencing using the the Gibson nah1F and nah4R primers (each w/ 20 bp overhangs).
-
*Ran undigested miniprep with [http://2011.igem.org/Team:Cornell/Protocols gel electrophoresis], looking for large bands corresponding to supercoiled DNA. The gel shows distinct bands for all three lanes. We interpreted this to mean that we got product. Submitted for [http://2011.igem.org/Team:Cornell/Protocols sequencing]
+
*Ran undigested miniprep with [http://2011.igem.org/Team:Cornell/Protocols gel electrophoresis], looking for large bands corresponding to supercoiled DNA. The gel shows distinct bands for all three lanes. We interpreted this to mean that we got product. Submitted for [[sequencing]]
::[[File:Cornell2012_0621_Gibson-entire-plasmid.jpg|600px]]
::[[File:Cornell2012_0621_Gibson-entire-plasmid.jpg|600px]]
===June 24th-30th===
===June 24th-30th===
====June 27th, Wednesday====
====June 27th, Wednesday====
-
*Ran digest of gibson-assembled nah operon with [http://2011.igem.org/Team:Cornell/Protocols gel electrophoresis]
+
*Ran digest of gibson-assembled nah operon with [[gel electrophoresis]]
====June 28th, Thursday====
====June 28th, Thursday====

Revision as of 14:57, 2 July 2012

Home Team Project Parts Modeling Notebook Protocols Safety Attributions

Contents

The purpose of this subproject is to make the nah operon biobrick compatible for the use of future iGEM teams. The nah operon codes for a pathway that converts naphthalene into salicylate. In our system, this will allow naphthalene to be detected by the salicylate reporter. There are three standard cut sites internal to the operon which we are removing - PstI, and two NotI sites. This biobrick compatible piece could be useful to future teams in projects that involve bioremediation or detection of naphthalene.

June

June 10th-16th

June 13th, Wednesday

  • Set up PCR for four fragments of the nah operon as well as the pBMT-1 backbone, using primers designed to mutate cut-sites concurrently with Gibson Assembly. Also set up a PCR for the entire nah operon. Due to length of the fragments, a longer extension time was chosen.
  • If Gibson Assembly fails, but we are able to PCR the entire 10kb nah operon using Phusion polymerase, an alternate method of mutation using Phusion will be pursued.
    • Work done by: Caleb, Claire, Dylan, Spencer, Steven, and Swati

June 14th, Thursday

  • PCR only amplified nah1, nah3, and nah4 - longer fragments (nah2, the full nah operon, and pBMT-1) were not identified on the PCR product gel. Set up another PCR with shorter extension time.

June 15th, Friday

  • PCR of four out of five products visible on gel. Set up PCR of pBMT-1, final fragment required for Gibson Assembly of the nah operon.

June 17th-23rd

June 17th, Sunday

June 19th, Tuesday

  • Ran Gibson Assembly of nah operon fragments into pBMT-1 backbone and transformed into DH5a electrocompotent E. coli cells.
  • Set up PCR to amplify the Gibson Assembly products.
    • Work done by: Dylan and Swati

June 20th, Wednesday

  • Set up a digestion of the PCR of Gibson Assembly products and ran the digested products on a gel to see if Gibson worked.
  • Three colonies on plates of DH5a transformed with Gibson Assembly product. Made liquid cultures to miniprep and sequence.
    • Work done by: Dylan and Swati

June 22nd, Friday

  • Miniprepped directly transformed Gibson Assembly product for sequencing using the the Gibson nah1F and nah4R primers (each w/ 20 bp overhangs).
  • Ran undigested miniprep with gel electrophoresis, looking for large bands corresponding to supercoiled DNA. The gel shows distinct bands for all three lanes. We interpreted this to mean that we got product. Submitted for sequencing
Cornell2012 0621 Gibson-entire-plasmid.jpg

June 24th-30th

June 27th, Wednesday

====June 28th, Thursday====