title: Selection of RNA amide synthases.
abstract: BACKGROUND
  It is generally accepted that, during evolution, replicating RNA molecules emerged from pools of random polynucleotides. This prebiotic RNA world was followed by an era of RNA-mediated catalysis of amide-bond formation. RNA would thus have provided the machinery responsible for the assembly of peptides and the beginning of the protein world of today. Naturally occurring ribozymes, which catalyze the cleavage or ligation of oligonucleotide phosphodiester bonds, support the idea that RNA could self-replicate. But was RNA constrained to this path and were RNA-acylated carriers required before RNA could catalyze the formation of amide bonds?
  
  
  RESULTS
  We have isolated RNA catalysts that are capable of mediating amide-bond synthesis without the need for specifically designed templates to align the substrates, and we have kinetically characterized these catalysts. The rate enhancement observed for these RNA amide synthases exceeds the noncatalyzed amidation rate by a factor of approximately 10(4). In addition, Cu2+ ions caused a change in the affinity of RNA for the substrate rather than being directly involved in amide-bond formation.
  
  
  CONCLUSIONS
  The discovery of these new amide synthases shows how functionally modified nucleic acids can facilitate covalent-bond formation without templating. Previously unforeseen RNA-evolution pathways can, therefore, be considered; for example, to guide amide-bond formation, en route to the protein world, it appears that substrate-binding pockets were formed that are analogous to those of protein enzymes.
authors.affiliation: NeXstar Pharmaceuticals Incorporated, Boulder, CO 80301, USA.
authors.forename: T W
authors.initials: TW
authors.lastname: Wiegand
authors.forename: R C
authors.initials: RC
authors.lastname: Janssen
authors.forename: B E
authors.initials: BE
authors.lastname: Eaton
mesh_terms: D019732:Amide Synthases / Q000096:biosynthesis* / Q000737:chemistry / Q000378:metabolism*; D001483:Base Sequence; D002413:Cations, Divalent; D003300:Copper / Q000378:metabolism; D019020:Directed Molecular Evolution / Q000379:methods; D007700:Kinetics; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D016337:RNA, Catalytic / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism*; D012689:Sequence Homology, Nucleic Acid; D013379:Substrate Specificity
chemical_list: D002413:Cations, Divalent; D016337:RNA, Catalytic; D003300:Copper; D019732:Amide Synthases