An RNA-Cleaving Catalytic DNA Accelerated by Freezing

Detection of intracellular microRNA-21 for cancer diagnosis by a nanosystem containing a ZnO@polydopamine and DNAzyme probe

MicroRNAs (miRNAs) are a series of single-stranded non-coding ribonucleic acid (RNA) molecules which associated closely with various human diseases. Efficient strategies for detecting miRNAs are of great significance to cancer diagnosis and prognosis. Here we provide a novel nanosystem that can be applied for the detection of miRNAs. The nanosystem consists of a single-stranded deoxyribonucleic acid (DNA) probe and a probe carrier. The DNA probe was designed based on a deoxyribozyme (DNAzyme) with several necessary functional sequences and two fluorescent dyes labeled at proper sites. The ZnO@polydopamine (ZnO@PDA) nanomaterial serves not only as a probe carrier, but also as a supplier of Zn2+ that can activate the DNAzyme. The DNA probe will undergo a conformation alteration induced by miRNA-21, which then trigger the DNAzyme catalyzed self-cleavage reaction with the assist of Zn2+ provided by ZnO decomposition under weak acid environment. A change of fluorescent color will occur due to the interruption of fluorescence resonance energy transfer between the two fluorescent dyes, and the dissociated miRNA-21 can repeatedly induce the above responses to amplify the fluorescence signal. The feasibility of the whole procedure was demonstrated by various experiments. This nanosystem showed a good selectivity towards miRNA-21, and under the optimal incubation time of 2 hours, a good linear relationship was obtained in a concentration range of 0.01-2.0 nM with a detection limit of 3.8 pM. In in vivo detection, an obvious fluorescence color change from red to green can be observed in the presence of miRNA-21. The results proved that this miRNA detection strategy has a broad application prospect in tumor diagnosis and miRNA related biological studies.

Generation of RNA with 2', 3'-Cyclic Phosphates by Deoxyribozyme Cleavage in Frozen Solutions

The generation of terminal 2', 3'-cyclic phosphates on RNA oligomers is an important process in the study of tRNA splicing and repair, ribozyme catalysis, and RNA circularization. Here, we describe a simple method for producing 2', 3'-cyclic phosphate functionalized RNA by the deoxyribozyme-catalyzed cleavage of a short 3'-RNA overhang in frozen solution. This method avoids the nonspecific modification and degradation of RNA and attached functional groups (e.g., fluorophores) inherent in other methods, and the use of frozen conditions enables cleavage at very low divalent metal ion concentrations, limiting RNA hydrolysis.

Modulation of DNAzyme Activity via Butanol Dehydration

Understanding the activity of biomolecules in cosolvent systems is important for catalysis, separation and developing biosensors. The majority of previously studied solvents are either phase separated with water or miscible with water. Butanol was recently used to extract water for the conjugation of DNA to gold nanoparticles. In this work, the effect of butanol on the activity of a few RNA-cleaving DNAzymes was studied. A 130-fold improvement in sensitivity for the Na⁺ -specific EtNa DNAzyme was observed, and butanol also improved the activity of another Na⁺ -specific DNAzyme, NaA43T by a few folds. However, when divalent metal ions were used for both EtNa and 17E DNAzymes, the activity was inhibited. A main driven force for enhanced DNAzyme activity is the concentration effect due to butanol dehydration. This study provides insights into the interplay between DNA, metal ions and organic solvents, and such an understanding might be useful for developing sensitive biosensors.

Self-paired dumbbell DNA -assisted simple preparation of stable circular DNAzyme and its application in Pb2+ sensor

During its development in recent decades, DNAzyme has become a promising candidate for application in biosensor field. However, it still suffers from the problem of thermodynamic and biological instability such as nuclease digestion, which limits its applications in complex samples. Here we have presented a simple and common strategy to resolve this problem by engineering the linear DNAzyme into a circular shape DNAzyme based on the integration of substrate and enzyme parts into one single-stranded sequence. This circular DNAzyme system is indeed endowed with excellent stability due to the stable intramolecular double-stranded formation and extraordinary resistance to nuclease digestion due to the closed structure. We demonstrated that this circular DNAzyme system gained excellent stability and could active under conditions across a broader range of temperature, salt concentrations, and pH. Depending on this circular DNAzyme, combing with Terminal deoxynucleotidyl transferase (TdT)-generated G-quadruplexes, a label free colorimetric sensing platform for Pb²⁺ quantitation was developed, and a detection limit of 0.085 nM was achieved. Then the enzyme digestion cycle amplification was introduced to further improve the sensitivity of the sensing system, an ultralow detection limit of 0.0015 nM for this fluorescence method was achieved. Based on the two sensing platforms, ultrasensitive analysis of Pb²⁺ in environmental water and food samples was successfully realized. It is anticipated that this stable circular DNAzyme design will be helpful for trace detection in complex samples.

Freezing-Assisted Conjugation of Unmodified Diblock DNA to Hydrogel Nanoparticles and Monoliths for DNA and Hg2+ Sensing

Acrydite-modified DNA is the most frequently used reagent to prepare DNA-functionalized hydrogels. Herein, we show that unmodified penta-adenine (A₅ ) can reach up to 75 % conjugation efficiency in 8 h under a freezing polymerization condition in polyacrylamide hydrogels. DNA incorporation efficiency was reduced by forming duplex or other folded structures and by removing the freezing condition. By designing diblock DNA containing an A₅ block, various functional DNA sequences were attached. Such hydrogels were designed for ultrasensitive DNA hybridization and Hg²⁺ detection, with detection limits of 50 pM and 10 nM, respectively, demonstrating the feasibility of using unmodified DNA to replace acrydite-DNA. The same method worked for both gel nanoparticles and monoliths. This work revealed interesting reaction products by exploiting freezing and has provided a cost-effective way to attach DNA to hydrogels.

Functional Nucleic Acids Under Unusual Conditions

Functional nucleic acids (FNAs), including naturally occurring ribozymes and riboswitches as well as artificially created DNAzymes and aptamers, have been popular molecular toolboxes for diverse applications. Given the high chemical stability of nucleic acids and their ability to fold into diverse sequence-dependent structures, FNAs are suggested to be highly functional under unusual reaction conditions. This review will examine the progress of research on FNAs under conditions of low pH, high temperature, freezing conditions, and the inclusion of organic solvents and denaturants that are known to disrupt nucleic acid structures. The FNA species to be discussed include ribozymes, riboswitches, G-quadruplex-based peroxidase mimicking DNAzymes, RNA-cleaving DNAzymes, and aptamers. Research within this space has not only revealed the hidden talents of FNAs but has also laid important groundwork for pursuing these intriguing functional macromolecules for unique applications.

Nucleic Acid Catalysis under Potential Prebiotic Conditions

Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5-4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.

DNAzyme–gold nanoparticle-based probes for biosensing and bioimaging

The design and applications of DNAzyme–gold nanoparticle-based probes in biosensing and bioimaging are summarized here.

Freezing promoted hybridization of very short DNA oligonucleotides

Shorter DNA probes provide better specificity for hybridization, but they may not form stable duplexes at room temperature. In this study, we used thiazole orange to follow DNA hybridization upon freezing and achieved stable 5-mer duplex DNA. Using multiple short probes in tandem, long DNA could also be studied. This study provides insights into DNA hybridization in the frozen state and expands the application of freezing for nucleic acid chemistry.

An in Vitro-Selected DNAzyme Mutant Highly Specific for Na+ under Slightly Acidic Conditions

Sodium is one of the most common metal ions in biology; however, DNA-based sodium probes have only been reported recently. A Na⁺ -specific RNA-cleaving DNAzyme named NaA43 is active with Na⁺ alone. In this work, we were using Co(NH₃ )₆ ³⁺ as the intended metal cofactor for in vitro selection, but obtained a mutant of the NaA43 DNAzyme. The mutant was named NaH1, and differs from NaA43 by only two nucleotides. NaA43 has an optimal pH of 7.0, whereas the optimal pH for NaH1 is 6.0. This difference might be due to our selection having been performed at pH 6.0. NaH1 also displays an excellent selectivity for sodium relative to other competing monovalent ions, as well as a fast catalytic rate of (0.11±0.01) min^-1 with 50 mm Na⁺ . At low Na⁺ concentrations, the selected DNAzyme exhibited a higher cleavage rate than NaA43 and thus a tighter apparent K_d of (12.0±1.6) mm Na⁺ . Furthermore, the NaH1 DNAzyme was engineered into a fluorescent Na⁺ biosensor by attaching a fluorophore/quencher pair to the DNAzyme with a detection limit of 223 μm Na⁺ . Preliminary work on detection of Na⁺ in serum was demonstrated as well. This study provides a useful mutant that works in a slightly acidic environment, which might be useful for sensing Na⁺ in acidic in vivo environments.