The Programmable Catalytic Core of 8-17 DNAzymes

• Published in: Molecules (Basel, Switzerland) Vol. 29; no. 11; p. 2420
• Main Authors: Zhang, Fumei, Shi, Weiguo, Guo, Lei, Liu, Shihui, He, Junlin
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 21.05.2024; MDPI
• Subjects: Base Sequence; Catalysis; catalytic core; Catalytic Domain; Catalytic RNA; DNA, Catalytic - chemistry; DNA, Catalytic - metabolism; DNAzyme; Hydrogen-Ion Concentration; metal ion dependence; Metals - chemistry; Nucleic Acid Conformation; China; DNAzyme; catalytic core; metal ion dependence
• ISSN: 1420-3049; 1420-3049
• DOI: 10.3390/molecules29112420

8-17 DNAzymes (8-17, 17E, Mg5, and 17EV1) are in vitro-selected catalytic DNA molecules that are capable of cleaving complementary RNAs. The conserved residues in their similar catalytic cores, together with the metal ions, were suggested to contribute to the catalytic reaction. Based on the contribution of the less conserved residues in the bulge loop residues (W12, A15, A15.0) and the internal stem, new catalytic cores of 8-17 DNAzymes were programmed. The internal stem CTC-GAG seems to be more favorable for the DNAzymes than CCG-GGC, while an extra W12.0 led to a significant loss of activity of DNAzymes, which is contrary to the positive effect of A15.0, by which a new active DNAzyme 17EM was derived. It conducts a faster reaction than 17E. It is most active in the presence of Pb2+, with the metal ion preference of Pb2+ >> Zn2+ > Mn2+ > Ca2+ ≈ Mg2+. In the Pb2+ and Zn2+-mediated reactions of 17EM and 17E, the same Na+- and pH dependence were also observed as what was observed for 17E and other 8-17 DNAzymes. Therefore, 17EM is another member of the 8-17 DNAzymes, and it could be applied as a potential biosensor for RNA and metal ions.