title: Differential dependence on DNA ligase of type II restriction enzymes: a practical way toward ligase-free DNA automaton.
abstract: DNA computing study is a new paradigm in computer science and biological computing fields. As one of DNA computing approaches, DNA automaton is composed of the hardware, input DNA molecule and state transition molecules. By now restriction enzymes are key hardware for DNA computing automaton. It has been found that DNA computing efficiency may be independent on DNA ligases when type IIS restriction enzymes like FokI are used as hardware. In this study, we compared FokI with four other distinct enzymes HgaI, BsmFI, BbsI, and BseMII, and found their differential independence on T4 DNA ligase when performing automaton reactions. Since DNA automaton is a potential powerful tool to tackle gene relationship in genomic network scale, the feasible ligase-free DNA automaton may set an initial base to develop functional DNA automata for various DNA technology development and implications in genetics study in the near future.
authors.affiliation: Bio-X Life Science Research Center, Shanghai Jiao Tong University, Shanghai 200030, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Chen
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.forename: Jian
authors.initials: J
authors.lastname: Zhao
authors.forename: Lin
authors.initials: L
authors.lastname: He
authors.forename: Zhizhou
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D001331:Automation; D003201:Computers; D039301:Computers, Molecular; D004247:DNA; D011088:DNA Ligases / Q000378:metabolism*; D004262:DNA Restriction Enzymes / Q000378:metabolism; D015280:DNA Restriction-Modification Enzymes / Q000378:metabolism; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism*
chemical_list: D015280:DNA Restriction-Modification Enzymes; D004247:DNA; C427307:BseMII endonuclease; D004262:DNA Restriction Enzymes; C418602:endodeoxyribonuclease BsmFI; C035042:endodeoxyribonuclease FokI; C114463:endodeoxyribonuclease HgaI; D015252:Deoxyribonucleases, Type II Site-Specific; D011088:DNA Ligases