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. 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
7. Conjugation
   2. 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