DNase II Can Efficiently Digest RNA and Needs to Be Redefined as a Nuclease.

DNase II, identified in 1947 and named in 1953, is an acidic DNA endonuclease prevalent across organisms and crucial for normal growth. Despite its expression in nearly all human tissues, as well as its biological significance, DNase II's detailed functions and corresponding mechanisms remain unclear. Although many groups are trying to figure this out, progress is very limited.

Facile Splint-Free Circularization of ssDNA with T4 DNA Ligase by Redesigning the Linear Substrate to Form an Intramolecular Dynamic Nick.

The efficient preparation of single-stranded DNA (ssDNA) rings, as a macromolecular construction approach with topological features, has aroused much interest due to the ssDNA rings' numerous applications in biotechnology and DNA nanotechnology. However, an extra splint is essential for enzymatic circularization, and by-products of multimers are usually present at high concentrations. Here, we proposed a simple and robust strategy using permuted precursor (linear ssDNA) for circularization by forming an intramolecular dynamic nick using a part of the linear ssDNA substrate itself as the template.

Formation of an instantaneous nick for highly efficient adenylation of oligonucleotides by ligase without subsequent jointing.

By forming a nick at the adenylation site instantaneously, nucleic acids are efficiently adenylated by T4 DNA ligase. The subsequent ligation is successfully suppressed in terms of rapid conversion of the instantaneous nick to a more stable gap. It is helpful to understand enzymatic ligation dynamics, and the adenylated products can be used for various practical applications.

Unexpected Mechanism and Inhibition Effect for Nonspecific Amplification Involving Dynamic Binding of Primers with Background DNA.

Nonspecific amplification is a serious issue in DNA detection as it can lead to false-positive results and reduce specificity. It is very important to well understand its mechanism through sequencing nonspecific products. Here, an approach is developed using a nanopore sequencing technique after acquiring the long repetitive sequence of DNA products from nonspecific amplification.

Effects of ribonucleotide supplementation in modulating the growth of probiotic Bacillus subtilis and the synergistic benefits for improving the health performance of Asian seabass (Lates calcarifer).

In aquaculture, due to the requirements for high-density culture, the diseases caused by bacterial pathogens have become a serious issue. To solve this problem, we performed synbiotic application of RNA and Bacillus subtilis as a sustainable and eco-friendly approach to improve the health and immunity of Asian seabass (Lates calcarifer) during cultivation without using any harmful antibiotics or chemicals. Among various forms of nucleic acids, such as mononucleotides and DNA, RNA was found to be most effective in promoting the growth performance of probiotic B.

Direct dsRNA preparation by promoter-free RCT and RNase H cleavage using one circular dsDNA template with a mismatched bubble.

Double-stranded RNA (dsRNA) has aroused widespread interest due to its effects on immunity and applications based on RNAi. However, the in vitro preparation of dsRNA is costly and laborious. In this study, we have developed a novel and interesting method designated as pfRCT (promoter-free rolling-circle transcription) for direct, facile, and efficient dsRNA preparation.

Ultralow background one-pot detection of Lead(II) using a non-enzymatic double-cycle system mediated by a hairpin-involved DNAzyme.

A double-cycle system has been developed for specifically detecting trace amounts of Pb by significantly decreasing the background signal. The detection involves two types of RNA cleavage reactions: one using a Pb-specific GR5 DNAzyme (PbDz) and the other utilizing a newly constructed 10-23 DNAzyme with two hairpins embedded in its catalytic center (hpDz). The ring-structured hpDz (c-hpDz) exhibits significantly lower activity compared to the circular 10-23 DNAzyme without hairpin structures, which plays a crucial role in reducing the background signal.

Can Eat DNA as an Excellent Nitrogen Source to Grow Quickly.

Is DNA or RNA a good nutrient? Although scientists have raised this question for dozens of years, few textbooks mention the nutritional role of nucleic acids. Paradoxically, mononucleotides are widely added to infant formula milk and animal feed. Interestingly, competent bacteria can bind and ingest extracellular DNA and even integrate it into their genome.

Construction of ssDNA-Attached LR-Chimera Involving Z-DNA for ZBP1 Binding Analysis.

The binding of proteins to Z-DNA is hard to analyze, especially for short non-modified DNA, because it is easily transferred to B-DNA. Here, by the hybridization of a larger circular single-stranded DNA (ssDNA) with a smaller one, an LR-chimera (involving a left-handed part and a right-handed one) with an ssDNA loop is produced. The circular ssDNAs are prepared by the hybridization of two ssDNA fragments to form two nicks, followed by nick sealing with T4 DNA ligase.

Anti-Interference Detection of from Aquatic Food Based on Target-Cyclized RCA with Dynamic Adapter Followed by LAMP.

() is considered the most concerning pathogen for seafood. Like other pathogens in food samples, its gene detection suffers from a problem of background interference when isothermal detection methods are used. The sensitivity and specificity greatly decrease due to large amounts of background genome.

Nonalternating purine pyrimidine sequences can form stable left-handed DNA duplex by strong topological constraint.

In vivo, left-handed DNA duplex (usually refers to Z-DNA) is mainly formed in the region of DNA with alternating purine pyrimidine (APP) sequence and plays significant biological roles. It is well known that d(CG)n sequence can form Z-DNA most easily under negative supercoil conditions, but its essence has not been well clarified. The study on sequence dependence of Z-DNA stability is very difficult without modification or inducers.

Plasmon switching of gold nanoparticles through thermo-responsive terminal breathing of surface-grafted DNA in hydrated ionic liquids.

Self-assembly performed in ionic liquids (ILs) as a unique solvent promises distinct functions and applications in sensors, therapeutics, and optoelectronic devices due to the rich interactions between nanoparticle building blocks and ILs. However, the general consideration that common nanoparticles are readily destabilized by counterions in an IL has largely prevented researchers from investigating controlled nanoparticle assembly in IL-based systems. This study explores the assembling behaviour of double-stranded (ds) DNA-functionalized gold nanoparticles (dsDNA-AuNPs) in hydrated ionic liquids.

Interfacing DNA with Gold Nanoparticles for Heavy Metal Detection.

The contamination of heavy metals (e.g., Hg, Pb, Cd and As) poses great risks to the environment and human health.

Stepwise Strategy for One-Pot Synthesis of Single-Stranded DNA Rings from Multiple Short Fragments.

Cyclic rings of single-stranded (ss) DNA have various unique properties, but wider applications have been hampered by their poor availability. This paper reports a convenient one-pot method in which these rings are efficiently synthesized by using T4 DNA ligase through convergent cyclization of easily available short DNA fragments. The key to the present method is to separate all the splint oligonucleotides into several sets, and add each set sequentially at an appropriate interval to the solutions containing all the short DNA fragments.

DNA Base Pair Stacking Assembly of Anisotropic Nanoparticles for Biosensing and Ordered Assembly.

Anisotropic gold nanoparticles have attracted great interest due to their unique physicochemical properties derived from the shape anisotropy. Manipulation of their interfacial interactions, and thereby the assembling behaviors are often requisite in their applications ranging from optical sensing and diagnosis to self-assembly. Recently, the control of interfacial force based on base pair stacking of DNA terminals have offered a new avenue to surface engineering of nanostructures.

Opposite Effects of Flexible Single-Stranded DNA Regions and Rigid Loops in DNAzyme on Colloidal Nanoparticle Stability for "Turn-On" Plasmonic Detection of Lead Ions.

Strains in biomolecules greatly restrict their structural flexibility. The effects of DNA's structural flexibility on nanoparticle stability have remained less explored in the field of plasmonic biosensors. In the present study, we discover the opposite effects of a rigid loop and a flexible single-stranded DNA (ssDNA) region in DNAzyme on the colloidal stability of gold nanoparticles (AuNPs), which afford "turn-on" plasmonic detection of Pb.

Preferential production of RNA rings by T4 RNA ligase 2 without any splint through rational design of precursor strand.

Rings of single-stranded RNA are promising for many practical applications, but the methods to prepare them in preparative scale have never been established. Previously, RNA circularization was achieved by T4 RNA ligase 2 (Rnl2, a dsRNA ligase) using splints, but the yield was low due to concurrent intermolecular polymerization. Here, various functional RNAs (siRNA, miRNA, ribozyme, etc.

Accelerated non-crosslinking assembly of DNA-functionalized nanoparticles in alcoholic solvents: for application in the identification of clear liquors.

Colorimetric detection of various target molecules in aqueous solutions based on the non-crosslinking assembly of DNA-functionalized Au nanoparticles (DNA-AuNPs) has been well established in recent years. The extension of DNA-AuNPs to other solvents remains much less explored, despite the practical importance of detection in non-aqueous solutions, such as those containing an organic ingredient that is required or not removable in many contexts. However, the general consideration that DNA is easily denatured and precipitated in organic solvents has been hampering the use of DNA-AuNPs in low polar solvents.

Facile Characterization of Topology of DNA Catenanes.

During the preparation of single-stranded DNA catenanes, topological isomers of different linking numbers (Lk) are intrinsically produced, and they must be separated from each other to construct sophisticated nanostructures accurately. In many previous studies, however, mixtures of these isomers were directly employed to construct nanostructures without sufficient characterization. Here, we present a method that easily and clearly characterizes the isomers by polyacrylamide gel electrophoresis.

Effect of sulfated polysaccharides on the digestion of DNA by pepsin under simulated gastric juice in vitro.

The effect of sulfated polysaccharides on the digestion of dietary DNA by pepsin was studied using in vitro simulated gastric juice. The results showed that fucoidan (FUC), dextran sulfate (DS) and chondroitin sulfate (CS) could inhibit the digestion of DNA in a dose-dependent manner. Polysaccharides with high sulfate group content have stronger inhibition ability.

The Astaxanthin Aggregation Pattern Greatly Influences Its Antioxidant Activity: A Comparative Study in Caco-2 Cells.

Astaxanthin is an excellent antioxidant that can form unstable aggregates in biological or artificial systems. The changes of astaxanthin properties caused by molecular aggregation have gained much attention recently. Here, water-dispersible astaxanthin H- and J-aggregates were fabricated and stabilized by a natural DNA/chitosan nanocomplex (respectively noted as H-ADC and J-ADC), as evidenced by ultraviolet and visible spectrophotometry, Fourier transform infrared spectroscopy, and Raman spectroscopy.

DNA Ligase Connects Two Fragments Having Exceptionally Short Complementary Termini at High Temperatures.

DNA ligase ( DNA ligase) is widely employed for cloning, enzymatic synthesis, and molecular diagnostics at high temperatures (e.g., 65 °C).

Nanotetrahedron-assisted electrochemical aptasensor with cooperatively-folding aptamer chimera for sensitive and selective detection of lysozyme in red wines.

Although aptamers show great potential in the field of analytical chemistry, their intrinsic shortcomings of relatively weak affinity and selectivity in complex working environment limit their applicability to real analysis, because the flexibility of aptamers makes the specific aptatopes (i.e., binding sites for targets) in the conformational structure unstable and deficient.

Colorimetric determination of mercury(II) ion based on DNA-assisted amalgamation: a comparison study on gold, silver and Ag@Au Nanoplates.

Inspired by the increasing use of plasmonic gold and silver nanoplates as probes for diverse analytes, the research community often questions which metal nanoplates should be chosen for a given application. A comparative study was performed on the performance and physicochemical properties of three types of metal nanoplates for use in plasmonic detection of Hg(II) ion. Specifically, gold, silver and Ag@Au nanoplates were studied.

Engineering Aptamer with Enhanced Affinity by Triple Helix-Based Terminal Fixation.

The affinity of aptamers relies on their adaptive folding, but the excessive flexibility of the aptamer backbone usually hampers the folding process. Thus, there is an urgent need to engineer aptamers with more stable and defined structures. Herein, we report a postselection strategy for stabilizing aptamer structures, by fixing both termini of the aptamer with a length-optimized triple helix structure.