Molecular biology

From CSBLwiki

Revision as of 03:14, 16 July 2010 (view source) Igchoi (Talk | contribs) (→protocols) ← Older edit		Revision as of 13:09, 23 November 2010 (view source) Igchoi (Talk | contribs) Newer edit →
Line 17:		Line 17:
	*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
		+	<biblio>LIC pmid=2235490</biblio>
	**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]

---

Revision as of 13:09, 23 November 2010

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

Reagents & Protocols

recipes

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

protocols

• PCR - General rules for primer design
• Genomic DNA extraction
• Competent cell preparation BSGC protocol (PDF)
  • Easy & rapid competent cell preparation reference link - by HJKo
• Electrocompetent cell Protocol (PDF)
• LIC cloning introduction LIC introduction - Ligation Independent Cloning

1. Error fetching PMID 2235490: [LIC]

• • LIC cloning protocol (Berkeley Structural Genomics Center)
    • Vector preparation
    • Insert preparation
    • LIC transformation:
      • mix insert and vector in appropriate amounts
      • incubate 5~30 min(20 min) at room temperature
      • do transformation in E. coli (recommend to use electro-competent cells)
• NCBE practical protocols: very good illustration for undergraduate students
• Conjugation
  • Donor: E. coli S17-1
• E. coli knockout by the Wanner method (Lambda Red Recombinase)

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