Typical Structure of Trans Cleaving DNAzymes

A trans-cleaving DNAzyme contains two components, a substrate strand and an enzyme strand (Fig. 1A), whereas a ds-cleaving DNAzyme is a self-cleaving DNAzyme comprised of only a single strand. In this chapter, we focus on the trans-cleaving system. Most trans-cleaving DNAzymes identified thus far share similar structural features, i.e., the enzyme strand has two substrate recognition arms and a catalytic core. A primary example is the Pb2+-

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Fig. 1. Structure and function of the "8-17" DNAzyme. (A) Secondary structure of the DNAzyme. (B) Schematics of the cleavage of the substrate by the enzyme strand in the presence of Pb2+.

dependent DNAzyme, named the "8-17" DNAzyme (see Fig. 1A) (5,16,17). The substrate strand, named 17DS, is a DNA/RNA chimer with a single RNA linkage (rA). The enzyme strand is named 17E. The two Watson-Crick basepair regions on the two sides of the DNAzyme are the substrate recognition arms, and the bulged structure of 17E is the catalytic core. The base sequences of the recognition arms can be changed so long as the basepairing is maintained, whereas mutations in the catalytic core region may result in significant changes of the DNAzyme activities. The substrate is cleaved by the enzyme strand in the presence of Pb2+ (Fig. 1B) (6).

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