Alpha-LNA (locked nucleic acid with alpha-D-configuration): synthesis and selective parallel recognition of RNA

Alpha-LNA is presented as a stereoisomer of LNA (locked nucleic acid) with alpha-D-configuration. Three different approaches towards the thymine alpha-LNA monomer as well as the 5-methylcytosine alpha-LNA monomer are presented. Different alpha-LNA sequences have been synthesised and their hybridisation with complementary DNA and RNA has been evaluated by means of thermal stability experiments and circular dichroism spectroscopy. In a mixed pyrimidine sequence, alpha-LNA displays unprecedented parallel-stranded and selective RNA binding. Furthermore, a remarkable selectivity for hybridisation with RNA over DNA is indicated.     

Polymer functionalized submicrometric emulsions as potential synthetic DNA vectors

Triglyceride-based emulsions were first prepared by a solvent displacement procedure which was modified to achieve their functionalization by surface deposition of various amphiphilic comb-like copolymers. These emulsions have been characterized as regards to hydrodynamic particle size and surface charges using dynamic light scattering and electrophoretic mobility measurements. The adsorption isotherms of a polydT15 oligonucleotide and a model plasmid showed that the process was dependent on the nature of the interfaces, the affinity for the nucleic acid increasing with more cationic charges, together with improved accessibility. The binding process was found to proceed according to two regimes: one at low nucleic acid coverage, independent of the initial plasmid concentration, and the second one at high coverage, which was nucleic-acid-concentration dependent. This behavior was considered to occur because of the development of repulsive interactions upon increasing the amount of immobilized nucleic acid. The complexation of plasmid complexed at the interface was finally investigated using the ethidium bromide displacement technique. The level of compaction of plasmid complexed onto the functionalized emulsions was lower than that obtained with the parent free polymer.     

Convergent strategies for the attachment of fluorescing reporter groups to peptide nucleic acids in solution and on solid phase

The site-selective conjugation of peptide nucleic acids (PNA) with fluorescent reporter groups is essential for the construction of hybridisation probes that can report the presence of a particular DNA sequence. This paper describes convergent methods for the solution- and solid-phase synthesis of multiply labelled PNA oligomers. The solid-phase synthesis of protected PNA enabled the selective attachment of fluorescent labels at the C-terminal end (3' in DNA) which demonstrated that further manipulations on protected PNA fragments are feasible. For the conjugation to internal sites, a method is introduced that allows for the on-resin assembly of modified monomers thereby omitting the need to synthesise an entire monomer in solution. Furthermore, it is shown that the application of a highly orthogonal protecting group strategy in combination with chemoselective conjugation reactions provides access to a rapid and automatable solid-phase synthesis of dual labelled PNA probes. Real-time measurements of nucleic acid hybridisation were possible by taking advantage of the fluorescence resonance energy transfer (FRET) between suitably appended fluorophoric groups. Analogously to DNA-based molecular beacons, the dual labelled PNA probes were only weakly fluorescing in the single-stranded state. Hybridisation to a complementary oligonucleotide, however, induced a structural reorganisation and conferred a vivid fluorescence enhancement.     

Synthetic oligonucleotides: AFM characterisation and electroanalytical studies

One of the most important steps in designing more sensitive and stable DNA based biosensors is the immobilisation procedure of the nucleic acid probes on the transducer surface, while maintaining their conformational flexibility. MAC Mode AFM images in air demonstrated that the oligonucleotide sequences adsorb spontaneously on the electrode surface, showing the existence of pores in the adsorbed layer that reveal big parts of the electrode surface, which enables non-specific adsorption of other molecules on the uncovered areas. The electrostatic immobilisation onto a glassy carbon electrode followed by hybridisation with a complementary sequence and control with a non-complementary sequence was studied using differential pulse voltammetry and electrochemical impedance spectroscopy. Changes in the oxidation currents of guanosine and adenosine were observed after hybridisation events as well as after control experiments. Modification of the double layer capacitance that took place after hybridisation or control experiments showed that non-specific adsorption of complementary or non-complementary sequences occur allowing the formation of a mixed multilayer.     

Retention mechanism of L-glutamide-derived noncrystalline stationary phases in reversed-phase high-performance liquid chromatography and application for separation of nucleic acid constituents

Double alkylated L-glutamide-derived noncrystalline stationary phases Sil-DSG and Sil-DBG have been prepared by coupling N',N'-dioctadecyl-N-[4-carboxybutanoyl]-L-glutamide (DSG) and N',N',-dibutyl-N-[4-carboxybutanoyl]-L-glutamide (DBG) with aminopropylated silica (Sil-APS). TEM observations of DSG and DBG showed that lipid DSG can aggregate in organic solvents (methanol, chloroform, toluene, etc.) and self-assembled nano fibers are observed while such fibrous aggregations are not observed for DBG. The resulting chromatographic data have been provided information about its selective interaction with guest molecules (PAHs) in RP-HPLC. We have observed that the carbonyl groups in Sil-DSG exist in ordered state by forming a condensing thin layer over silica surface while DBG cannot form such an ordered state due to its lower order of short alkyl chain. The ordered carbonyl groups present in Sil-DSG promotes multiple carbonyl pi-benzene pi interactions with guest PAHs isomers which enhance the selectivity for these compounds. The contribution of pi-pi interactions was also supported by the substantial effects on the selectivity of benzene and nitrobenzenes. The effect of pi-electron containing solvent on the retention behavior of the PAHs was also studied. The selectivity for nucleic acid constituents, i.e. nucleosides and its bases were also evaluated by Sil-DSG and the selectivity for these compounds on Sil-DSG was compared with the selectivity of conventional polymeric ODS phase. It has been found that Sil-DSG provided higher selectivity for nucleic acid constituents than polymeric ODS and that HPLC packing materials can be efficiently employed for routine analysis of these compounds. The effect of methanol content on the separation behavior of nucleosides was also studied.     

A label-free electrochemical DNA biosensor based on a Zr(IV)-coordinated DNA duplex immobilised on a carbon nanofibre|chitosan layer

A label-free electrochemical biosensor for detecting DNA hybridisation was developed by monitoring the change in the voltammetric activity of ferrocenecarboxylic acid at the biosensor–solution interface. The biosensor was constructed by initially immobilising on a glassy carbon electrode an anchoring layer consisting of chitosan, carboxyl group functionalised carbon nanofibres and glutaraldehye. Chitosan acted as an adhering agent and carbon nanofibres were strategically used to provide a large surface area with binding points for DNA immobilisation, while glutaraldehye was a linker for DNA probes on the electrode surface. Based on a two-factorial design, cyclic voltammetry of [Fe(CN)₆]^3−/4− was performed to optimise the composition of the anchoring layer. Next, a 17-base pair DNA probe was attached to the anchoring layer, followed by its complementary target. Zr(IV) ion, known to exhibit affinity for oxygen-containing electroactive markers, for example, ferrocenecarboxylic acid, was then coordinated in the DNA duplex. In this way, ferrocenecarboxylic acid was attracted towards the biosensor for oxidation. A change in the voltammetric oxidation current of ferrocenecarboxylic acid pre- and post-hybridisation was used to provide an indication of hybridisation. A linear dynamic range between 0.5 and 40 nM and a detection limit of 88 pM of DNA target were then achieved. In addition, the biosensor exhibited good selectivity, repeatability and stability for the determination of DNA sequences.     

Solid composite electrodes for DNA enrichment and detection

New plastic composite electrodes with appliance in medical diagnostic are described. The new electrode material offers the possibility of specific electrical enrichment and electrochemical analysis of nucleic acid sequences. To facilitate selective enrichment of target nucleic acids, specific probe oligonucleotides were attached covalently to free carboxyl groups of conducting polycarbonate/carbon fiber electrodes. Complementary oligonucleotides were enriched from analyte solutions by electric field supported methods. The analysis of the PCR product shows the efficiency and selectivity of the electrical enrichment. We have also shown that inexpensive and robust solid electrodes made of polycarbonate and conductive carbon powder are suitable for electrochemical examination of nucleic acids. The combination of electrochemical enrichment of DNA and subsequent electrochemical detection is a promising approach towards an inexpensive molecular diagnosis kit.     

Impedimetric immunosensor using avidin-biotin for antibody immobilization

A newly developed electrochemical method--Elimination Voltammetry with Linear Scan (EVLS)--has been applied to the electrochemical study of nucleic acids (NAs) on a silver electrode. Using the linear combination of the currents measured at different scan rates, the EVLS is capable of eliminating one or two selected particular currents. It was shown that the elimination function conserving the reversible diffusion current and eliminating the charging and kinetic currents provides the significant increase of voltammetric signals of DNA. Due to the high sensitivity and resolution power, the EVLS can contribute to study behaviour of nucleic acids on the charged interface and can be applied to nucleic acid analyses and the development of DNA sensors.     

Electrochemical genosensors for the detection of Bonamia parasite. Selection of single strand-DNA (ssDNA) probes by simulation of the secondary structure folding

A post-PCR nucleic acid work by comparing experimental data, from electrochemical genosensors, and bioinformatics data, derived from the simulation of the secondary structure folding and prediction of hybridisation reaction, was carried out in order to rationalize the selection of ssDNA probes for the detection of two Bonamia species, B. exitiosa and B. ostreae, parasites of Ostrea edulis.Six ssDNA probes (from 11 to 25 bases in length, 2 thiolated and 4 biotinylated) were selected within different regions of B. ostreae and B. exitiosa PCR amplicons (300 and 304 bases, respectively) with the aim to discriminate between these parasite species. ssDNA amplicons and probes were analyzed separately using the “Mfold Web Server” simulating the secondary structure folding behaviour. The hybridisation of amplicon-probe was predicted by means of “Dinamelt Web Server”. The results were evaluated considering the number of hydrogen bonds broken and formed in the simulated folding and hybridisation process, variance in gaps for each sequence and number of available bases. In the experimental part, thermally denatured PCR products were captured at the sensor interface via sandwich hybridisation with surface-tethered probes (thiolated probes) and biotinylated signalling probes. A convergence between analytical signals and simulated results was observed, indicating the possibility to use bioinformatic data for ssDNA probes selection to be incorporated in genosensors.     

Detection of short oligonucleotide sequences of hepatitis B virus using electrochemical DNA hybridisation biosensor

A novel, sensitive and selective electrochemical hybridisation biosensor was developed for the detection of the hepatitis B virus (HBV) using a manganese(II) complex as electrochemical indicator and a DNA probe-modified carbon paste electrode as the biosensor (DNA/CPE). The results showed that this complex could be accumulated electrochemically the immobilised dsDNA layer rather than in the single-stranded DNA (ssDNA) layer. On the basis of this, the manganese complex was used as an electrochemical hybridisation indicator for the detection of oligonucleotides related to HBV. The hybridisation event was evaluated on the basis of the difference between the reduction signals of the manganese(II) complex with the probe DNA prior to and post hybridisation with a target sequence using a differential pulse mode. Several factors affecting the immobilisation and hybridisation of oligonucleotides as well as the indicator’s accumulation were investigated. Experiments with a non-complementary and mismatch sequences demonstrated the good selectivity of the biosensor. Using this approach, the HBV target oligonucleotide’s sequence could be quantified over arange from 0.22 ng L^?1 to 5.40 ng L^?1, with a linear correlation coefficient of 0.9994 and the limit of detection of 0.07 ng L^?1.     

Detection of Tumor Necrosis Factor Gene by Piezoelectric Nucleic Acid Sensor

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Label-free DNA electrochemical sensor based on a PNA-functionalized conductive polymer

An electrochemical hybridization biosensor based on peptide nucleic acid (PNA) probe is presented. PNA were attached covalently onto a quinone-based electroactive polymer. Changes in flexibility of the PNA probe strand upon hybridization generates electrochemical changes at the polymer-solution interface. A reagentless and direct electrochemical detection was obtained by detection of the electrochemical changes using square wave voltammetry (SWV). An increase in the peak current of quinone was observed upon hybridization of probe on the target, whereas no change is observed with non-complementary sequence. In addition, the biosensor is highly selective to effectively discriminate a single mismatch on the target sequence. The sensitivity is also presented and discussed.     

PNA-based probe for quantitative chemiluminescent in situ hybridisation imaging of cellular parvovirus B19 replication kinetics

To allow the ultrasensitive localization and the quantitative detection of parvovirus B19 nucleic acids in single infected cells at various times post-infection, a peptide nucleic acid (PNA)-based in situ hybridisation (ISH) assay with chemiluminescent detection has been developed. The assay is based on the use of a biotin-labelled PNA probe detected by a streptavidin-linked alkaline phosphatase and a chemiluminescent dioxetane phosphate derivative substrate. The luminescent signal was quantified and imaged with an ultrasensitive nitrogen-cooled CCD camera connected to an epifluorescence microscope. The assay was used to analyze the parvovirus B19 infection process in cell cultures and to quantify the amount of viral nucleic acids at different times after infection.The chemiluminescent ISH-PNA assay is characterized by high resolution providing a sharp localization of B19 nucleic acids within single cells, with higher sensitivity with respect to conventional colorimetric ISH detection. Thanks to the high detectability and wide linear range of chemiluminescence detection, an objective evaluation of the percentage of infected cells, which reached its maximum at 24 h after infection, following a B19 virus infectious cycle could be accurately evaluated. Chemiluminescence detection also allowed the quantitative analysis of viral nucleic acids at the single-cell level, showing a continuous increase of the content of viral nucleic acids in infected cells with time after infection.The developed chemiluminescent ISH-PNA assay could thus represent a potent tool for the assessment of viral infections and for the quantitative evaluation of the virus nucleic acid load of infected cells in virus studies and diagnostics.     

Ratiometric fluorescence transduction by hybridization after isothermal amplification for determination of zeptomole quantities of oligonucleotide biomarkers with a paper-based platform and camera-based detection

Paper is a promising platform for the development of decentralized diagnostic assays owing to the low cost and ease of use of paper-based analytical devices (PADs). It can be challenging to detect on PADs very low concentrations of nucleic acid biomarkers of lengths as used in clinical assays. Herein we report the use of thermophilic helicase-dependent amplification (tHDA) in combination with a paper-based platform for fluorescence detection of probe-target hybridization. Paper substrates were patterned using wax printing. The cellulosic fibers were chemically derivatized with imidazole groups for the assembly of the transduction interface that consisted of immobilized quantum dot (QD)–probe oligonucleotide conjugates. Green-emitting QDs (gQDs) served as donors with Cy3 as the acceptor dye in a fluorescence resonance energy transfer (FRET)-based transduction method. After probe-target hybridization, a further hybridization event with a reporter sequence brought the Cy3 acceptor dye in close proximity to the surface of immobilized gQDs, triggering a FRET sensitized emission that served as an analytical signal. Ratiometric detection was evaluated using both an epifluorescence microscope and a low-cost iPad camera as detectors. Addition of the tHDA method for target amplification to produce sequences of ∼100 base length allowed for the detection of zmol quantities of nucleic acid targets using the two detection platforms. The ratiometric QD-FRET transduction method not only offered improved assay precision, but also lowered the limit of detection of the assay when compared with the non-ratiometric QD-FRET transduction method. The selectivity of the hybridization assays was demonstrated by the detection of single nucleotide polymorphism.     

稀土及其配合物对核酸的断裂作用

人工核酸酶是一类具有限制性内切酶的功能、能高效高选择性地催化水解DNA 或RNA 的断裂工具。它们一般由核酸结构识别系统及催化断裂系统组成, 将两种功能有效地结合起来, 可模拟核酸的酶切反应。本文综述了稀土及其配合物对核酸的断裂作用, 并对其断裂机制进行了探讨。     

Detection of Tumor Necrosis Factor Gene by Piezoelectric Nucleic Acid Senosr

A piezoelectric nucleic acid sensor was constructed ofr detection of tumor necrosis factor gene.Two methods were employed for immobilization of nucleic acid probe on gold electrode of piezoelectric crystal.The results show that polyethyleneimine adbesion and glutaraldehyde cross-linking method has higher sensitivity,stability and selectivity than protein A method.The solid-phase nucleic acid hybridization of oligo unclecotides and tumor necrosis factor target gene sequence were monitorde using this sensor.Tumor necrosis factor gene sequence(580bp) was detected by this nucleic acid sensor for the first time.     

Single-molecule studies on DNA and RNA.

DNA and RNA are the most individual molecules known. Therefore, single-molecule experiments with these nucleic acids are particularly useful. This review reports on recent experiments with single DNA and RNA molecules. First, techniques for their preparation and handling are summarised including the use of AFM nanotips and optical or magnetic tweezers. As important detection techniques, conventional and near-field microscopy as well as fluorescence resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) are touched on briefly. The use of single-molecule techniques currently includes force measurements in stretched nucleic acids and in their complexes with binding partners, particularly proteins, and the analysis of DNA by restriction mapping, fragment sizing and single-molecule hybridisation. Also, the reactions of RNA polymerases and enzymes involved in DNA replication and repair are dealt with in some detail, followed by a discussion of the transport of individual nucleic acid molecules during the readout and use of genetic information and during the infection of cells by viruses. The final sections show how the enormous addressability in nucleic acid molecules can be exploited to construct a single-molecule field-effect transistor and a walking single-molecule robot, and how individual DNA molecules can be used to assemble a single-molecule DNA computer.     

酶放大DNA电化学传感器的研究进展

DNA电化学传感器灵敏度高、选择性好、分析时间短和检测成本低,极大地推动了生物传感器的发展. 结合蛋白质酶、功能核酸酶的催化效率高与特异性好,可提高检测灵敏度和选择性. 本文评述了酶放大DNA电化学传感器的研究进展,并分析现存问题,展望发展趋势.     

用于检测生物体系中线粒体活性氧的荧光探针

In addition to being the energy powerhouse of the cell, mitochondria are an important source of reactive oxygen species (ROS) during the process of molecular oxygen metabolism. Mitochondrial ROS are closely associated with normal physiological functions as well as human diseases, and participate in cell signaling, nucleic acid and protein damage, and oxidative stress induction. However, the complicated interplay between mitochondrial ROS and the cellular pathological state has not been fully elucidated. It is expected that research on the mitochondrial ROS undertaking in the molecular pathogenesis of human diseases would benefit from development of efficient tools for the detection of these ROS. In recent years, an increasing number of fluorescent probes for mitochondrial ROS with high sensitivity and selectivity have been developed. Here, we present a review of the recent advances in small molecular fluorescent probes for selective detection of ROS inside the mitochondria. In this review, the design, synthesis, characteristics, and applications of the published fluorescent probes for mitochondrial ROS are discussed in detail.