%0 Journal Article
%T Beyond allostery: Catalytic regulation of a deoxyribozyme through an entropy-driven DNA amplifier
%A Grace Eckhoff
%A Vlad Codrea
%A Andrew D Ellington
%A Xi Chen
%J Journal of Systems Chemistry
%D 2010
%I BioMed Central
%R 10.1186/1759-2208-1-13
%X A variety of functional nucleic acids have been engineered over the past two decades, including not only simple binding elements (aptamers [1,2]) and catalysts (ribozymes [3] and deoxyribozymes [4]), but also more 'intelligent' molecular parts, such as aptamer beacons and allosteric ribozymes that can sense biomolecules [5,6], process molecular information [7,8], and regulate biochemical systems [9]. However, most regulatory nucleic acid elements are based on allosteric control, which has a fundamental limitation: one input molecule generally yields only one output molecule. Such stoichiometric or sub-stoichiometric regulation is often insufficient for effective metabolic regulation or diagnostic signal transduction, especially when the concentrations of input molecules are low.In contrast, natural catalytic cascades, such as the phosphorylation of proteins by kinases, readily amplify low input signals. Although in principle ribozymes and deoxyribozymes could participate in similar cascades as catalysts [10-12], no generalizable method for implementing such cascades has yet been established. On the other hand, DNA and RNA can catalyze chemical reactions not only by forming intricate tertiary structures, but also by simply forming Watson-Crick base pairs. In fact, by serving as a hybridization template, DNA can control and catalyze a wide range of chemical reactions [13], some of which can yield products capable of regulating downstream reactions. More recently, Zhang and coworkers have designed a scheme for highly efficient, enzyme-free, entropy-driven catalytic reactions that relies only on the dynamic hybridization of DNA strands [14-17]. Because of its chemical simplicity, this scheme is expected to allow the development of enzyme-free DNA circuits substantially more complex and robust [18] than previous enzyme-dependent examples [19-22]. Similar strand displacement-based schemes using DNA hairpins as substrates have also been devised [23,24]. Moreover, it has be
%U http://www.jsystchem.com/content/1/1/13