Molecular biology

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Revision as of 16:19, 1 January 2009 (view source) Igchoi (Talk | contribs) (→softwares) ← Older edit		Revision as of 09:24, 3 April 2009 (view source) Igchoi (Talk | contribs) (→protocols) Newer edit →
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	#Electrocompetent cell [[media:ElectrocompetentEcoli.pdf|Protocol (PDF)]]		#Electrocompetent cell [[media:ElectrocompetentEcoli.pdf|Protocol (PDF)]]
	#LIC cloning introduction [[media:LICnovagen.pdf|LIC introduction]] - Ligation Independent Cloning		#LIC cloning introduction [[media:LICnovagen.pdf|LIC introduction]] - Ligation Independent Cloning
-	*LIC cloning protocol (Berkeley Structural Genomics Center)	+	##LIC cloning protocol (Berkeley Structural Genomics Center)
-	#[http://www.strgen.org/protocols/lic-vector-prep.pdf Vector preparation]	+	###[http://www.strgen.org/protocols/lic-vector-prep.pdf Vector preparation]
-	#[http://www.strgen.org/protocols/lic-insert-prep.pdf Insert preparation]	+	###[http://www.strgen.org/protocols/lic-insert-prep.pdf Insert preparation]
-	#[http://www.strgen.org/protocols/lic-rxn-transf.pdf LIC transformation]:	+	###[http://www.strgen.org/protocols/lic-rxn-transf.pdf LIC transformation]:
-	##mix insert and vector in appropriate amounts	+	####mix insert and vector in appropriate amounts
-	##incubate 5~30 min(20 min) at room temperature	+	####incubate 5~30 min(20 min) at room temperature
-	##do transformation in E. coli (recommend to use electro-competent cells)	+	####do transformation in E. coli (recommend to use electro-competent cells)
		+	#[http://www.ncbe.reading.ac.uk/ncbe/protocols/ NCBE practical protocols]: very good illustration for undergraduate students
	==Tools==		==Tools==

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Revision as of 09:24, 3 April 2009

Contents 1 Reagents & Protocols 1.1 recipes 1.2 protocols 2 Tools 2.1 webtools 2.2 softwares

Reagents & Protocols

recipes

1. Chemicals
2. Commonly used reagents and equipment in molecular biology (PDF)
3. Concentration of antibiotics commonly used
4. For DNA extraction (to remove some protein contaminants & inactivate enzymes): Phenol:Chloroform=1:1(v:v) solution
5. DNA sequencing check list
   1. quality score
   2. good sequencing result vs. bad sequencing result (see below example)
      

      

protocols

1. PCR - General rules for primer design
2. Genomic DNA extraction
3. Competent cell preparation BSGC protocol (PDF)
4. Electrocompetent cell Protocol (PDF)
5. LIC cloning introduction LIC introduction - Ligation Independent Cloning
   1. LIC cloning protocol (Berkeley Structural Genomics Center)
      1. Vector preparation
      2. Insert preparation
      3. LIC transformation:
         1. mix insert and vector in appropriate amounts
         2. incubate 5~30 min(20 min) at room temperature
         3. do transformation in E. coli (recommend to use electro-competent cells)
6. NCBE practical protocols: very good illustration for undergraduate students

Tools

webtools

1. Oligo Tm calculation

softwares

1. NIH Image: Gel analysis software
2. Serial Cloner: DNA sequence management (PCR, restriction maps, etc.)
3. BioX (Mac OS X only)
4. Biological sequence editor Bioedit
5. Jmol