title: In vitro evolution of molecular cooperation in CATCH, a cooperatively coupled amplification system.
abstract: BACKGROUND
  One of the key issues in the investigation of evolution is how complex systems evolved from simple chemical replicators. Theoretical work proposed several models in which complex replicating systems are kinetically stabilized. The development of powerful isothermal amplification technique allows complex nucleic acid based evolving in vitro systems to be set up, which may then serve to verify experimentally current theories of evolution. Recently such a system based on the 3SR (self-sustained sequence replication) reaction has been established to investigate the evolution of cooperation: the trans-cooperatively coupled CATCH (cooperative amplification by cross hybridization).
  
  
  RESULTS
  Over four rounds of serial transfer, the cooperatively coupled two species CATCH system evolved into a more complex cooperative four species system, which then was overgrown by CATCH-derived RNA-Z-like hairpin species. In contrast to the classical RNA-Z species, these molecules have complementary loop sequences and self-amplify using a dual mechanism that includes concentration-dependent phases of noncooperative and cooperative amplification.
  
  
  CONCLUSIONS
  The evolution of a cooperative system, under conditions that were alternately unfavorable and favorable for cooperative amplification, led to a system showing facultative cooperation. This principle of facultative cooperation preserves the complexity of the system investigated and could have general implications for the evolution and stabilization of cooperation under oscillating reaction conditions.
authors.affiliation: Department of Molecular Information Processing Institute of Molecular Biotechnology Beutenbergstrasse 11 07745 Clondiag Chip Technologies Löbstedter Strasse 105 D 07743 Jena Germany. telli@clondiag.com
authors.forename: T
authors.initials: T
authors.lastname: Ellinger
authors.forename: R
authors.initials: R
authors.lastname: Ehricht
authors.forename: J S
authors.initials: JS
authors.lastname: McCaskill
mesh_terms: D017794:Alfalfa mosaic virus / Q000201:enzymology; D001483:Base Sequence; D003001:Cloning, Molecular; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization / Q000379:methods*; D009841:Oligonucleotides / Q000737:chemistry / Q000235:genetics; D017354:Point Mutation; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic; D012313:RNA / Q000737:chemistry / Q000235:genetics*; D012194:RNA-Directed DNA Polymerase / Q000378:metabolism; D011995:Recombination, Genetic; D016914:Ribonuclease H / Q000378:metabolism; D013698:Templates, Genetic; D014764:Viral Proteins
chemical_list: D009841:Oligonucleotides; D014764:Viral Proteins; D012313:RNA; C062210:bacteriophage T7 RNA polymerase; D012194:RNA-Directed DNA Polymerase; D012321:DNA-Directed RNA Polymerases; D016914:Ribonuclease H