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From 2012.igem.org

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You should make use of the calendar feature on the wiki and start a lab notebook. This may be looked at by the judges to see how your work progressed throughout the summer. It is a very useful organizational tool as well.

Contents 1 Labwork 1.1 May and June 2012 1.2 July 2012 1.3 August 2012 1.4 September 2012 1.5 October 2012 2 Methods and Protocols 2.1 Plasmid Preparation 2.1.1 Plasmid Preparation of E.coli (Mini Preparation) 2.1.2 Plasmid Preparation of Saccharomyces cerevisia 2.2 Transformation 2.2.1 Yeast Transformation 2.2.2 E.coli Transformation 2.3 PCR 2.4 Culture Medium 2.5 Agar Plate 2.5.1 LBampicillin-Agar 2.5.2 SCD-Agar 2.5.3 YEPDG418-Agar 2.6 Gel Electrophoresis 2.7 Kit

Labwork

May and June 2012

• Arrangements for labwork
  preparation of competent cells (E.coli, S.cerevisiae), agarose plates (LB, YEPD, SCD-ura,…), medium for E.coli and S.cerevisiae

• Purchasing of the equipment (reaction tubes, glass bottles, pipette tips,..)

• Primer design

July 2012

• Plasmid isolation of p426, p423, pUD8e, pUD22e from E.coli

• Isolation of chromosomal DNA of CEN.PK2-1C

• Trials to get the genes, promoters and terminators via PCR

August 2012

• PCR of the genes, promoters and terminators
  all genes (without KO and KAH), promoters and terminators could be amplified
  

Templates	Amplified DNA Fragments
synthesized sequence of HMG-CoA	HMG-CoA
synthesized sequence of GGPPS	GGPPS
synthesized sequence of Cps/Ks	CPS/KS
chromosomal DNA of CEN.PK2-1C	ERG20

• Linearization of p426 and p423 with SpeI and XhoI
• Biobrick production of the genes HMG-CoA, ERG20, CPS/KS
  
  • restriction of 3 µg of the genes with EcoRI and PstI
    
  • ligation of biobrick genes with linear pSB1C3
    
  • transformation of the ligation in E.coli
    
  • plasmid isolation of E.coli clones
    
  • control restriction of biobrick plasmids with EcoRI and SpeI
    
• Formation of the mevalonate overexpression plasmid via gap repair
  • first and second yeast transformation with equimolar quantities of DNA fragments for mevalonate overexpression (p426 with 7 inserts): only very small colonies could grow after the first and second transformation
  • using pure GGPPS (purification of a preparative gel) for the third yeast transformation: normal size of the colonies
  • inoculation of several clones of the third yeast transformation
  • plasmid preparation of the clones
  • transformation of the plasmids in E.coli
    
• Amplifying pSB1C3 for biobrick production
  • trials to amplify pSB1C3, whose blunt ends were ligated and transformed in E.coli
  • pSB1C3 should be linearized by EcoRI and PstI : did not work (two fragments instead of one)
    
  • preparative gel of the linear fragment: very low concentration of linear pSB1C3 (was not sufficient for ligation)

September 2012

October 2012

Methods and Protocols

Plasmid Preparation

Plasmid Preparation of E.coli (Mini Preparation)

Plasmid Preparation of Saccharomyces cerevisia

Transformation

Yeast Transformation

E.coli Transformation

PCR

Culture Medium

Full Medium (YEPD) for Yeast
Yeast Extract	1 % (weight/volume)
Pepton	2 % (w/v)
Glucose	2 % (w/v)

Synthetic Complete Medium (SC) for Yeast
Yeast Nitrogen Base	0.17 % (w/v)
Ammoniumsulfate	0.5 % (w/v)
Glucose	2 % (w/v)
Amino Acid Mix*	50 ml/l
Histidin**	0.25 mM
Tryptophan**	0.19 mM
Leucin**	0.35 mM
Uracil**	0.44 mM

pH has to be regulated with KOH to pH=6.3

• contains no His, Leu, Trp and Uracil
  ** addition of this components depents on the respective selection medium

SOC-Medium for Regeneration of transformed Escherichia coli`s after Electroporation
Trypton	2 % (w/v)
Yeast Extract	0.5 % (w/v)
NaCl	10 mM
KCl	2,5 mM
MgCl2	10 mM
MgSO4	10 mM
Glucose	20 mM

pH has to be regulated to pH=6.8-7.0

Full Medium (LB) for E.coli
Yeast Extract	0.5 % (w/v)
Trypton	1 % (w/v)
NaCl	0.5 % (w/v)

pH has to be regulated with NaOH to pH=7.5

Every cluture medium has to be autoclaved to be sterile.

Agar Plate

LB_ampicillin-Agar

Add 2 % agar to LB-medium. After autoclaving and cooling-down to 60 °C steril ampicillin is added. Plates were poured.

SCD-Agar

Add 2 % agar to SCD-medium. After autoclaving and cooling-down steril amino acid solution is added. Dependent on the respective selective medium Histidin (0.25 mM), Trypthophan (0.19 mM), Uracil (0.44 mM) or Leucin (0.35 mM) are added. Plates were poured.

YEPD_G418-Agar

Add 2 % agar to YEPD-medium. After autoclaving and cooling-down sterile G418 (final concentration 2g/l) is added. Plates were poured.

Gel Electrophoresis

Agarose Gel (1x)
TAE puffer	1x
Agarose	1 % (w/v)

Solve agarose in TAE by boiling it. After cooling-down to 55-60 °C gel is poured.

TAE Puffer (50x) for Gel Electrophoresis
EDTA	18,6 g
Tris	242g
Glacial Acetic Acid	57,2 ml
Purified Water	1000ml

pH has to be regulated with glacial acetic acid to pH=8.

Kit

PCR Purification Kit
Gel Extraction Kit
Midi Plasmid Preparation Kit