title: Laboratory evolution of artificially expanded DNA gives redesignable aptamers that target the toxic form of anthrax protective antigen.
abstract: Reported here is a laboratory in vitro evolution (LIVE) experiment based on an artificially expanded genetic information system (AEGIS). This experiment delivers the first example of an AEGIS aptamer that binds to an isolated protein target, the first whose structural contact with its target has been outlined and the first to inhibit biologically important activities of its target, the protective antigen from Bacillus anthracis We show how rational design based on secondary structure predictions can also direct the use of AEGIS to improve the stability and binding of the aptamer to its target. The final aptamer has a dissociation constant of ∼35 nM. These results illustrate the value of AEGIS-LIVE for those seeking to obtain receptors and ligands without the complexities of medicinal chemistry, and also challenge the biophysical community to develop new tools to analyze the spectroscopic signatures of new DNA folds that will emerge in synthetic genetic systems replacing standard DNA and RNA as platforms for LIVE.
authors.affiliation: Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA.
authors.forename: Elisa
authors.initials: E
authors.lastname: Biondi
authors.affiliation: Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA.
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Lane
authors.affiliation: School of Dentistry, The University of Maryland, Baltimore, MD 21201, USA.
authors.forename: Debasis
authors.initials: D
authors.lastname: Das
authors.affiliation: Department of Chemistry, University of Chicago, Chicago, IL 60637, USA.
authors.forename: Saurja
authors.initials: S
authors.lastname: Dasgupta
authors.affiliation: Department of Chemistry, University of Chicago, Chicago, IL 60637, USA.|Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Piccirilli
authors.affiliation: Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA.
authors.forename: Shuichi
authors.initials: S
authors.lastname: Hoshika
authors.affiliation: Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA.
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Bradley
authors.affiliation: School of Dentistry, The University of Maryland, Baltimore, MD 21201, USA.
authors.forename: Bryan A
authors.initials: BA
authors.lastname: Krantz
authors.affiliation: Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA sbenner@ffame.org.|Firebird Biomolecular Sciences LLC, Alachua, FL 32615, USA.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Benner
mesh_terms: D000942:Antigens, Bacterial / Q000737:chemistry* / Q000235:genetics* / Q000276:immunology; D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000235:genetics*; D001408:Bacillus anthracis / Q000235:genetics / Q000276:immunology; D001427:Bacterial Toxins / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics* / Q000276:immunology; D001483:Base Sequence; D001665:Binding Sites; D001667:Binding, Competitive; D002942:Circular Dichroism; D054856:G-Quadruplexes; D007700:Kinetics; D009154:Mutation; D009690:Nucleic Acid Conformation; D052156:SELEX Aptamer Technique; D013329:Structure-Activity Relationship; D058615:Synthetic Biology
chemical_list: D000942:Antigens, Bacterial; D052157:Aptamers, Nucleotide; D001427:Bacterial Toxins; C030325:anthrax toxin