Evolution of high-branching deoxyribozymes from a catalytic DNA with a three-way junction

Chem Biol. 2006 Oct;13(10):1061-9. doi: 10.1016/j.chembiol.2006.08.009.


Here, we report the evolution of two star-shaped (five-way junction) deoxyribozymes from a catalytic DNA containing a three-way junction scaffold. The transition was shown to be a switch rather than a gradual progression. The star-shaped motifs, surprisingly, only took five selection cycles to be detected, and another four to dominate the evolving population. Chemical probing experiments indicated that the two deoxyribozymes belong to the same family despite noticeable variations in both the primary sequence and the secondary structure. Our findings not only describe the evolution of high-branching nucleic acid structures from a low-branching catalytic module, but they also illustrate the idea of deriving a rare structural motif by sampling the sequence variants of a given functional nucleic acid.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Catalysis
  • Conserved Sequence
  • DNA, Catalytic / chemistry*
  • DNA, Catalytic / genetics
  • Directed Molecular Evolution / methods*
  • Kinetics
  • Metals / chemistry
  • Metals / metabolism
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Sequence Analysis, DNA / methods


  • DNA, Catalytic
  • Metals