title: Modular Synthetic Inverters from Zinc Finger Proteins and Small RNAs.
abstract: Synthetic zinc finger proteins (ZFPs) can be created to target promoter DNA sequences, repressing transcription. The binding of small RNA (sRNA) to ZFP mRNA creates an ultrasensitive response to generate higher effective Hill coefficients. Here we combined three "off the shelf" ZFPs and three sRNAs to create new modular inverters in E. coli and quantify their behavior using induction fold. We found a general ordering of the effects of the ZFPs and sRNAs on induction fold that mostly held true when combining these parts. We then attempted to construct a ring oscillator using our new inverters. Our chosen parts performed insufficiently to create oscillations, but we include future directions for improvement upon our work presented here.
authors.affiliation: Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, United States of America.
authors.forename: Justin
authors.initials: J
authors.lastname: Hsia
authors.affiliation: Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, United States of America.|Joint BioEnergy Institute, Emeryville, California, United States of America.
authors.forename: William J
authors.initials: WJ
authors.lastname: Holtz
authors.affiliation: Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, United States of America.
authors.forename: Michel M
authors.initials: MM
authors.lastname: Maharbiz
authors.affiliation: Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, United States of America.
authors.forename: Murat
authors.initials: M
authors.lastname: Arcak
authors.affiliation: Joint BioEnergy Institute, Emeryville, California, United States of America.|Department of Bioengineering, University of California, Berkeley, California, United States of America.|Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America.|Biological Systems & Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
authors.forename: Jay D
authors.initials: JD
authors.lastname: Keasling
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D001483:Base Sequence; D004926:Escherichia coli; D008969:Molecular Sequence Data; D010957:Plasmids / Q000378:metabolism; D011401:Promoter Regions, Genetic; D034741:RNA, Small Interfering / Q000378:metabolism*; D012097:Repressor Proteins / Q000378:metabolism; D016335:Zinc Fingers
chemical_list: D020121:5' Untranslated Regions; D034741:RNA, Small Interfering; D012097:Repressor Proteins