title: Quantification of DNA fragmentation in processed foods using real-time PCR.
abstract: DNA analysis of processed foods is performed widely to detect various targets, such as genetically modified organisms (GMOs). Food processing often causes DNA fragmentation, which consequently affects the results of PCR analysis. In order to assess the effects of DNA fragmentation on the reliability of PCR analysis, we investigated a novel methodology to quantify the degree of DNA fragmentation. We designed four real-time PCR assays that amplified 18S ribosomal RNA gene sequences common to various plants at lengths of approximately 100, 200, 400, and 800 base pairs (bp). Then, we created an indicator value, "DNA fragmentation index (DFI)", which is calculated from the Cq values derived from the real-time PCR assays. Finally, we demonstrated the efficacy of this method for the quality control of GMO detection in processed foods by evaluating the relationship between the DFI and the limit of detection.
authors.affiliation: Food Research Institute, National Agriculture and Food Research Organization, 2-1-12, Kannondai, Tsukuba, Ibaraki 305-8642, Japan. Electronic address: jmano@affrc.go.jp.
authors.forename: Junichi
authors.initials: J
authors.lastname: Mano
authors.affiliation: Nisshin Seifun Group Inc., 5-3-1, Tsurugaoka, Fujimino, Saitama 356-8511, Japan. Electronic address: nishitsuji.yasuyuki@nisshin.com.
authors.forename: Yasuyuki
authors.initials: Y
authors.lastname: Nishitsuji
authors.affiliation: Nisshin Seifun Group Inc., 5-3-1, Tsurugaoka, Fujimino, Saitama 356-8511, Japan. Electronic address: kikuchi.yosuke@nisshin.com.
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Kikuchi
authors.affiliation: Nisshin Seifun Group Inc., 5-3-1, Tsurugaoka, Fujimino, Saitama 356-8511, Japan. Electronic address: fukudome.shinichi@nisshin.com.
authors.forename: Shin-Ichi
authors.initials: SI
authors.lastname: Fukudome
authors.affiliation: Nippon Flour Mills Co., Ltd., 5-1-3, Midorigaoka, Atsugi, Kanagawa 243-0041, Japan. Electronic address: t-hayashida@nippn.co.jp.
authors.forename: Takuya
authors.initials: T
authors.lastname: Hayashida
authors.affiliation: Nippon Flour Mills Co., Ltd., 5-1-3, Midorigaoka, Atsugi, Kanagawa 243-0041, Japan. Electronic address: h-kawakami@nippn.co.jp.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kawakami
authors.affiliation: Nippon Flour Mills Co., Ltd., 5-1-3, Midorigaoka, Atsugi, Kanagawa 243-0041, Japan. Electronic address: you-kuri@nippn.co.jp.
authors.forename: Youichi
authors.initials: Y
authors.lastname: Kurimoto
authors.affiliation: National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan. Electronic address: noguchi@nihs.go.jp.
authors.forename: Akio
authors.initials: A
authors.lastname: Noguchi
authors.affiliation: National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan. Electronic address: kondo@nihs.go.jp.
authors.forename: Kazunari
authors.initials: K
authors.lastname: Kondo
authors.affiliation: National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan. Electronic address: rteshima@nihs.go.jp.
authors.forename: Reiko
authors.initials: R
authors.lastname: Teshima
authors.affiliation: Food Research Institute, National Agriculture and Food Research Organization, 2-1-12, Kannondai, Tsukuba, Ibaraki 305-8642, Japan. Electronic address: reona@affrc.go.jp.
authors.forename: Reona
authors.initials: R
authors.lastname: Takabatake
authors.affiliation: Food Research Institute, National Agriculture and Food Research Organization, 2-1-12, Kannondai, Tsukuba, Ibaraki 305-8642, Japan. Electronic address: kaz@affrc.go.jp.
authors.forename: Kazumi
authors.initials: K
authors.lastname: Kitta
mesh_terms: D053938:DNA Fragmentation; D018744:DNA, Plant / Q000235:genetics*; D030841:Food, Genetically Modified; D016133:Polymerase Chain Reaction / Q000379:methods*; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*
chemical_list: D018744:DNA, Plant
keywords: DNA; Fragmentation; Genetically modified organisms; Processed food; Real-time PCR