Selection of a self-cleaving ribozyme activated in a chemically and thermally denaturing environment

A Threose Nucleic Acid (TNA) Enzyme Catalyzing Native 3'-5' Ligation of RNA

Threose nucleic acid (TNA) is a synthetic genetic polymer of both prebiotic significance and practical utility. Identification of TNA molecules with enzymatic activities (TNAzymes) not only lends experimental support for TNA as a potential primitive catalyst but also offers intrinsically stable biotechnological and biomedical molecular tools. Here, we report the in vitro selection of TNAzymes capable of catalyzing the native 3'-5' ligation of two RNA oligonucleotides. The Zn2+-dependent TNAzyme facilitates the formation of a canonical phosphoester bond between a terminal 3'-hydroxyl group on one substrate and a 5'-triphosphate on the other. Under optimal conditions (pH 7.3 and 23 °C), the TNAzyme exhibits a catalytic rate constant of 0.39 h-1. Lastly, we demonstrate that the TNAzyme-catalyzed ligation of two RNA fragments could yield a functional RNA product such as a ribozyme. These findings showcase the potential role of TNA as a primordial catalyst during the emergence of the RNA world, as well as its prospective application in RNA synthesis.

An RNA-Cleaving DNAzyme That Requires an Organic Solvent to Function

Engineering functional nucleic acids that are active under unusual conditions will not only reveal their hidden abilities but also lay the groundwork for pursuing them for unique applications. Although many DNAzymes have been derived to catalyze diverse chemical reactions in aqueous solutions, no prior study has been set up to purposely derive DNAzymes that require an organic solvent to function. Herein, we utilized in vitro selection to isolate RNA-cleaving DNAzymes from a random-sequence DNA pool that were "compelled" to accept 35 % dimethyl sulfoxide (DMSO) as a cosolvent, via counter selection in a purely aqueous solution followed by positive selection in the same solution containing 35 % DMSO. This experiment led to the discovery of a new DNAzyme that requires 35 % DMSO for its catalytic activity and exhibits drastically reduced activity without DMSO. This DNAzyme also requires divalent metal ions for catalysis, and its activity is enhanced by monovalent ions. A minimized, more efficient DNAzyme was also derived. This work demonstrates that highly functional, organic solvent-dependent DNAzymes can be isolated from random-sequence DNA libraries via forced in vitro selection, thus expanding the capability and potential utility of catalytic DNA.

Protection of DNA by metal ions at 95 °C: from lower critical solution temperature (LCST) behavior to coordination-driven self-assembly

While polyvalent metal ions and heating can both degrade nucleic acids, we herein report that a combination of them leads to stabilization. After incubating 4 mM various metal ions and DNA oligonucleotides at 95 °C for 3 h at pH 6 or 8, metal ions were divided into four groups based on gel electrophoresis results. Mg²⁺ can stabilize DNA at pH 6 without forming stable nanoparticles at room temperature. Co²⁺, Cu²⁺, Cd²⁺, Mn²⁺ and Zn²⁺ all protected the DNA and formed nanoparticles, whereas the nanoparticles formed with Fe²⁺ and Ni²⁺ were so stable that they remained even in the presence of EDTA. At pH 8, Ce³⁺ and Pb²⁺ showed degraded DNA bands. For Mg²⁺, better protection was achieved with higher metal and DNA concentrations. By monitoring temperature-programmed fluorescence change, a sudden drop in fluorescence intensity attributable to the lower critical solution temperature (LCST) transition of DNA was found to be around 80 °C for Mg²⁺, while this transition temperature decreased with increasing Mn²⁺ concentration. The unexpected thermal stability of DNA enabled by metal ions is useful for extending the application of DNA at high temperatures, forming coordination-driven nanomaterials, and it might offer insights into the origin of life on the early Earth.