Sensors DNAzymes

In addition to chemical sensors, DNAzymes have found applications in molecular logic gates [68-70] and molecular motors [71, 72],... 

Fig. 23 (a) DNAzyme-based sensor design with two dabcyl quenchers and a FAM fluorophore (top) and mechanism of operation (bottom), (b) Fluorescence response before and after complete cleavage through Pb2+ inset contains the corresponding image of the DNAzyme probe in the absence (left) and presence of Pb2+ (after 2 min of reaction time, right). (Reprinted with permission from [150]. Copyright 2003 American Chemical Society)... 

The preparation of DNAzyme sensors is usually done in a combinatorial way by producing a random set of DNA strands and selecting the analyte-responsive strands on an affinity column followed by elimination of strands that are sensitive to a broader group of metal ions. In case of success, a DNAzyme with high selectivity and sensitivity is obtained after several iterative cycles. DNAzymes have been found by this process for Cu2+, Pb2+, and U02+ [151-153]. 

Liu J, Lu Y (2007) A DNAzyme catalytic beacon sensor for paramagnetic Cu2+ ions in aqueous solution with high sensitivity and selectivity. J Am Chem Soc 129 9838-9839... 

Since some DNAzymes depend on specific metal ions for activity, they can be employed for the detection of those ions, hi the first example, a previously reported [59] DNAzyme was labeled with a Dabcyl fluorescence quencher at the 3 -end and the corresponding RNA substrate with a TAMRA fluorophore at the 5 -end [60]. Upon addition of Pb " ions, the substrate was cleaved, resulting in dissociation from the DNA enzyme strand. This led to spatial separation of the fluorophore-quencher pair, resulting in fluorescence (Fig. 5). The sensor system was over 80 times more responsive to Pb than to other metal ions, and had a quantifiable detection range of 10 nM to 4 pM. A similar strategy was developed for the detection of Ctf by a DNAzyme that oxidatively cleaves DNA [61]. The system showed a dynamic range of 35 nM to 20 pM and had a metal ion selectivity of a factor of 2000 for Cu over other metal ions. A comparable system was reported for the detection of the uranyl cation (UO/ ), with millionfold selectivity over other metal ions and parts-per-trillion sensitivity. 

A different approach to DNAzyme sensors relies on the visual properties of aggregated gold nanoparticles [62-64]. The substrate for the DNAzyme is designed so that... 

Fig. 5 Schematic representation of a fluorophore F) and quencher (g)-labeled DNAzyme-substrate complex serving as a selective sensor for metal ions...

Dong s group reports a simple, sensitive, and label-free I7E DNAzyme-based sensor for Pb + detection. The catalytic activity of some DNAzymes is divalent metal ion-specific, just as the catalytic activity of some protein enzymes is metal ion cofactor-dependent (Santoro and Joyce, 1997 Carmi et al., 1998). In this work, the authors focus on 17E DNAzyme, which is a divalent Pb -specific enzyme employed widely in Pb + sensors (Santoro and Joyce, 1997). As shown in Figure 12.16A, in the presence of Pb, 17E DNAzyme could cleave the substrate 17DS, which could release ssDNA (including 17E and fragments from 17DS)... 

Shen et al. [16] have recently reported the development of an electrochemical DNAzyme biosensor based on DNA-Au bio-bar code amplification, which provides a platform for fabrication of sensors for analysis of many small molecules, especially for metal ions. For example, a specific DNAzyme for Pb + was immobilized onto an Au electrode surface via a thiol-Au interaction, taking advantage of cataljAic reactions of a DNAzyme upon its binding to Pb + and the use of DNA-Au bio-bar codes to achieve signal enhancement [16]. The presence of gold nanoparticles, enhancing the active surface... 

Kim, J. H. Han, S. H. Chung, B. H. Improving Pb + detection using DNAzyme-based fluorescence sensors by pairing fluorescence donors with gold nanoparticles. Biosens. Bioelectron. 2011, 26, 2125-2129. 

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