title: Restriction enzyme cutting site distribution regularity for DNA looping technology.
abstract: The restriction enzyme cutting site distribution regularity and looping conditions were studied systematically. We obtained the restriction enzyme cutting site distributions of 13 commonly used restriction enzymes in 5 model organism genomes through two novel self-compiled software programs. All of the average distances between two adjacent restriction sites fell sharply with increasing statistic intervals, and most fragments were 0-499 bp. A shorter DNA fragment resulted in a lower looping rate, which was also directly proportional to the DNA concentration. When the length was more than 500 bp, the concentration did not affect the looping rate. Therefore, the best known fragment length was longer than 500 bp, and did not contain the restriction enzyme cutting sites which would be used for digestion. In order to make the looping efficiencies reach nearly 100%, 4-5 single cohesive end systems were recommended to digest the genome separately.
authors.affiliation: Laboratory of Food Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China. Electronic address: shangying1986@163.com.
authors.forename: Ying
authors.initials: Y
authors.lastname: Shang
authors.affiliation: Laboratory of Food Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China. Electronic address: nan000108@126.com.
authors.forename: Nan
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Laboratory of Food Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China. Electronic address: zhupengyu3638@163.com.
authors.forename: Pengyu
authors.initials: P
authors.lastname: Zhu
authors.affiliation: The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China. Electronic address: lyb@cau.edu.cn.
authors.forename: Yunbo
authors.initials: Y
authors.lastname: Luo
authors.affiliation: Laboratory of Food Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China. Electronic address: huangkl009@sina.com.
authors.forename: Kunlun
authors.initials: K
authors.lastname: Huang
authors.affiliation: The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China. Electronic address: wytian07@163.com.
authors.forename: Wenying
authors.initials: W
authors.lastname: Tian
authors.affiliation: Laboratory of Food Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China. Electronic address: xuwentaoboy@yahoo.cn.
authors.forename: Wentao
authors.initials: W
authors.lastname: Xu
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence / Q000235:genetics*; D004247:DNA / Q000235:genetics*; D004262:DNA Restriction Enzymes / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics; D016678:Genome; D006801:Humans; D008025:Ligases / Q000378:metabolism; D012275:Oryza / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software
chemical_list: D004247:DNA; D004262:DNA Restriction Enzymes; D008025:Ligases
keywords: Cohesive end; Ct; DNA looping technology; Distribution regularity; IPCR; Inverse-PCR; Restriction enzyme; Restriction enzyme cutting sites; threshold cycle