High-throughput SNP detection using nano-scale engineered biomagnetite

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

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)-β1 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.

Original languageEnglish
Pages (from-to)2315-2321
Number of pages7
JournalBiosensors and Bioelectronics
Volume22
Issue number9-10
DOIs
Publication statusPublished - 2007 Apr 15

Fingerprint

Nucleotides
Polymorphism
Single Nucleotide Polymorphism
DNA
Throughput
Denaturation
Oligonucleotides
Nucleic Acid Repetitive Sequences
Base Composition
Transforming Growth Factors
Hot Temperature
Genes
Alleles
Polymerase Chain Reaction

Keywords

  • Automated system
  • Bacterial magnetic particles (BacMPs)
  • Hybridization
  • Nano-scale engineered biomagnetite
  • Single nucleotide polymorphism (SNP)
  • Transforming growth factor (TGF)-β1

ASJC Scopus subject areas

  • Biotechnology
  • Analytical Chemistry
  • Electrochemistry

Cite this

High-throughput SNP detection using nano-scale engineered biomagnetite. / Matsunaga, Tadashi; Maruyama, Kohei; Takeyama, Haruko; Katoh, Takahiko.

In: Biosensors and Bioelectronics, Vol. 22, No. 9-10, 15.04.2007, p. 2315-2321.

Research output: Contribution to journalArticle

@article{4e5ec8767a7a459a9abb1f4b21974784,
title = "High-throughput SNP detection using nano-scale engineered biomagnetite",
abstract = "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)-β1 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.",
keywords = "Automated system, Bacterial magnetic particles (BacMPs), Hybridization, Nano-scale engineered biomagnetite, Single nucleotide polymorphism (SNP), Transforming growth factor (TGF)-β1",
author = "Tadashi Matsunaga and Kohei Maruyama and Haruko Takeyama and Takahiko Katoh",
year = "2007",
month = "4",
day = "15",
doi = "10.1016/j.bios.2006.12.022",
language = "English",
volume = "22",
pages = "2315--2321",
journal = "Biosensors",
issn = "0956-5663",
publisher = "Elsevier Limited",
number = "9-10",

}

TY - JOUR

T1 - High-throughput SNP detection using nano-scale engineered biomagnetite

AU - Matsunaga, Tadashi

AU - Maruyama, Kohei

AU - Takeyama, Haruko

AU - Katoh, Takahiko

PY - 2007/4/15

Y1 - 2007/4/15

N2 - 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)-β1 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.

AB - 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)-β1 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.

KW - Automated system

KW - Bacterial magnetic particles (BacMPs)

KW - Hybridization

KW - Nano-scale engineered biomagnetite

KW - Single nucleotide polymorphism (SNP)

KW - Transforming growth factor (TGF)-β1

UR - http://www.scopus.com/inward/record.url?scp=33847349678&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33847349678&partnerID=8YFLogxK

U2 - 10.1016/j.bios.2006.12.022

DO - 10.1016/j.bios.2006.12.022

M3 - Article

VL - 22

SP - 2315

EP - 2321

JO - Biosensors

JF - Biosensors

SN - 0956-5663

IS - 9-10

ER -