Evolution of high-branching deoxyribozymes from a catalytic DNA with a three-way junction.
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.
Chiuman
William
W
Department of Biochemistry and Biomedical Sciences and Department of Chemistry, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada.
Li
Yingfu
Y
D001483:Base Sequence; D002384:Catalysis; D017124:Conserved Sequence; D021881:DNA, Catalytic / Q000737:chemistry* / Q000235:genetics; D019020:Directed Molecular Evolution / Q000379:methods*; D007700:Kinetics; D008670:Metals / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D017422:Sequence Analysis, DNA / Q000379:methods
D021881:DNA, Catalytic; D008670:Metals