Oligonucleotide probes containing polylysine residues for fabrication of DNA chips on various solid surfaces

Methods of the Synthesis of Silicon-Containing Nanoparticles Intended for Nucleic Acid Delivery

A promising new approach to the treatment of viral infections and genetic diseases associated with damaged or foreign nucleic acids in the body is gene therapy, i.e., the use of antisense oligonucleotides, ribozymes, deoxyribozymes, siRNA, plasmid DNA, etc. (therapeutic nucleic acids). Selective recognition of target nucleic acids by these compounds based on highly specific complementary interaction can minimize negative side effects, which occur with currently used low molecular weight drugs. To apply a new generation of therapeutic agents in medical practice, it is necessary to solve the problem of their delivery into cells. Silicon-containing nanoparticles are considered as promising carriers for this purpose due to their biocompatibility, low toxicity, ability to biodegradation and excretion from the body, as well as the simplicity of the synthesis and modification. Silicon-containing nanoparticles are divided into two broad categories: solid (nonporous) and mesoporous silicon nanoparticles (MSN). This review gives a brief overview of the creation of mesoporous, multilayer, and other silicon-based nanoparticles. The publications concerning solid silicon-organic nanoparticles capable of binding and delivering nucleic acids into cells are discussed in more detail with emphasis on methods for their synthesis. The review covers publications over the past 15 years, which describe the classical Stöber method, the microemulsion method, modification of commercial silica nanoparticles, and other strategies.

Efficient inhibition of influenza A viral replication in cells by deoxyribozymes delivered by nanocomposites

Nucleic-acid-based drugs are a promising class of novel therapeutics; however, their use in medicine is widely limited because of insufficient delivery into cells. This article proposes a new delivery strategy of nucleic acid fragments into cells as components of TiO₂-based nanocomposites. For the first time, unmodified Dz molecules were non-covalently immobilized on TiO₂ nanoparticles precovered with polylysine (TiO₂•PL) with the formation of (TiO₂•PL)•Dz nanocomposites. DNAzymes in the proposed nanocomposites were shown to retain their ability to cleave the RNA target in a cell-free system with the same selectivity as unbound Dz molecules. It was shown by confocal laser microscopy that the fluorescein-labelled (TiO₂•PL)•Dz^Flu nanocomposites penetrate into eukaryotic cells, where Dz^Flu is internalized in the cytoplasm and predominantly in nuclei. Delivery of deoxyribozymes into cells in the proposed nanocomposites permits very efficient interactions with RNA targets inside cells. This was demonstrated by an example of inhibition of H5N1 influenza A virus replication (inhibition by a factor of ca. 3000). This effect was one order of magnitude higher than with using lipofectamine as the transfection agent. The proposed (TiO₂•PL)•Dz nanocomposites demonstrated high antiviral activity and are thus potent as nucleic-acid-based drugs.

SiO₂ nanoparticles as platform for delivery of 3'-triazole analogues of AZT-triphosphate into cells

A system for delivery of analogues of AZT-triphosphates (AZT*TP) based on SiO₂ nanoparticles was proposed. For this purpose, a simple and versatile method was developed for the preparation of SiO₂∼dNTP conjugates using the 'click'-reaction between AZTTP and premodified nanoparticles containing the alkyne groups. The substrate properties of SiO₂∼AZT*TP were tested using Klenow fragment and HIV reverse transcriptase. The 3'-triazole derivatives of thymidine triphosphate being a part of the SiO₂∼AZT*TP nanocomposites were shown to be incorporated into the growing DNA chain. It was shown by confocal microscopy that the proposed SiO₂∼AZT*TP nanocomposites penetrate into cells. These nanocomposites were shown to inhibit the reproduction of POX and Herpes viruses at nontoxic concentrations.

[TiO2-DNA nanocomposites capable of penetrating into cells]

Methods of noncovalent immobilization of DNA fragments onto titanium dioxide nanoparticles (TiO2) were developed, which led to TiO2-DNA nanocomposites capable of penetrating through cell membranes. TiO2 nanoparticles of different forms (amorphous, anatase, brookit) with enhanced agglomeration stability were synthesized. The particles were characterized by X-ray diffraction, small angle X-ray scattering, infrared spectroscopy and atomic force microscopy. Three approaches to the preparation of nanocomposites are described: (1) sorption of polylysine-containing oligonucleotides onto TiO2-nanoparticles, (2) the electrostatic binding of oligonucleotides to TiO2 nanoparticles bearing immobilized polylysine, and (3) sorption of oligonucleotides on TiO2 nanoparticles in the presence of cetavlon. All three methods provide an efficient and stable immobilization of DNA fragments onto nanoparticles, which leads to nanocomposites with a density for an oligonucleotide up to 40 nmol/mg. It is shown that DNA fragments in nanocomposites retain their ability to form complementary complexes and can be delivered into cells without transfection agents and other methods of exposure.

High-performance method for specific effect on nucleic acids in cells using TiO2~DNA nanocomposites

Nanoparticles are used to solve the current drug delivery problem. We present a high-performance method for efficient and selective action on nucleic acid target in cells using unique TiO₂·PL-DNA nanocomposites (polylysine-containing DNA fragments noncovalently immobilized onto TiO₂ nanoparticles capable of transferring DNA). These nanocomposites were used for inhibition of human influenza A (H3N2) virus replication in infected MDCK cells. They showed a low toxicity (TC₅₀ ≈ 1800 μg/ml) and a high antiviral activity (>99.9% inhibition of the virus replication). The specificity factor (antisense effect) appeared to depend on the delivery system of DNA fragments. This factor for nanocomposites is ten-times higher than for DNA in the presence of lipofectamine. IC₅₀ for nanocomposites was estimated to be 1.5 μg/ml (30 nM for DNA), so its selectivity index was calculated as ~1200. Thus, the proposed nanocomposites are prospective for therapeutic application.

An examination of the ability of titanium dioxide nanoparticles and its conjugates with oligonucleotides to penetrate into eucariotis cells

In this study we examine the possibility that TiO₂ nanoparticles and their conjugates can penetrate into cultivated cells without any special transfection procedures. Oligonucleotides and their derivates were conjugated with the TiO₂ nanoparticles, which were obtained as colloidal solutions at a concentration of TiO₂ 0.3M by TiCl₄ hydrolysis. The electronic microscopy of various cell cultures (KCT, Vero, and MDCK) treated with nanoparticle solutions (20 µg/µl) showed that nanoparticles could enter the cells and accumulate in the vacuoles and phagosomes and form inclusions in cytoplasm. Thus, we demonstrated the penetration of TiO₂ nanoparticles and their oligonucleotide conjugates into intracellular space without any auxiliary operations. Most other researches used electroporation techniques for similar purposes [1, 2, 5].

An inexpensive and simple method for thermally stable immobilization of DNA on an unmodified glass surface: UV linking of poly(T)10-poly(C)10-tagged DNA probes

Microarrays printed on glass slides are often constructed by covalently linking modified oligonucleotide probes to a derivatized surface at considerable expense. In this article, we demonstrate that 14-base oligonucleotides with a poly(T)10 - poly(C)10 tail (TC tag), but otherwise unmodified, can be linked by UV light irradiation onto a plain, unmodified glass surface. Probes immobilized onto unmodified glass microscope slides performed similarly to probes bound to commercial amino-silane-coated slides and had comparable detection limits. The TC-tagged probes linked to unmodified glass did not show any significant decrease in hybridization performance after a 20 min incubation in water at 100 degrees C prior to rehybridization, indicating a covalent bond between the TC tag and unmodified glass. The probes were used in thermal minisequencing cycling reactions. Furthermore, the TC tag improved the hybridization performance of the immobilized probes on the amino-silane surface, indicating a general benefit of adding a TC tag to DNA probes. In conclusion, our results show that using TC-tagged DNA probes immobilized on an unmodified glass surface is a robust, heat-stable, very simple, and inexpensive method for manufacturing DNA microarrays.