An RNA-Cleaving Catalytic DNA Accelerated by Freezing.

The EtNa DNAzyme was isolated during the isopropanol precipitation step of an in vitro selection effort. Although inactive with the intended cofactor, its RNA cleavage activity was observed under a few conditions. With Na , EtNa was highly active in ∼50 % ethanol, whereas in water, it was highly active with Ca .

Headgroup-Inversed Liposomes: Biointerfaces, Supported Bilayers and Applications.

Phospholipids are a major component of the cell membrane. In most natural phospholipids, the phosphate acts as a bridge, connecting the other portion of the polar headgroup with the hydrophobic tails. Such bridging phosphate is chemically quite inert.

Fluorescent DNA Probing Nanoscale MnO: Adsorption, Dissolution by Thiol, and Nanozyme Activity.

Manganese dioxide (MnO) is an interesting material due to its excellent biocompatibility and magnetic properties. Adsorption of DNA to MnO is potentially of interest for drug delivery and sensing applications. However, little fundamental understanding is known about their interactions.

Transition Metal Dichalcogenide Nanosheets for Visual Monitoring PCR Rivaling a Real-Time PCR Instrument.

Monitoring the progress of polymerase chain reactions (PCRs) is of critical importance in bioanalytical chemistry and molecular biology. Although real-time PCR thermocyclers are ideal for this purpose, their high cost has limited their applications in resource-poor areas. Direct visual detection would be a more attractive alternative.

Interfacing DNA Oligonucleotides with Calcium Phosphate and Other Metal Phosphates.

Calcium phosphate (CaP) has long been used for DNA delivery, although its fundamental interaction with DNA, especially with single-stranded DNA oligonucleotides, remains to be fully understood. Using fluorescently labeled oligonucleotides, we herein studied DNA adsorption isotherm and the effect of DNA length and sequence. Longer DNAs are adsorbed more strongly, and at neutral pH, poly-C DNAs are adsorbed more than the other three DNA homopolymers.

Selection and Screening of DNA Aptamers for Inorganic Nanomaterials.

Searching for DNA sequences that can strongly and selectively bind to inorganic surfaces is a long-standing topic in bionanotechnology, analytical chemistry and biointerface research. This can be achieved either by aptamer selection starting with a very large library of ≈10 random DNA sequences, or by careful screening of a much smaller library (usually from a few to a few hundred) with rationally designed sequences. Unlike typical molecular targets, inorganic surfaces often have quite strong DNA adsorption affinities due to polyvalent binding and even chemical interactions.

Zn Induced Irreversible Aggregation, Stacking, and Leakage of Choline Phosphate Liposomes.

The interaction between lipids and metal ions is important for metal sensing, cellular signal transduction, and oxidative lipid damage. While most previous work overlooked the phosphate group of lipids for metal binding, we herein highlight its importance. Phosphocholine (PC) and its headgroup inversed choline phosphate (CP) lipids were used to prepare liposomes.

Filling in the Gaps between Nanozymes and Enzymes: Challenges and Opportunities.

Using nanomaterials to mimic the function of protein enzymes is an interesting idea. Many nanomaterials have a similar size as enzymes and they also possess catalytic activity. Over the past decade, a surge of nanozyme work has emerged, likely due to the advancement in the synthesis and characterization of inorganic nanoparticles.

Photosensitization of Molecular Oxygen on Graphene Oxide for Ultrasensitive Signal Amplification.

H O and horseradish peroxidase (HRP) are commonly used together in bioassays. HRP is required to accelerate the reaction between a chromogenic substrate (e.g.

A Cell-Mimicking Structure Converting Analog Volume Changes to Digital Colorimetric Output with Molecular Selectivity.

We herein report a three-component cell-mimicking structure with a peroxidase-like iron oxide nanozyme as the nucleus, a molecularly imprinted hydrogel shell as cytoplasm, and a lipid bilayer membrane. The structure was characterized by cryo and negative stain TEM and also by a calcein leakage test. By introducing charged monomers, the gel shell can swell or shrink in response to salt concentration.

Multi-metal-dependent nucleic acid enzymes.

Nucleic acid enzymes (NAEs) are catalytically active RNA and DNA molecules. NAEs with RNA-cleaving activity are most extensively studied for applications in analytical chemistry, gene therapy and nanotechnology. Most NAEs require metal ions for activity.

Ultrasensitive DNAzyme-Based Ca Detection Boosted by Ethanol and a Solvent-Compatible Scaffold for Aptazyme Design.

Functional DNA includes aptamers and DNAzymes, and metal ions are often important for achieving the chemical functions of such DNA. Biosensors based on functional DNA have mainly been tested in aqueous buffers. By introducing organic solvents with much lower dielectric constants, the interaction between metal ions and DNA can be significantly enhanced, and this might affect the performance of DNA-based biosensors.

Length-Dependent Diblock DNA with Poly-cytosine (Poly-C) as High-Affinity Anchors on Graphene Oxide.

DNA-functionalized graphene oxide (GO) is a popular system for biosensor development and directed materials assembly. Compared to covalent attachment, simple physisorption of DNA has been more popular, and a DNA sequence with a strong affinity on GO is highly desirable. Recently, we found that poly-cytosine (poly-C) DNA can strongly adsorb on many common nanomaterials, including GO.

Site-Selective Labeling of Chromium(III) as a Quencher on DNA for Molecular Beacons.

Molecular beacons typically use organic molecules or nanomaterials as quenchers. Many transition-metal ions have excellent fluorescence quenching ability, and the aim of this study was to recruit them as small quenchers in DNA detection. Cr has a slow ligand exchange rate, forming stable adducts with DNA.

Hybrid nanomaterials of WS or MoS nanosheets with liposomes: biointerfaces and multiplexed drug delivery.

Lipid containing hybrid materials are of significant interest for biointerface research and drug delivery applications, and a large number of previous studies have focused on graphene oxide (GO). In this work, novel hybrid materials made of transition metal dichalcogenides (TMDCs) and phosphocholine (DOPC) liposomes were prepared and compared with GO. All these inorganic materials are 2D nanosheets.

Splitting a DNAzyme enables a Na-dependent FRET signal from the embedded aptamer.

Recently, a few Na-specific RNA-cleaving DNAzymes have been reported, and a Na aptamer was identified from the NaA43 and Ce13d DNAzymes. These DNAzymes and the embedded aptamer have been used for Na detection. In this work, we studied the Na-dependent folding of the Ce13d DNAzyme using fluorescence resonance energy transfer (FRET).

Kinetic Discrimination of Metal Ions Using DNA for Highly Sensitive and Selective Cr Detection.

Most metal sensors are designed for a strong binding affinity toward target metal ions, and the underlying principle relies on binding thermodynamics. The kinetic aspect of binding, however, was rarely explored for sensing. In this work, the binding kinetics of 19 common or toxic metal ions are compared based on a fluorescence quenching assay using DNA oligonucleotides as ligands.

Folding of the silver aptamer in a DNAzyme probed by 2-aminopurine fluorescence.

The RNA-cleaving Ag10c DNAzyme was recently isolated via in vitro selection and it can bind two Ag ions for activity. The Ag10c contains a well-defined Ag binding aptamer as indicated by DMS footprinting. Since aptamer binding is often accompanied with conformational changes, we herein used 2-aminopurine (2AP) to probe its folding in the presence of Ag.

Freezing Directed Construction of Bio/Nano Interfaces: Reagentless Conjugation, Denser Spherical Nucleic Acids, and Better Nanoflares.

While nanoparticle solutions cannot freeze in general, they may remain stable in the presence of polymer stabilizers. We herein communicate that gold nanoparticles (AuNPs) are stable in the presence of thiolated DNA after a freeze-thaw cycle. The DNA is conjugated to AuNPs during freezing without additional reagents and the conjugation can be completed in a few minutes.

Two Completely Different Mechanisms for Highly Specific Na Recognition by DNAzymes.

Our view of the interaction between Na and nucleic acids was changed by a few recently discovered Na -specific RNA-cleaving DNAzymes. In addition to nonspecific electrostatic interactions, highly specific recognition is also possible. Herein, two such DNAzymes, named EtNa and Ce13d, are compared to elucidate their mechanisms of Na binding.

Metal Sensing by DNA.

Metal ions are essential to many chemical, biological, and environmental processes. In the past two decades, many DNA-based metal sensors have emerged. While the main biological role of DNA is to store genetic information, its chemical structure is ideal for metal binding via both the phosphate backbone and nucleobases.

New insights into a classic aptamer: binding sites, cooperativity and more sensitive adenosine detection.

The DNA aptamer for adenosine (also for AMP and ATP) is a highly conserved sequence that has recurred in a few selections. It it a widely used model aptamer for biosensor development, and its nuclear magnetic resonance structure shows that each aptamer binds two AMP molecules. In this work, each binding site was individually removed by rational sequence design, while the remaining site still retained a similar binding affinity and specificity as confirmed by isothermal titration calorimetry.

Enhanced DNA sensitized Tb luminescence in organic solvents for more sensitive detection.

DNA-sensitized Tb luminescence spectroscopy is a powerful method for probing nucleic acids and developing biosensors. Its performance in organic solvents has yet to be explored. In this study, Tb luminescence with nucleosides, nucleotides and DNA oligonucleotides in various organic solvents is studied.

Dipole Orientation Matters: Longer-Circulating Choline Phosphate than Phosphocholine Liposomes for Enhanced Tumor Targeting.

Zwitterionic phosphocholine (PC) liposomes are widely used in drug delivery because of their high biocompatibility and long blood circulation time. We herein report that by flipping the direction of the PC dipole, the resulting choline phosphate (CPe) liposomes have an even longer circulation time, as confirmed at both cellular and animal-model levels. Even when 33% cholesterol was included in the lipid formulation with a poly(ethylene glycol) layer, the CPe liposome still had a longer blood circulation time.

Poly-cytosine DNA as a High-Affinity Ligand for Inorganic Nanomaterials.

Attaching DNA to nanomaterials is the basis for DNA-directed assembly, sensing, and drug delivery using such hybrid materials. Poly-cytosine (poly-C) DNA is a high affinity ligand for four types of commonly used nanomaterials, including nanocarbons (graphene oxide and single-walled carbon nanotubes), transition metal dichalcogenides (MoS and WS ), metal oxides (Fe O and ZnO), and metal nanoparticles (Au and Ag). Compared to other homo-DNA sequences, poly-C DNA has the highest affinity for the first three types of materials.