The role of Na<sup>+</sup> in catalysis by the 8–17 DNAzyme

Parra-Meneses, Virginia; Rojas-Hernández, Francisca; Cepeda-Plaza, Marjorie

doi:10.1039/d2ob01075e

Cited by 4 publications

(4 citation statements)

References 43 publications

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“…As shown in Figure 7 , the positively cooperative role of Na + is significant in the case of Pb 2+ -, Zn 2+ -, and Mn 2+ -assisted reactions, but not in the case of Ca 2+ and Mg 2+ . A similar contribution of Na + was also observed for the 8-17 DNAzyme [ 35 ]. Na + was supposed to play a promotive role, probably by strengthening the electrostatic interaction within the catalytic residue–metal ion complex [ 19 ].…”

Section: Resultssupporting

confidence: 79%

The Programmable Catalytic Core of 8-17 DNAzymes

Zhang,

Shi,

Guo

et al. 2024

Molecules

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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.

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Section: Resultssupporting

confidence: 79%

The Programmable Catalytic Core of 8-17 DNAzymes

Zhang,

Shi,

Guo

et al. 2024

Molecules

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“…The 8-17 DNAzyme is one of the most studied DNAzymes in terms of structure and mechanism. [28][29][30][31] Its three-dimensional structure in the presence of an uncleavable substrate was determined by X-ray crystallography, 32 further confirming its compact structure. To endow the metal-responsiveness to the 8-17 DNAzyme, we employed the artificial Im C -Cu II -Im C base pair, which is one of the metal-mediated base pairs with the greatest stabilizing effect.…”

mentioning

confidence: 88%

Metal-dependent activity control of a compact-sized 8–17 DNAzyme based on metal-mediated unnatural base pairing

Takezawa,

Hu,

Nakama

et al. 2024

Chem. Commun.

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“…Another study showed that the insertion of a C3 spacer in the catalytic core did not corrupt 39E activity but enhanced about 10–fold UO 2 2+ –sensitivity [ 29 ]. Some simulation works also investigated the effects of pH values and monovalent metal ions on the activities of DNAzymes [ 26 , 27 , 30 , 31 ]. These suggest that DNAzymes might adopt much more complicated configuration arrangements toward the catalytic functions.…”

Section: Introductionmentioning

confidence: 99%

Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics

Zhang

Wang

et al. 2023

IJMS

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DNAzyme is a class of DNA molecules that can perform catalytic functions with high selectivity towards specific metal ions. Due to its potential applications for biosensors and medical therapeutics, DNAzyme has been extensively studied to characterize the relationships between its biochemical properties and functions. Similar to protein enzymes and ribozymes, DNAzymes have been found to undergo conformational changes in a metal–ion–dependent manner for catalysis. Despite the important role the conformation plays in the catalysis process, such structural and dynamic information might not be revealed by conventional approaches. Here, by using the single–molecule fluorescence resonance energy transfer (smFRET) technique, we were able to investigate the detailed conformational dynamics of a uranyl–specific DNAzyme 39E. We observed conformation switches of 39E to a folded state with the addition of Mg2+ and to an extended state with the addition of UO22+. Furthermore, 39E can switch to a more compact configuration with or without divalent metal ions. Our findings reveal that 39E can undergo conformational changes spontaneously between different configurations.

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The role of Na⁺ in catalysis by the 8–17 DNAzyme

Abstract: The 8-17 DNAzyme is the most studied deoxyribozyme in terms of its molecular mechanism, hence it has become a model system to understand the basis behind DNA catalysis. New functional...

Cited by 4 publications

References 43 publications

The Programmable Catalytic Core of 8-17 DNAzymes

The Programmable Catalytic Core of 8-17 DNAzymes

Metal-dependent activity control of a compact-sized 8–17 DNAzyme based on metal-mediated unnatural base pairing

Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics

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The role of Na+ in catalysis by the 8–17 DNAzyme

Abstract: The 8-17 DNAzyme is the most studied deoxyribozyme in terms of its molecular mechanism, hence it has become a model system to understand the basis behind DNA catalysis. New functional...

Cited by 4 publications

References 43 publications

The Programmable Catalytic Core of 8-17 DNAzymes

The Programmable Catalytic Core of 8-17 DNAzymes

Metal-dependent activity control of a compact-sized 8–17 DNAzyme based on metal-mediated unnatural base pairing

Single–Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics

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The role of Na⁺ in catalysis by the 8–17 DNAzyme