title: Development of the Handy Bio-Strand and its application to genotyping of OPRM1 (A118G).
abstract: We previously developed a three-dimensional microarray system, the Bio-Strand, which exhibits advantages in automated DNA analysis in combination with our Magtration Technology. In the current study, we have developed a compact system for the Bio-Strand, the Handy Bio-Strand, which consists of several tools for the preparation of Bio-Strand Tip, hybridization, and detection. Using the Handy Bio-Strand, we performed single nucleotide polymorphism (SNP) genotyping of OPRM1 (A118G) by allele-specific oligonucleotide competitive hybridization (ASOCH). DNA fragments containing SNP sites were amplified from genomic DNA by PCR and then were fixed on a microporous nylon thread. Thus, prepared Bio-Strand Tip was hybridized with allele-specific Cy5 probes (<15mer), on which the SNP site was designed to be located in the center. By optimizing the amount of competitors, the selectivity of Cy5 probes increased without a drastic signal decrease. OPRM1 (A118G) genotypes of 23 human genomes prepared from whole blood samples were determined by ASOCH using the Handy Bio-Strand. The results were perfectly consistent with those determined by PCR direct sequencing. ASOCH using the Handy Bio-Strand would be a very simple and reliable method for SNP genotyping for small laboratories and hospitals.
authors.affiliation: Precision System Science, Kamihongou, Matsudo, Chiba 271-0064, Japan. harumi.ginya@pss.co.jp
authors.forename: Harumi
authors.initials: H
authors.lastname: Ginya
authors.forename: Junko
authors.initials: J
authors.lastname: Asahina
authors.forename: Mamiko
authors.initials: M
authors.lastname: Yoshida
authors.forename: Osamu
authors.initials: O
authors.lastname: Segawa
authors.forename: Tsutomu
authors.initials: T
authors.lastname: Asano
authors.forename: Hideo
authors.initials: H
authors.lastname: Ikeda
authors.forename: Yukiko Miyashita
authors.initials: YM
authors.lastname: Hatano
authors.forename: Madoka
authors.initials: M
authors.lastname: Shishido
authors.forename: Britt-Marie
authors.initials: BM
authors.lastname: Johansson
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhou
authors.forename: Mathias
authors.initials: M
authors.lastname: Hallberg
authors.forename: Masaaki
authors.initials: M
authors.lastname: Takahashi
authors.forename: Fred
authors.initials: F
authors.lastname: Nyberg
authors.forename: Hideji
authors.initials: H
authors.lastname: Tajima
authors.forename: Masafumi
authors.initials: M
authors.lastname: Yohda
mesh_terms: D000483:Alleles; D001483:Base Sequence; D004247:DNA / Q000235:genetics / Q000302:isolation & purification; D004867:Equipment Design; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods; D015345:Oligonucleotide Probes / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D017450:Receptors, Opioid, mu / Q000235:genetics*
chemical_list: C485764:OPRM1 protein, human; D015345:Oligonucleotide Probes; D017450:Receptors, Opioid, mu; D004247:DNA