An Efficient Lanthanide-Dependent DNAzyme Cleaving 2'-5'-Linked RNA.

Area of Science:

• Biochemistry
• Molecular Biology
• Synthetic Biology

Background:

• RNA exists in two main linkage forms: the predominant 3′-5′ and the biologically significant 2′-5′.
• Understanding and manipulating 2′-5′ RNA is vital for biological, medical, and prebiotic research.

Purpose of the Study:

• To isolate a DNAzyme capable of specifically cleaving 2′-5′ linked RNA.
• To characterize the activity and cofactor requirements of the novel DNAzyme.
• To demonstrate potential applications in chemical biology and studying RNA-metal interactions.

Main Methods:

• In vitro selection was employed to identify a DNA sequence with catalytic activity.
• The DNAzyme's cleavage specificity for 2′-5′ RNA over 3′-5′ RNA was assessed.
• The reaction kinetics were measured using cerium(III) [Ce(3+)] as the primary metal cofactor.
• The influence of other trivalent lanthanide ions on DNAzyme activity was investigated.

Main Results:

• A DNAzyme (Ce5 DNAzyme) was successfully isolated that specifically cleaves 2′-5′ RNA.
• The DNAzyme requires trivalent light lanthanide ions, with optimal activity observed for Ce(3+).
• The observed reaction rate of 0.16 min⁻¹ with 10 μm Ce(3+) is the fastest reported for this reaction.
• Activity decreased with heavier lanthanide ions, and the DNAzyme was used to study phosphorothioate-modified RNA reactions.

Conclusions:

• The Ce5 DNAzyme represents a highly efficient and specific tool for cleaving 2′-5′ RNA.
• This discovery provides a valuable tool for chemical biology applications, including RNA analysis.
• The DNAzyme facilitates the study of interactions between modified RNA and specific metal ions.