Molecular biology

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Revision as of 08:33, 21 July 2009 (view source) Igchoi (Talk | contribs) (→recipes) ← Older edit		Revision as of 08:33, 21 July 2009 (view source) Igchoi (Talk | contribs) (→recipes) Newer edit →
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	==Reagents & Protocols==		==Reagents & Protocols==
	===recipes===		===recipes===
-	#[[Chemicals]]	+	*[[Chemicals]]
-	#[[media:mba.pdf|Commonly used reagents and equipment in molecular biology (PDF)]]	+	*[[media:mba.pdf|Commonly used reagents and equipment in molecular biology (PDF)]]
-	#[[Concentration of antibiotics commonly used]]	+	*[[Concentration of antibiotics commonly used]]
-	#For DNA extraction (to remove some protein contaminants & inactivate enzymes): Phenol:Chloroform=1:1(v:v) solution	+	*For DNA extraction (to remove some protein contaminants & inactivate enzymes): Phenol:Chloroform=1:1(v:v) solution
-	#DNA sequencing check list	+	*DNA sequencing check list
-	##[http://en.wikipedia.org/wiki/Phred_quality_score quality score]	+	**[http://en.wikipedia.org/wiki/Phred_quality_score quality score]
-	##good sequencing result vs. bad sequencing result (see below example)	+	**good sequencing result vs. bad sequencing result (see below example)
	[[image:sequencingresult.jpg|left|thumb|good vs. bad sequencing example]]		[[image:sequencingresult.jpg|left|thumb|good vs. bad sequencing example]]

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Revision as of 08:33, 21 July 2009

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)
• Electrocompetent cell Protocol (PDF)
• LIC cloning introduction LIC introduction - Ligation Independent Cloning
  • 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

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