Self-assembly of stable monomolecular nucleic acid lipid particles with a size of 30 nm

The design of efficient nucleic acid complexes is key to progress in genetic research and therapies based on RNA interference. For optimal transport within tissue and across extracellular barriers, nucleic acid carriers need to be small and stable. In this Article, we prepare and characterize mono-nucleic acid lipid particles (mono-NALPs). The particles consist of single short double-stranded oligonucleotides or single siRNA molecules each encapsulated within a closed shell of a cationic-zwitterionic lipid bilayer, furnished with an outer polyethylene glycol (PEG) shield. The particles self-assemble by solvent exchange from a solution containing nucleic acid mixed with the four lipid components DOTAP, DOPE, DOPC, and DSPE-PEG(2000). Using fluorescence correlation spectroscopy, we monitor the formation of mono-NALPs from short double-stranded oligonucleotides or siRNA and lipids into monodisperse particles of approximately 30 nm in diameter. Small angle neutron and X-ray scattering and transmission electron microscopy experiments substantiate a micelle-like core-shell structure of the particles. The PEGylated lipid shell protects the nucleic acid core against degradation by nucleases, sterically stabilizes the mono-NALPs against disassembly in collagen networks, and prevents nonspecific binding to cells. Hence, PEG-lipid shielded mono-NALPs are the smallest stable siRNA lipid system possible and may provide a structural design to be built upon for the development of novel nucleic acid delivery systems with enhanced biodistribution in vivo.     

RESISTANCE OF THE SCRAPIE AGENT TO INACTIVATION BY PSORALENS

–In searching for a nucleic acid within the scrapie agent, we employed psoralens which penetrate the coats of most conventional viruses, form photoadducts with their genomes, and block replication of the viruses. Five psoralens, at concentrations up to 500 times greater than those required to inactivate conventional viruses, did not influence scrapie agent titers in partially purified preparations from murine spleen and hamster brain. ³H-psoralens were used to monitor the formation of photoadducts within nucleic acid standards added to preparations of the scrapie agent. Since no inhibition of psoralen photoadduct formation was observed in these preparations, one of three possibilities seems likely: the scrapie agent is devoid of nucleic acid, the psoralens failed to penetrate the protein coat of the agent, or its nucleic acid is unreactive with psoralens.     

Nucleic acid biosensors for environmental pollution monitoring

Nucleic acid-based biosensors are finding increasing use for the detection of environmental pollution and toxicity. A biosensor is defined as a compact analytical device incorporating a biological or biologically-derived sensing element either integrated within or intimately associated with a physicochemical transducer. A nucleic acid-based biosensor employs as the sensing element an oligonucleotide, with a known sequence of bases, or a complex structure of DNA or RNA. Nucleic acid biosensors can be used to detect DNA/RNA fragments or either biological or chemical species. In the first application, DNA/RNA is the analyte and it is detected through the hybridization reaction (this kind of biosensor is also called a genosensor). In the second application, DNA/RNA plays the role of the receptor of specific biological and/or chemical species, such as target proteins, pollutants or drugs. Recent advances in the development and applications of nucleic acid-based biosensors for environmental application are reviewed in this article with special emphasis on functional nucleic acid elements (aptamers, DNAzymes, aptazymes) and lab-on-a-chip technology.     

Programming Non-Nucleic Acid Molecules into Computational Nucleic Acid Systems

Nucleic acid (NA) computation has been widely developed in the past years to solve kinds of logic and mathematic issues in both information technologies and biomedical analysis. However, the difficulty to integrate non-NA molecules limits its power as a universal platform for molecular computation. Here, we report a versatile prototype of hybridized computation integrated with both nucleic acids and non-NA molecules. Employing the conformationally controlled ligand converters, we demonstrate that non-NA molecules, including both small molecules and proteins, can be computed as nucleic acid strands to construct the circuitry with increased complexity and scalability, and can be even programmed to solve arithmetical calculations within the computational nucleic acid system. This study opens a new door for molecular computation in which all-NA circuits can be expanded with integration of various ligands, and meanwhile, ligands can be precisely programmed by the nuclei acid computation.     

Progress on Detection of Metals Ions by Functional Nucleic Acids Biosensor

Functional nucleic acids are natural or artificial nucleic acid sequences with specific functions and special structures. A part of metal ions are essential trace elements of human health, but excessive metal ions will be harmful to human health. The functional nucleic acids are widely used for detection of metal ions because of its advantages such as easy modification, low price, high stability and strong specificity. This paper detailed the interaction between functional nucleic acids and metal ions, mainly including cutting type, link type, metal ion-mediated base pairing, click chemistry type, conformational change type, and other types. The biosensors based on the combination of functional nucleic acid with different signal output were then introduced. Finally, the research significance and existing problems of functional nucleic acid for metal ion detection were discussed. The future development trends and applications of functional nucleic acid biosensor were prospected.     

Invited Article Liquid-crystalline dispersions of nucleic acids

The formation and properties of dispersions of double stranded natural and synthetic nucleic acids are described. Evidence is given for the liquid-crystalline state of the nucleic acid within the dispersed droplets in these phases. The exploitation of nucleic acid dispersions in biosensors is discussed.     

Supramolecular Materials Comprising Nucleic Acid Biopolymers

We have generated a supramolecular self-assembling film by exchanging the counter-ions of the phosphate moieties in nucleic acid with those of cationic amphiphiles as didodecyldimethylammonium bromide (or DDAB). SAXS and WAXS data for all film samples showed similar harmonic peaks suggesting a lamellar multilayer structure with layers of nucleic acids being separated by lipid bilayers of DDAB. AFM height images also showed that double stranded nucleic acid film can form the step or plateau type of structure and shorter nucleic acid film showed shorter step feature. Moreover, the length and the molecular structure of DNA and RNA can be used to manipulate the mechanical properties of these self-assembled films.     

Chimeric GNA/DNA metal-mediated base pairs

DNA double helices comprising chimeric GNA/DNA metal-mediated base pairs have been synthesized and characterized (GNA = glycol nucleic acid). The possibility to combine different nucleic acid backbones within one metal-mediated base pair expands the applicability of metal-functionalized nucleic acids.     

Mapping of surrogate markers of cellular components and structures using laser desorption/ionization mass spectrometry

Laser desorption/ionization mass spectrometry (LDI-MS) has been used to assess the potential of using surrogate markers, bound to cellular structures containing nucleic acids, to image or map the position of these structures within biological samples. In this study, organic dyes were used as markers because of their established use in the histochemical marking of nucleic acids, and also because they are amenable to LDI-MS. Eight cationic dyes were tested and all could be desorbed from nucleic acid samples without additional matrix after specifically binding to these molecules. Methylene Blue was the best of these based on its sensitivity to detection by LDI-MS and the fact that it can be washed from the tissue in areas where it was not specifically bound to provide low-intensity background signals. Experiments are reported which characterize the M(+) ion signal obtained from Methylene Blue with regard to sensitivity, reproducibility and possible use for quantitation. This dye was used to map (with a lateral resolution of 25 microm) several nucleic acid-containing samples spotted on prepared surfaces, and to image the location of nucleic acids in two model tissues, retinal vertical sections and thyroid whole mount sections.     

A microfluidic device that generates hydroxyl radicals to probe the solvent accessible surface of nucleic acids

We describe a microfluidic device containing a mineral matrix capable of rapidly generating hydroxyl radicals that enables high-resolution structural studies of nucleic acids. Hydroxyl radicals cleave the solvent accessible backbone of DNA and RNA; the cleavage products can be detected with as fine as single nucleotide resolution. Protection from hydroxyl radical cleavage (footprinting) can identify sites of protein binding or the presence of tertiary structure. Here we report preparation of micron sized particles of iron sulfide (pyrite) and fabrication of a microfluidic prototype that together generate enough hydroxyl radicals within 20 ms to cleave DNA sufficiently for a footprinting analysis to be conducted. This prototype enables the development of high-throughput and/or rapid reaction devices with which to probe nucleic acid folding dynamics and ligand binding.     

Nucleic Acid Nanoprobes for Biosensor Development in Complex Matrices

Nucleic acid probes in living organisms play an essential role in therapeutics and diagnosis.Through the imaging and sensing of nucleic acid probes in complex biological matrices,a variety of diseases-related biological process,pathogenic process,or pharmacological responses to a therapeutic intervention have been discovered.However,a critical challenge of nucleic acid probes applied in complex matrices lies in enhancing the stability of nucleic acid probes,especially when it suffers from nuclease degradation and protein adsorption.In order to enhance the application of nucleic acid nanoprobes in complex matrices,great efforts have been devoted to improving the stability of probes operated in complex media,including construction of nucleic acid nanoprobes with nuclease resistance and protein adsorption resistance,sample pretreatment,anti-biofouling and signal correction.In this review,we aim to summarize recent advances in the stability of nucleic acid nanoprobes in complex matrices,including the methods of enhancing the stability of probes or signals,and the application of nucleic acid nanoprobes for disease diagnosis.     

Surface-modified silica colloid for diagnostic imaging

A method of preparing nanometer-sized oxide colloids suitable as substance carriers for size-sensitive diagnostic imaging and other biomedical applications is described. The nanometer-sized silica particles prepared by the Stober process were reacted with silane to obtain amine-terminated colloidal surfaces under aqueous conditions. The surface-modified colloids can be further treated to combine or conjugate with imaging agents and other diagnostic or therapeutic substances. The water-stable colloidal carriers are spherical and have a narrow size distribution that can be controlled to range from 10 to 200 nm.     

Electron radiation damage of MCM-41 and related materials.

The article compares the relative stability of MCM-41 and related mesoporous materials in electron beam at an accelerating voltage of 100-300 kV. The work encountered in electron microscopy presents a comparison with similar research that has been carried out on nonporous and microporous silicates, especially alpha-quartz and zeolite Y. The trends in stability are analyzed, classifying the effects of sample preparation, organic and inorganic moieties, and electron accelerating voltage on beam stability. A higher synthesis temperature, the use of an acid catalyst in the synthesis, and the presence of additional organic or inorganic material within the channels were all found to stabilize these materials. The dose required to completely disrupt the structure increased with accelerating voltage for nearly all samples, suggesting a primarily radiolytic damage mechanism. The exception, MCM-41 containing nanometer-sized titania particles in its channels, was found to be almost insensitive to accelerating voltage.     

(S,S)-trans-cyclopentane-constrained peptide nucleic acids. a general backbone modification that improves binding affinity and sequence specificity

Replacing the ethylenediamine portion of aminoethylglycine peptide nucleic acids (aegPNAs) with one or more (S,S)-trans-cyclopentane diamine units significantly increases binding affinity and sequence specificity to complementary DNA, making these modified PNAs ideal for use as nucleic acid probes in genomic analysis. The synthesis and study of this new class of PNAs (tcypPNAs) is described in which trans-cyclopentane diamine has been incorporated into several positions, and in varying number, within PNA backbones of mixed-base sequences.     

Rapid automatic nucleic acid purification system based on gas–liquid immiscible phase

The continuous expansion of nucleic acid detection applications has resulted in constant developments in rapid, low-consumption, and highly automated nucleic acid extraction methods. Nucleic acid extraction using magnetic beads across an immiscible phase interface offers significant simplification and parallelization potential. The gas–liquid immiscible phase valve eliminates the requirement for complicated cassettes and is suitable for automation applications. By analyzing the process of magnetic beads crossing the gas-liquid interface, we utilized a low magnetic field strength to drive large magnetic bead packages to cross the gas-liquid interface, providing a solution of high magnetic bead recovery rate for solid-phase extraction with a low-surfactant system based on gas-liquid immiscible phase valve. The recovery rate of magnetic beads was further improved to 90%–95% and the carryover of the reagents was below 1%. Consequently, a chip and an automatic system were developed to verify the applicability of this method for nucleic acid extraction. The Hepatitis B virus serum standard was used for the extraction test. The extraction of four samples was performed within 7 minutes, with nucleic acid recovery maintained above 80% and good purity. Thus, through analysis and experiments, a fast, highly automated, and low-consumption nucleic acid recovery method was proposed in this study.     

Subnanomolar Detection of Oligonucleotides through Templated Fluorogenic Reaction in Hydrogels: Controlling Diffusion to Improve Sensitivity

Oligonucleotide‐templated reactions are valuable tools for nucleic acid sensing both in vitro and in vivo. They are typically carried out under conditions that make any reaction in the absence of template highly unfavorable (most commonly by using a low concentration of reactants), which has a negative impact on the detection sensitivity. Herein, we report a novel platform for fluorogenic oligonucleotide‐templated reactions between peptide nucleic acid probes embedded within permeable agarose and alginate hydrogels. We demonstrate that under conditions of restricted mobility (that is, limited diffusion), non‐specific interactions between probes are prevented, thus leading to lower background signals. When applied to nucleic acid sensing, this accounts for a significant increase in sensitivity (that is, lower limit of detection). Optical nucleic acid sensors based on fluorogenic peptide nucleic acid probes embedded in permeable, physically crosslinked, alginate beads were also engineered and proved capable of detecting DNA concentrations as low as 100 pm .     

Point of attachment and sequence of immobilized peptide-acridine conjugates control affinity for nucleic acids

Screening of combinatorial libraries by spatial arraying strategies requires library members to be solid-phase immobilized. However, for nucleic acid ligands that bind via intercalation, immobilization may inhibit binding if the tethering functionality is present at the edge of the heterocyle that approaches the duplex during the binding reaction. We report here a method for immobilizing peptide-acridine conjugates (PACs) via either their C- or their N-terminus, corresponding to functionalization at either the 4- or the 9-position of acridine, respectively, and for assaying the nucleic acid binding properties of the resulting resins. We find that both the amino acid sequence of the PAC as well as its point of attachment to the solid support are important in determining affinity for duplex nucleic acids. These results have implications for the design of future on-bead and microarray-based selections and in understanding the nucleic acid binding of functionalized intercalators.     

Study on the interaction between nucleic acids and cationic surfactants

The interactions of nucleic acids and cationic surfactants (cetylpyridine bromide (CPB) and cetyltrimethylammonium bromide (CTMAB)) in aqueous solution have been studied using the techniques of resonance light scattering (RLS) spectroscopy, the absorption spectroscopy, zeta potential assay and NMR assignment measurement. It is considered that CPB or CTMAB can assemble on the surface of nucleic acid via electrostatic and hydrophobic forces, which results in the formation of large associate of nucleic acid-cationic surfactant and RLS enhancement of nucleic acid. Besides these forces, the pi-pi stacking force between CPB and nucleic acid also exists in the associate. In comparison with CTMAB, CPB has larger enhancement on RLS of nucleic acid, which is attributed to that the enhancement of the former is only due to the absorption of the bases of nucleic acid, while the enhancement of the latter is own to the synergetic resonance caused by the absorption of both bases of nucleic acid and the pyridyl in CPB. These results have important implication for understanding the influence of surfactants on nucleic acid functionality in life science.     

Nucleic acid encoding to program self-assembly in chemical biology

This tutorial review serves as an introduction to the use of oligonucleotides and in particular peptide nucleic acids (PNAs) to encode function beyond heredity. Applications in chemical biology are reviewed starting with the use of nucleic acid tags to program self-assembled microarrays of small and macromolecules, followed by the use of nucleic acid templated reactions for the purpose of DNA or RNA sensing and finally, the use of nucleic acid templates to display ligands.     

Microfluidic bead-based multienzyme-nanoparticle amplification for detection of circulating tumor cells in the blood using quantum dots labels

This study reports the development of a microfluidic bead-based nucleic acid sensor for sensitive detection of circulating tumor cells in blood samples using multienzyme-nanoparticle amplification and quantum dot labels. In this method, the microbeads functionalized with the capture probes and modified electron rich proteins were arrayed within a microfluidic channel as sensing elements, and the gold nanoparticles (AuNPs) functionalized with the horseradish peroxidases (HRP) and DNA probes were used as labels. Hence, two signal amplification approaches are integrated for enhancing the detection sensitivity of circulating tumor cells. First, the large surface area of Au nanoparticle carrier allows several binding events of HRP on each nanosphere. Second, enhanced mass transport capability inherent from microfluidics leads to higher capture efficiency of targets because continuous flow within micro-channel delivers fresh analyte solution to the reaction site which maintains a high concentration gradient differential to enhance mass transport. Based on the dual signal amplification strategy, the developed microfluidic bead-based nucleic acid sensor could discriminate as low as 5 fM (signal-to-noise (S/N) 3) of synthesized carcinoembryonic antigen (CEA) gene fragments and showed a 1000-fold increase in detection limit compared to the off-chip test. In addition, using spiked colorectal cancer cell lines (HT29) in the blood as a model system, the detection limit of this chip-based approach was found to be as low as 1 HT29 in 1 mL blood sample. This microfluidic bead-based nucleic acid sensor is a promising platform for disease-related nucleic acid molecules at the lowest level at their earliest incidence.