Molecular biology

From CSBLwiki

Contents 1 Reagents & Protocols 1.1 recipes 1.2 protocols 2 Tools 2.1 Webtools 2.2 Softwares

Reagents & Protocols

recipes

1. Commonly used reagents and equipment in molecular biology (PDF)
2. Concentration of antibiotics commonly used
3. For DNA extraction (to remove some protein contaminants & inactivate enzymes): Phenol:Chloroform=1:1(v:v) solution
4. 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
   1. Takara PCR protocol
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

• 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)

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 test