Module 1: Degenerate PCR and Topoisomerase (TOPO)-based DNA Cloning

Equipment and Materials

Week 1

  • Previously harvested frozen grape leaves
  • Qiagen DNeasy Plant Mini Kit (50) (Qiagen, Valencia, CA)
  • 70% EtOH
  • Liquid N2
  • Mortar and pestle
  • Homogenization pestle for 1.5 ml microcentrifuge tubes
  • 0.2 ml PCR tubes
  • Degenerate PCR primers
    • LM 638 (5′-GGIGGIGTIGGIAAIACIAC-3′)
    • LM 637 (5′-A(A/G)IGCTA(A/G)IGGIA(A/G)ICC-3′)
  • NanoDrop™ One microvolume UV-Vis spectrophotometer (Thermo Scientific, Wilmington, DE)
  • T-100 Thermal Cycler (BioRad USA, Hercules, CA)
  • Promega 2X PCR Master Mix (Promega US, Madison, WI)
  • JumpStart Taq DNA polymerase (MilliporeSigma, Burlington, MA)

Week 2

  • 1000X GelRed (Phenix Research Products, Candler, NC)
  • 50X TAE buffer
  • Agarose
  • Power supply
  • Ice bucket
  • QIAquick PCR Purification Kit (Qiagen, Valencia, CA)
  • Agarose gel electrophoresis apparatus
  • Biospectrum UVP GelDoc-It®2 Imager (Analytik Jena, Upland, CA)

Week 3

  • Pre-cut parafilm strips
  • 37°C incubator
  • Ice bucket
  • L-shape spreader
  • 42°C water bath
  • 37°C shaker

LB Agar (per Liter)

  • 10 g of NaCl; 10 g of tryptone; 5 g of yeast extract; 20 g of agar
  • Add deionized H2O to a final volume of 1 liter.
  • Autoclave, pour into Petri dishes (~25 ml/100 mm plate)

LB Broth (per Liter)

  • 10 g of NaCl, 10 g of tryptone, 5 g of yeast extract
  • Add deionized H2O to 1 liter
  • Autoclave

LB-Ampicillin Agar (per Liter)

  • 1 liter of LB agar, autoclaved, cool to 55°C
  • Add 10 ml of 10 mg/ml filter-sterilized ampicillin
  • Pour into Petri dishes (~25 ml/100 mm plate)

LB-Kanamycin Agar (per Liter)

  • 1 liter of LB agar, autoclaved
  • Cool to 55°C; add 2.5 ml of 20 mg/ml filter-sterilized kanamycin
  • Pour into Petri dishes (~25 ml/100 mm plate)

2% X-gal (per 10 ml)

  • 0.2 g of 5-Bromo-4-chloro-3-indolyl-β-Dgalactopyranoside (X-gal)
  • 10 ml of dimethylformamide (DMF)
  • Store at -20°C. Spread 40 µl per LB agar plate.

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Molecular Techniques Copyright © 2026 by Ming-Mei Chang is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License, except where otherwise noted.

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