title: A universal RNAi-based logic evaluator that operates in mammalian cells.
abstract: Molecular automata that combine sensing, computation and actuation enable programmable manipulation of biological systems. We use RNA interference (RNAi) in human kidney cells to construct a molecular computing core that implements general Boolean logic to make decisions based on endogenous molecular inputs. The state of an endogenous input is encoded by the presence or absence of 'mediator' small interfering RNAs (siRNAs). The encoding rules, combined with a specific arrangement of the siRNA targets in a synthetic gene network, allow direct evaluation of any Boolean expression in standard forms using siRNAs and indirect evaluation using endogenous inputs. We demonstrate direct evaluation of expressions with up to five logic variables. Implementation of the encoding rules through sensory up- and down-regulatory links between the inputs and siRNA mediators will allow arbitrary Boolean decision-making using these inputs.
authors.affiliation: FAS Center for Systems Biology, Harvard University, 7 Divinity Ave., Cambridge, Massachusetts 02138 USA.
authors.forename: Keller
authors.initials: K
authors.lastname: Rinaudo
authors.forename: Leonidas
authors.initials: L
authors.lastname: Bleris
authors.forename: Rohan
authors.initials: R
authors.lastname: Maddamsetti
authors.forename: Sairam
authors.initials: S
authors.lastname: Subramanian
authors.forename: Ron
authors.initials: R
authors.lastname: Weiss
authors.forename: Yaakov
authors.initials: Y
authors.lastname: Benenson
mesh_terms: D001483:Base Sequence; D002469:Cell Separation; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D005434:Flow Cytometry; D053263:Gene Regulatory Networks; D020868:Gene Silencing; D006801:Humans; D007668:Kidney / Q000378:metabolism*; D008954:Models, Biological; D008957:Models, Genetic; D008969:Molecular Sequence Data; D034622:RNA Interference; D012333:RNA, Messenger / Q000378:metabolism; D034741:RNA, Small Interfering / Q000378:metabolism
chemical_list: D012333:RNA, Messenger; D034741:RNA, Small Interfering