SPE and purification of DNA using magnetic particles

Superparamagnetic particles have been attractive for molecular diagnostics and analytical chemistry applications due to their unique magnetic properties and their ability to interact with various biomolecules of interest. This paper presents a critical overview of magnetic nano ‐ and microparticles used as a solid phase for extraction and purification of DNAs. The mechanisms of DNA binding to the surface of functionalised magnetic particles are described. The most widely used materials including silica supports, organic polymers and other materials, mostly containing magnetite or paramagnetic metallic elements are reviewed. The main application areas of magnetic particles for DNA separation are briefly described.     

Attachment and detachment of particles to and from fluid interfaces

In this topical review, we commemorate some of the outstanding contributions of Prof. Peter Kralchevsky in the field of colloid and interface science. In particular, we focus on his achievements on phenomena involving the attachment and detachment of colloidal particles to and from fluid interfaces, giving a personal perspective on how his work has inspired our own research and the activities of a thriving scientific community. We specifically concentrate our presentation on the issues of emulsion stability via particle adsorption and desorption, particle organization via capillary immersion forces and on the relevance of electrostatic barriers to spontaneous particle adsorption. This review takes the reader through numerous developments, from the early ‘90s to the present day, and reflects on the importance of the legacy of the work of Prof. Kralchevsky for the years to come.     

Fabrication and characterization of gold nano particles for DNA biosensor applications

This research involves the preparation of a biosensor using silicon oxide for biomedical applications, and its effective use for the detection of target DNA hybridization. An electrochemical DNA biosensor was successfully fabricated by using(3-aminopropyl) tri-ethoxysilane(APTES) as a linker molecule combined with gold nanoparticles(GNPs) on a thermally oxidized SiO_2 thin film. The size of the GNPs was calculated by utilizing UV–vis data with an average calculated particle size within the range of 30±5 nm, and characterization by transmission electron microscopy(TEM) and atomic force microscopy(AFM). The GNP-modified SiO_2 thin films were electrically characterized through the measurement of capacitance, permittivity and conductivity using a low-cost dielectric analyzer. The capacitance, permittivity and conductivity profiles of the fabricated sensor clearly differentiated DNA immobilization and hybridization.     

Isolation of microbial DNA by newly designed magnetic particles

Carboxyl group-containing magnetic nonporous poly(2-hydroxyethyl methacrylate-co-glycidyl methacrylate) (P(HEMA-co-GMA)) microspheres and cobalt ferrite nanoparticles modified with alginic acid (natural carboxylic polysaccharide) were used for isolation of microbial DNA of lactic acid bacteria (LAB) from dairy products, lyophilised cell cultures, and bacterial colonies grown on hard media, and Trichophyton fungi DNA from lyophilised cells. DNA from the samples with lysed cells was reversibly adsorbed to the particles in the presence of high poly(ethylene glycol) (PEG 6000) and sodium chloride concentrations. The optimal final PEG and NaCl concentrations were 9.1 wt.% and 2.0 M, respectively. The adsorbed DNA was released from the particles in low ionic strength TE buffer. The quality of isolated DNA was checked by PCR amplification. Moreover, PCR amplicons were isolated on cobalt ferrite nanoparticles modified with alginic acid and checked by restriction analysis.     

From structure to function: methods and applications

The rapid increase in experimental data along with recent progress in computational methods has brought modern biology a step closer toward solving one of the most challenging problems: prediction of protein function. Comprehension of protein function at its most basic level requires understanding of molecular interactions. Currently, it is becoming universally accepted that the scale of the accumulated data for analysis and for prediction necessitate highly efficient computational tools with appropriate application capabilities. The review presents the up-to-date advances in computational methods for structural pattern discovery and for prediction of molecular associations. We focus on their applications toward a range of biological problems and highlight the advantages of the combination of these methods and their integration with biological experiments. We provide examples, synergistically merging structural modeling, rigid and flexible structural alignment and detection of conserved structural patterns and docking (rigid and flexible with hinge-bending movements). We hope the review will lead to a broader utilization of computational methods, and their cross-fertilization with experiment.     

化学修饰的寡核苷酸: 合成、性质和应用

本文综述了近年来化学修饰的寡核苷酸研究的进展,介绍了化学修饰的寡核苷酸的种类, 化学合成方法, 生物作用原理及应用方面已达到的成継34This review deals with the progress in the research of chemically modified oligonucleotides: the synthesis, the chemical and biological properties and the potential applications as a new research tool and new therapeutic approach.     

Amplified DNA sensing and immunosensing by the rotation of functional magnetic particles

Amplified chemiluminescent detection of DNA-complementary DNA or of antigen-antibody interactions is accomplished in the presence of rotating functionalized magnetic particles.     

Hollow latex particles: synthesis and applications

One of the major developments in emulsion polymerization over the last two decades has been the ability to make hollow latex particles. This has contributed many fundamental insights into the synthesis and the development of structure in particles. Hollow latex particles also enhance the performance of industrial coatings and potentially are useful in other technologies such as microencapsulation and controlled release. Ever since the publication of the initial process patents describing these particles, there has been a global R&D effort to extend the synthetic techniques and applications. One prominent synthetic approach to hollow particles is based on osmotic swelling. This dominates the literature, and usually starts with the synthesis of a structured latex particle containing an ionizable core that is subsequently expanded with the addition of base. Fundamental to this approach are a sophisticated control of transport phenomena, chemical reactivity within the particle, and the thermoplastic properties of the polymer shell. Hydrocarbon encapsulation technology has also been employed to make hollow latex particles. One approach involves a dispersed ternary system that balances transport, conversion kinetics, and phase separation variables to achieve the hollow morphology. Other techniques, including the use of blowing agents, are also present in the literature. The broad range of approaches that affords particles with a hollow structure demonstrates the unique flexibility of the emulsion polymerization process.     

Click chemistry to construct fluorescent oligonucleotides for DNA sequencing

"Click chemistry" 1,3-dipolar cycloaddition between alkynyl 6-carboxyfluorescein (FAM) and azido-labeled single-stranded (ss) DNA was carried out under aqueous conditions to produce FAM-labeled ssDNA in quantitative yield. The FAM-labeled ssDNA was successfully used as a primer to produce DNA sequencing products with single-base resolution in a capillary electrophoresis DNA sequencer with laser-induced fluorescence detection.     

Attachment of Single-Stranded DNA to Certain SERS-Active Gold and Silver Substrates: Selected Practical Tips

Layers formed from single-stranded DNA on nanostructured plasmonic metals can be applied as “working elements” in surface–enhanced Raman scattering (SERS) sensors used to sensitively and accurately identify specific DNA fragments in various biological samples (for example, in samples of blood). Therefore, the proper formation of the desired DNA layers on SERS substrates is of great practical importance, and many research groups are working to improve the process in forming such structures. In this work, we propose two modifications of a standard method used for depositing DNA with an attached linking thiol moiety on certain SERS-active structures; the modifications yield DNA layers that generate a stronger SERS signal. We propose: (i) freezing the sample when forming DNA layers on the nanoparticles, and (ii) when forming DNA layers on SERS-active macroscopic silver substrates, using ω-substituted alkanethiols with very short alkane chains (such as cysteamine or mercaptopropionic acid) to backfill the empty spaces on the metal surface unoccupied by DNA. When 6-mercapto-1-hexanol is used to fill the unoccupied places on a silver surface (as in experiments on standard gold substrates), a quick detachment of chemisorbed DNA from the silver surface is observed. Whereas, using ω-substituted alkanethiols with a shorter alkane chain makes it possible to easily form mixed DNA/backfilling thiol monolayers. Probably, the significantly lower desorption rate of the thiolated DNA induced by alkanethiols with shorter chains is due to the lower stabilization energy in monolayers formed from such compounds.     

Parameter space minimization methods: applications to Lennard-Jones-dipole-dipole clusters

The morphology of the uniform Lennard-Jones-dipole-dipole cluster with 13 centers (LJDD)13 is investigated over a relatively wide range of values of the dipole moment. We introduce and compare several necessary modifications of the basin-hopping algorithm for global optimization to improve its efficiency. We develop a general algorithm for T=0 Brownian dynamics in curved spaces, and a graph theoretical approach necessary for the elimination of dissociated states. We find that the (LJDD)13 cluster has icosahedral symmetry for small to moderate values of the dipole moment. As the dipole moment increases, however, its morphology shifts to an hexagonal antiprism, and eventually to a ring.     

Oxazine ring construction: methods and applications to natural product synthesis

Although natural products containing a 1,2-oxazine ring are rare, more examples in this family of natural products have been discovered since trichodermamides A and B were reported in 2003. In addition to their structural novelty, these natural products possess very interesting bioactivities that are strongly dependent on their structures, making them attractive targets for investigating structure-activity relationships (SAR). In this feature article, we summarized the methodologies developed in recent years for constructing the 1,2-oxazine rings. Racemic and enantioselective total syntheses of trichodermamides A and B, based on these methodologies, are reviewed in detail.     

Foldamer simulations: novel computational methods and applications to poly-phenylacetylene oligomers

We apply several methods to probe the ensemble kinetic and structural properties of a model system of poly-phenylacetylene (pPA) oligomer folding trajectories. The kinetic methods employed included a brute force accounting of conformations, a Markovian state matrix method, and a nonlinear least squares fit to a minimalist kinetic model used to extract the folding time. Each method gave similar measures for the folding time of the 12-mer chain, calculated to be on the order of 7 ns for the complete folding of the chain from an extended conformation. Utilizing both a linear and a nonlinear scaling relationship between the viscosity and the folding time to correct for a low simulation viscosity, we obtain an upper and a lower bound for the approximate folding time within the range 70 ns相似文献   

Photoaddition of 4,6-dimethyltetrahydrobenzoangelicin to thymine in DNA: X-ray studies and experiments with model oligonucleotides

The crystal structures of 4,6-dimethyltetrahydrobenzoangelicin (THBA), a furocoumarin analog, and of its furan-side cis-syn cycloadduct with thymine formed in the photoreaction with DNA, have been determined. The crystal structure of the latter compound contained only one enantiomeric form corresponding to the addition to a 5'-XpT site. Contrary to most psoralen derivatives studied, THBA showed higher photoreactivity toward synthetic oligonucleotides containing that sequence than toward those with the 5'-TpX sequence.     

A guide to design the trajectory of active particles: From fundamentals to applications

Active particles convert external energy into motility, displaying a variety of dynamical features. Recent progress in the field has marked a shift in focus from understanding the origin and sources of active motion to controlling the dynamics and trajectory of individual microswimmers. This review explores the advancements made in a two-fold perspective—the role of particle design and that of external factors. Our main goal is to highlight the guiding principles, which determine active particle trajectory. These include, on the one hand, the role of the morphology of active particles and their assemblies in driving translation, rotation, and corresponding coupling between the two. On the other hand, the effect of environmental parameters such as the presence of physicochemical heterogeneities including interfaces, suspended obstacles, and boundaries on the modality and trajectory of active colloids. We discuss the potential of using active particles in biomedical and environmental applications through recent examples.     

Electron injection into DNA: synthesis and spectroscopic properties of pyrenyl-modified oligonucleotides

The nucleoside 5-(1-pyrenyl)-2'-deoxyuridine (1) was prepared by a Suzuki-Miyaura cross-coupling reaction and subsequently used as a DNA building block in order to prepare a range of modified oligonucleotides using phosphoramidite chemistry. The DNA duplexes contain a pyrenyl group covalently attached to the nucleobase uracil. Upon excitation at 340 nm an intramolecular electron transfer from the pyrenyl group to the uracil moiety takes place which represents an injection of an excess electron into the DNA base stack. Based on the results obtained by steady-state fluorescence and time-resolved pump-probe laser spectroscopy it was possible to show that base-to-base electron transfer can occur from the Py-dU group only to adjacent thymines.     

Quenching of fluorophore-labeled DNA oligonucleotides by divalent metal ions: implications for selection, design, and applications of signaling aptamers and signaling deoxyribozymes

Recent years have seen a dramatic increase in the use of fluorescence-signaling DNA aptamers and deoxyribozymes as novel biosensing moieties. Many of these functional single-stranded DNA molecules are either engineered to function in the presence of divalent metal ion cofactors or designed as sensors for specific divalent metal ions. However, many divalent metal ions are potent fluorescence quenchers. In this study, we first set out to examine the factors that contribute to quenching of DNA-bound fluorophores by commonly used divalent metal ions, with the goal of establishing general principles that can guide future exploitation of fluorescence-signaling DNA aptamers and deoxyribozymes as biosensing probes. We then extended these studies to examine the effect of specific metals on the signaling performance of both a structure-switching signaling DNA aptamer and an RNA-cleaving and fluorescence-signaling deoxyribozyme. These studies showed extensive quenching was obtained when using divalent transition metal ions owing to direct DNA-metal ion interactions, leading to combined static and dynamic quenching. The extent of quenching was dependent on the type of metal ion and the concentration of supporting monovalent cations in the buffer, with quenching increasing with the number of unpaired electrons in the metal ion and decreasing with the concentration of monovalent ions. The extent of quenching was independent of the fluorophore, indicating that quenching cannot be alleviated simply by changing the nature of the fluorescent probe. Our results also show that the DNA sequence and the local secondary structure in the region of the fluorescent tag can dramatically influence the degree of quenching by divalent transition metal ions. In particular, the extent of quenching is predominantly determined by the fluorophore location with respect to guanine-rich and duplex regions within the strand sequence. Examination of the effect of both the type and concentration of metal ions on the performance of a fluorescence-signaling aptamer and a signaling deoxyribozyme confirms that judicious choice of divalent transition metal ions is important in maximizing signals obtained from such systems.