Monatshefte für Chemie / Chemical Monthly

, Volume 122, Issue 10, pp 795–819 | Cite as

Statistics of landscapes based on free energies, replication and degradation rate constants of RNA secondary structures

  • Walter Fontana
  • Thomas Griesmacher
  • Wolfgang Schnabl
  • Peter F. Stadler
  • Peter Schuster
Anorganische Und Physikalische Chemie

Summary

RNA secondary structures are computed from primary sequences by means of a folding algorithm which uses a minimum free energy criterion. Free energies as well as replication and degradation rate constants are derived from secondary structures. These properties can be understood as highly sophisticated functions of the individual sequences whose values are mediated by the secondary structures. Such functions induce complex value landscapes on the space of sequences. The landscapes are analysed by random walk techniques, in particular autocorrelation functions and correlation lengths are computed. Free energy landscapes were found to be of AR(1) type. The rate constant landscapes, however, turned out to be more complex. In addition, gradient and adaptive walks are performed in order to get more insight into the complex structure of the landscapes.

Keywords

RNA secondary structures RNA free energies Value landscapes Autocorrelation functions Correlation lengths 

Statistik von Landschaften aus freien Energien, Replikations- und Abbaugeschwindigkeitskonstanten von RNA-Sekundärstrukturen

Zusammenfassung

RNA-Sekundärstrukturen werden aus den Primärsequenzen mit Hilfe eines Computeralgorithmus berechnet, welcher einem Kriterium minimaler freier Energien folgt. Freie Energien, Replikations- oder Abbaugeschwindigkeitskonstanten werden aus den Sekundärstrukturen berechnet. Man kann daher diese Eigenschaften als komplizierte Funktionen der Sequenzen auffassen, deren Zahlenwerte durch Vermittlung der Sekundärstrukturen erhalten werden. Diese Funktionen induzieren hochkomplexe Bewertungslandschaften im Raum der Sequenzen. Die Landschaften werden mit Hilfe von Irrflugtechniken analysiert. Im einzelnen werden Autokorrelationsfunktionen und Korrelationslängen berechnet. Die freien Energie-Landschaften sind vom AR(1) Typ. Die von den Reaktionsgeschwindigkeitskonstanten abgeleiteten Landschaften stellten sich hingegen als komplexer heraus. Zusätzlich werden die Bewertungslandschaften auch noch mit Hilfe vonGradient undAdaptive Walks untersucht, um mehr Einblick in ihre komplexe Struktur zu gewinnen.

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Copyright information

© Springer-Verlag 1991

Authors and Affiliations

  • Walter Fontana
    • 2
    • 3
  • Thomas Griesmacher
    • 1
  • Wolfgang Schnabl
    • 1
  • Peter F. Stadler
    • 1
  • Peter Schuster
    • 1
    • 3
  1. 1.Institut für Theoretische ChemieUniversität WienWienAustria
  2. 2.Los Alamos National LaboratoryUSA
  3. 3.Santa Fe InstituteUSA

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