Engineering DNA aptamers and DNA enzymes with fluorescence-signaling properties
R. Nutiu, S. Mei, Z. Liu, and Y. Li
Department of Biochemistry and Department of Chemistry,
McMaster University, Hamilton, Ontario L8N 3Z5, Canada
Abstract: Single-stranded DNA molecules with ligand-binding
ability and catalytic function, referred to as DNA aptamers and DNA
enzymes, respectively, are special DNA sequences isolated from random-sequence
DNA libraries by �in vitro selection�. These two new classes of artificial
DNA molecules have the potential of being used as molecular tools in
a variety of innovative applications ranging from biosensing to gene
regulation. Our laboratory is interested in engineering fluorescence-signaling
DNA aptamers and DNA enzymes that can be widely exploited for detection-directed
applications. In this article, we will first discuss our recent efforts
on the rational design of a new class of signaling aptamers denoted
�structure- switching signaling aptamers�, which report target binding
by switching structures from DNA/DNA duplex to DNA/target complex. We
will then describe the in vitro selection of fluorescence-signaling
DNA enzymes that exhibit a synchronized catalysis-signaling capability
by cleaving a chimeric RNA/DNA substrate at the lone RNA linkage surrounded
by closely spaced fluorophore-quencher pair. Potential utilities of
these signaling DNA molecules will also be discussed.
*Lecture presented at the symposium "Chemistry of nucleic acids", as part of the 39th IUPAC Congress and 86th Conference of the Canadian Society for Chemistry: Chemistry at the Interfaces, Ottawa, Canada, 10-15 August 2003. Other Congress presentations are published in this issue, pp. 1295-1603.
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