High-throughput SNP detection using nano-scale engineered biomagnetite.
A semi-automated system for the large-scale detection of single nucleotide polymorphisms (SNPs) has been developed based on allele-specific oligonucleotide hybridization and thermal dissociation curve analysis using nano-scale engineered biomagnetite (bacterial magnetic particles; BacMPs). For reliable detection in large numbers of samples, several conditions for the capture of target DNA on nano-sized BacMPs and the denaturation of double-stranded DNA were optimized. The most efficient target DNA capture was observed using short PCR amplicons (69 bp). Captured DNAs were denatured using 50 mM NaOH. With these optimizations, large-scale SNP detection was performed on 822 samples of the transforming growth factor (TGF)-beta1 gene, which is rich in both GC content and repetitive sequences. High reliability for the semi-automated BacMP-based SNP detection system was confirmed following comparison to traditional sequencing-based methods.
Matsunaga
Tadashi
T
Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan. tmatsuna@cc.tuat.ac.jp
Maruyama
Kohei
K
Takeyama
Haruko
H
Katoh
Takahiko
T
D015374:Biosensing Techniques; D052203:Ferrosoferric Oxide; D036103:Nanotechnology; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D053773:Transforming Growth Factor beta1 / Q000235:genetics
D053773:Transforming Growth Factor beta1; D052203:Ferrosoferric Oxide