Metal complex catalysis on a double stranded DNA template

Abstract

The reaction of ester hydrolysis catalysed by a DNA duplex in a sequence specific fashion has been developed, which is the fastest and most high yielding in comparison with the known reactions of this type.

Modular Assembly of a Pd Catalyst within a DNA Scaffold for the Amplified Colorimetric and Fluorimetric Detection of Nucleic Acids

“…ODNs on their own are versatile components for catalysis, able to adopt complex threedimensional structures to catalyze DNA/RNA ligation, [14] DNA phosphorylation, [15] and the formation of nucleopeptide linkages. [16] The same structural properties allow ODNs to serve as effective scaffolds for complex formation with transition metals to form hybrid catalytic systems; Michael addition, [17] Friedel-Craft alkylation, [18] ester hydrolysis, [19] and an enantioselective Diels-Alder reaction [20] have been demonstrated using this concept.Here we apply the concept of DNA-directed transitionmetal catalysts in an entirely new strategy for catalytic signal amplification. We use ligand-labeled probe strands to form a palladium complex in the presence of a specific target DNA sequence.…”

Modular Assembly of a Pd Catalyst within a DNA Scaffold for the Amplified Colorimetric and Fluorimetric Detection of Nucleic Acids

“…ODNs on their own are versatile components for catalysis, able to adopt complex threedimensional structures to catalyze DNA/RNA ligation, [14] DNA phosphorylation, [15] and the formation of nucleopeptide linkages. [16] The same structural properties allow ODNs to serve as effective scaffolds for complex formation with transition metals to form hybrid catalytic systems; Michael addition, [17] Friedel-Craft alkylation, [18] ester hydrolysis, [19] and an enantioselective Diels-Alder reaction [20] have been demonstrated using this concept.Here we apply the concept of DNA-directed transitionmetal catalysts in an entirely new strategy for catalytic signal amplification. We use ligand-labeled probe strands to form a palladium complex in the presence of a specific target DNA sequence.…”

Templated Chemistry for Sequence‐Specific Fluorogenic Detection of Duplex DNA

“…However, there do exist a few prior reports of templated chemistry being performed in the context of DNA triple helices. Nearly two decades ago, Dervan demonstrated triplex-mediated chemical ligation of dsDNA, [7a] and we described the cyclization of DNAs by triplex formation on a single-stranded DNA template. [15] In related work, Nicolaou described the use of N-cyanoimidazole to form a phosphodiester bond in templated formation of triplex structures as part of a self-replication scheme.…”

“…[15] In related work, Nicolaou described the use of N-cyanoimidazole to form a phosphodiester bond in templated formation of triplex structures as part of a self-replication scheme. [7b] More recently, Mokhir demonstrated templated ester hydrolysis in triple helices. [7c] …”

“…However, double–stranded DNA has received very limited attention as a template for acceleration of chemical reactions. The few existing examples include triple-helix-forming oligonucleotides that bind via Hoogsteen base pairs [7] or polyamides that associate in the minor groove. [8] These reactions had limitations such as little or no fluorescence activation, short recognition sequences or dependence on acidic pH conditions.…”