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Molecules 2010, 15(9), 6269-6284; doi:10.3390/molecules15096269

The Structural Diversity of Deoxyribozymes

1 Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada 2 Department of Chemistry and Chemical Biology, McMaster University, 1200 Main Street West, Hamilton, Ontario L8N 3Z5, Canada
* Author to whom correspondence should be addressed.
Received: 30 June 2010 / Revised: 23 August 2010 / Accepted: 2 September 2010 / Published: 6 September 2010
(This article belongs to the Special Issue Catalytic Nucleic Acids)
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When not constrained to long double-helical arrangements, DNA is capable of forming structural arrangements that enable specific sequences to perform functions such as binding and catalysis under defined conditions. Through a process called in vitro selection, numerous catalytic DNAs, known as deoxyribozymes or DNAzymes, have been isolated. Many of these molecules have the potential to act as therapeutic agents and diagnostic tools. As such, a better understanding of the structural arrangements present in these functional DNAs will aid further efforts in the development and optimization of these useful molecules. Structural characterization of several deoxyribozymes through mutagenesis, in vitro re-selection, chemical probing and circular dichroism has revealed many distinct and elaborate structural classes. Deoxyribozymes have been found to contain diverse structural elements including helical junctions, pseudoknots, triplexes, and guanine quadruplexes. Some of these studies have further shown the repeated isolation of similar structural motifs in independent selection experiments for the same type of chemical reaction, suggesting that some structural motifs are well suited for catalyzing a specific chemical reaction. To investigate the extent of structural diversity possible in deoxyribozymes, a group of kinase deoxyribozymes have been extensively characterized. Such studies have discovered some interesting structural features of these DNAzymes while revealing some novel DNA structures.
Keywords: deoxyribozyme; DNAzyme; catalytic DNA; in vitro selection; functional nucleic acid deoxyribozyme; DNAzyme; catalytic DNA; in vitro selection; functional nucleic acid
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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McManus, S.A.; Li, Y. The Structural Diversity of Deoxyribozymes. Molecules 2010, 15, 6269-6284.

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