Open AccessAdvantages of using the QIAshredder instead of restriction digestion to prepare DNA for droplet digital PCR
Author(s) -
Steven A. Yukl,
Philipp Kaiser,
Peggy Kim,
Peilin Li,
Joseph K. Wong
Publication year - 2014
Publication title -
biotechniques/biotechniques
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.617
H-Index - 131
eISSN - 1940-9818
pISSN - 0736-6205
DOI - 10.2144/000114159
Subject(s) - digital polymerase chain reaction , restriction digest , dna , genomic dna , restriction enzyme , digestion (alchemy) , biology , microbiology and biotechnology , polymerase chain reaction , restriction fragment , chromatography , chemistry , genetics , gene
The viscosity of genomic DNA can interfere with digital PCR systems that partition samples into oil droplets or microfluidic wells. Restriction digestion may reduce the viscosity, but the process is labor-intensive, and the buffer can alter the conditions for PCR. DNA fragmentation using the QIAshredder (a biopolymer spin column) is faster, may result in more predictable and uniformly-sized fragments, and avoids the need for restriction buffers that can inhibit downstream PCR. In 10 separate head-to-head experiments comparing aliquots of DNA processed using the QIAshredder to those digested with RsaI or BsaJI prior to droplet digital PCR, we found that the copy numbers measured from the QIAshredded DNA tended to be greater than those measured from the digested DNA (average of 1.35-fold compared with BsaJI; P < 0.0001), even for inputs as high as 1.8 µg or dilution down to the single copy level.