Novel method for high-throughput colony PCR screening in nanoliter-reactors

Nucleic Acids Res. 2009 May;37(8):e57. doi: 10.1093/nar/gkp160. Epub 2009 Mar 12.


We introduce a technology for the rapid identification and sequencing of conserved DNA elements employing a novel suspension array based on nanoliter (nl)-reactors made from alginate. The reactors have a volume of 35 nl and serve as reaction compartments during monoseptic growth of microbial library clones, colony lysis, thermocycling and screening for sequence motifs via semi-quantitative fluorescence analyses. nl-Reactors were kept in suspension during all high-throughput steps which allowed performing the protocol in a highly space-effective fashion and at negligible expenses of consumables and reagents. As a first application, 11 high-quality microsatellites for polymorphism studies in cassava were isolated and sequenced out of a library of 20,000 clones in 2 days. The technology is widely scalable and we envision that throughputs for nl-reactor based screenings can be increased up to 100,000 and more samples per day thereby efficiently complementing protocols based on established deep-sequencing technologies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alginates / chemistry
  • Base Sequence
  • Conserved Sequence
  • Escherichia coli / genetics
  • Gene Library*
  • Manihot / genetics
  • Microsatellite Repeats
  • Polymerase Chain Reaction / methods*
  • Polymorphism, Genetic
  • Sequence Analysis, DNA / methods*


  • Alginates