DNA extraction of bacterial cells using a semi-automated filtration system

K. B. Hoorzook, T. G. Barnard

Research output: Contribution to journalArticlepeer-review


The COVID-19 pandemic lockdown created problems with importing of commercial kits resulting in extended turnaround times for consumable deliveries. One way to circumvent this was to use an inexpensive optimized in-house method for DNA extraction from water. • The DNA extraction methods were optimized on a 96-well plate using a semi-automated filtration system to increase the number of samples from 24 to 96 at a time in 2 h. The DNA extraction method optimizations included: (a) Guanidium thiocyanate method plus dilution series of celite to determine DNA binding capacity; (b) QIamp 96 Qiacube HT kit (Qiagen®); (c) Guanidium thiocyanate with the celite replaced with a binding buffer. • The in-house DNA extraction methods and adapted in-house DNA extraction method were compared to QIamp 96 Qiacube HT kit (Qiagen®), which is used on a 96-well semi-automated filtration system. The results showed maximum capacity of the 96-well filter plates was 400 μℓ broth (OD600 = 0.45 = 3.6 × 108 cells/mℓ) before the 96-well filters blocked. • When the methods were compared, there was no significant difference between the in-house DNA extraction method with 1:420 celite dilution (P-value = 0.126) and the adapted in-house method with binding buffer (P-value = 0.298) DNA yield or amplification of PCR products.

Original languageEnglish
Article number101785
Publication statusPublished - Jan 2022


  • Celite
  • Environmental water
  • Escherichia coli
  • Genomic and plasmid extraction
  • Guanidium thiocyanate
  • Membrane filtration
  • Semi-automated DNA extraction method
  • Semi-automated filtration system

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Medical Laboratory Technology


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