title: A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair.
abstract: As one of its goals, synthetic biology seeks to increase the number of building blocks in nucleic acids. While efforts towards this goal are well advanced for DNA, they have hardly begun for RNA. Herein, we present a crystal structure for an RNA riboswitch where a stem C:G pair has been replaced by a pair between two components of an artificially expanded genetic-information system (AEGIS), Z and P, (6-amino-5-nitro-2(1H)-pyridone and 2-amino-imidazo[1,2-a]-1,3,5-triazin-4-(8H)-one). The structure shows that the Z:P pair does not greatly change the conformation of the RNA molecule nor the details of its interaction with a hypoxanthine ligand. This was confirmed in solution by in-line probing, which also measured a 3.7 nM affinity of the riboswitch for guanine. These data show that the Z:P pair mimics the natural Watson-Crick geometry in RNA in the first example of a crystal structure of an RNA molecule that contains an orthogonal added nucleobase pair.
authors.affiliation: Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA).
authors.forename: Armando R
authors.initials: AR
authors.lastname: Hernandez
authors.affiliation: Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA).
authors.forename: Yaming
authors.initials: Y
authors.lastname: Shao
authors.affiliation: Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA).
authors.forename: Shuichi
authors.initials: S
authors.lastname: Hoshika
authors.affiliation: Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA).
authors.forename: Zunyi
authors.initials: Z
authors.lastname: Yang
authors.affiliation: Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA).
authors.forename: Sandip A
authors.initials: SA
authors.lastname: Shelke
authors.affiliation: Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA).
authors.forename: Julien
authors.initials: J
authors.lastname: Herrou
authors.affiliation: Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA).
authors.forename: Hyo-Joong
authors.initials: HJ
authors.lastname: Kim
authors.affiliation: Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA).
authors.forename: Myong-Jung
authors.initials: MJ
authors.lastname: Kim
authors.affiliation: Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA). jpicciri@uchicago.edu.
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Piccirilli
authors.affiliation: Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA). sbenner@ffame.org.
authors.forename: Steven A
authors.initials: SA
authors.lastname: Benner
mesh_terms: D020029:Base Pairing; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA
keywords: crystal structure; expanded DNA; in-line probing; riboswitch; synthetic biology