DNAmoreDB - A Database of Deoxyribozymes

Published on 2006 in Chem. Biol. volume 13 issue 10.

PubMed ID: 17052610

DOI:10.1016/j.chembiol.2006.08.009

Abstract:

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.



DNAzymes linked to this article:

Name Isolated sequence Length Reaction
5J-B24 TTGAGGTACCAAATATTGTAAATATTGATGGCTGCCGGGCAGACAGTCGGTCCTCTGGAC      60 RNA cleavage
5J-B38 TCGAGGTACCAAATATTGTAAATATTGATGGCTGCCGGGCAGACAGTCGGTCTTCAGGAC      60 RNA cleavage
5J-A5 TCGAGGCACCAAATAATGTAAATATAGATCCCTAGGGGGAGTCGGCCCGCGTTATCGGGC      60 RNA cleavage
5J-A9 TCGAGGTACCAATTATTGTGAATAATGATGGCAATAGTCAGTCGGTACAGAGCTCTGTAC      60 RNA cleavage
5J-A11 TCGAGGTACCAATTATAGTGAATAATGATGGCGATAGTCAGTCGGTACAGAGTTCTGTAC      60 RNA cleavage
5J-A14 TCGAGGTACCAATAATAGTGGATAATGATGGCAGTAGTCAGTCGGTACAGAGTTCTGTAC      60 RNA cleavage
5J-A20 TCGAGGCACCAATTATTGTGAATAATGATGGCGATAGACAGTCGGTACAGAGTTTTGTAC      60 RNA cleavage
5J-A26 TCGAGGTACCAATTATTGTGAATAATGATGGCGATAGTCAGTCGGTACAGAGTTTTGTAC      60 RNA cleavage
5J-A28 TCGAGGAACCAAATATTGTGAATATTGATGCCTGGCGGCAGTCGGTACCGAGGTCGGTAC      60 RNA cleavage
5J-A30 TCGAGGAACCAAATATTGTGAATATTGATGCCTGGCGGCAGTCGGTACCGAGGTCGGTAC      60 RNA cleavage
5J-A36 TCGAGGTACCAATTATTGTGAATAATGATGGCGATAGCCAGTCGGTACAGAGTTTTGTAC      60 RNA cleavage
5J-A39 TCGAGGTACCAAATAATGTTAATATTGATCCCTTGGGGGAGTCGGCTCGCGTTTTCGGGC      60 RNA cleavage
5J-B12 TCGAGGTACCAAATATTGTAAATATTGATGGCTGCCGGGCAGACAGTCGGTCTTTAGGAC      60 RNA cleavage
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