Synthesis of thiol-modified peptide nucleic acids designed for post-assembly conjugation reactions

Two orthogonally protected PNA monomers were prepared having the mercaptomethyl moiety attached to the PNA backbone. These building blocks were employed in solid-phase PNA synthesis and it was shown that Boc/S-p-methoxybenzyl protection scheme was only satisfactory for the introduction of N-terminal thiol modification while the Fmoc/S-butylthio protected monomer proved to be amenable to elongation. The mercaptomethyl modification did not influence the thermal stability of a PNA/RNA duplex. The feasibility of PNA-PNA native ligation was demonstrated.     

High sensitivity detection of 16s rRNA using peptide nucleic acid probes and a surface plasmon resonance biosensor

A signal enhancing method allowing highly sensitive detection of E. coli 16s rRNA was developed using peptide nucleic acid (PNA) as a capture probe and a surface plasmon resonance (SPR) sensor as a detector. 16s rRNA has been used as a genetic marker for identification of organisms, and can be analyzed directly without PCR amplification due to the relatively high number of copies. PNA has a neutral backbone structure, therefore hybridization with 16s rRNA results in the ionic condition being changed from neutral to negative. A cationic Au nanoparticle was synthesized and used for signal amplification by ionic interaction with 16s rRNA hybridized on the PNA probe-immobilized SPR sensor chip. This method resulted in a detection limit of E. coli rRNA of 58.2 ± 1.37 pg mL⁻¹. Using this analytical method, Staphylococcus aureus was detected without purification of rRNA.     

Design of a new oligotriazole peptide nucleic acid analogue (oT-PNA)

We describe in this Letter the synthesis of an original thymine azido-heterotrimer generated by Click Chemistry. This trimer has been obtained from an azido-thymidine and a new chloroethyl-propargylated PNA monomer analogue, after two azidation/click-reaction cycles. Conformational preferences of a rotameric intermediate have also been studied     

核酸介导信号放大光学生物传感器在食品污染物检测中的应用EI北大核心CSCD

信号放大是新型生物传感分析过程中重要的环节。核酸介导的信号放大技术凭借核酸材料灵活的结构设计、低成本和易于制备等特点,在生物传感快速检测技术的开发上逐渐发展成为一项重要的分支,广泛应用于食品、环境和医药等新型检测方法开发。介绍了传统和新型核酸扩增技术、生物条形码和DNA walker等信号放大机理和应用,同时进一步综述核酸信号放大技术结合光学生物传感在食品污染物中检测的应用,如化学污染物、毒素类污染物、和重金属污染物等,并对核酸介导的信号放大技术在食品污染物检测中的问题和前景进行讨论。     

Versatile biosensor surface based on peptide nucleic acid with label free and total internal reflection fluorescence detection for quantification of endocrine disruptors

In recent years, the simultaneous detection of hundreds of substances has become increasingly important in medical diagnostics and environmental monitoring. This calls for methods that allow fast and simultaneous measurement of many analytes and require only a minimum of attendance. Biosensor-applications including easy implementation and long-term stability of the sensor element are more and more designed to meet these demands.In this paper, a surface based on covalently immobilised peptide nucleic acid (PNA) for the detection of different endocrine disruptors is used. The surface was characterised with a label free detection system, the reflectometric interference spectroscopy (RIfS). A hybridisation capacity with DNA oligonucleotides of 1.3 ng/mm² (180 fmol/mm²) on PNA-surfaces was achieved. The PNA transducer is stable for half a year and for more than 300 regeneration steps.With this modified surface various environmentally relevant endocrine disruptors could be detected by an immunoassay. The detection is done on an optical waveguide system, based on total internal reflection fluorescence (TIRF) by using an auxiliary-system consisting of a conjugate which is formed of DNA-oligomers and analyte-derivatives. The successive detection of different analytes on the same spot by using this auxiliary-system is demonstrated as one application of multianalyte detection. Quantification of different endocrine disruptors on the same PNA-surface is demonstrated by three calibration curves.     

Synthesis and photo activity of phenylazonaphthalene peptide nucleic acid monomers

Phenylazonaphthalene peptide nucleic acid （PNA） monomers were successfully synthesized, and their photoisomerization was examined. The new PNA monomers showed reversible trans-cis isomerization with UVand visible light irradiation, which might be the foundation of photo-regulating the hybridization between PNA containing phenylazonaphthalene unit and DNA. Simultaneously, the fluorescence of the new PNA monomers might make them especially useful as structural probes.     

Template tailoring: Accurate determination of heterozygous alleles using peptide nucleic acid and dideoxyNTP

Measurement of the length of DNA fragments plays a pivotal role in genetic mapping, disease diagnostics, human identification and forensic applications. PCR followed by electrophoresis is used for DNA length measurement of STRs, a process that requires labeled primers and allelic ladders as standards to avoid machine error. Sequencing‐based approaches can be used for STR analysis to eliminate the requirement of labeled primers and allelic ladder. However, the limiting factor with this approach is unsynchronized polymerization in heterozygous sample analysis, in which alleles with different lengths can lead to imbalanced heterozygote peak height ratios. We have developed a rapid DNA length measurement method using peptide nucleic acid and dideoxy dNTPs to “tailor” DNA templates for accurate sequencing to overcome this hurdle. We also devised an accelerated “dyad” pyrosequencing strategy, such that the combined approach can be used as a faster, more accurate alternative to de novo sequencing. Dyad sequencing interrogates two bases at a time by allowing the polymerase to incorporate two nucleotides to DNA template, cutting the analysis time in half. In addition, for the first time, we show the effect of peptide nucleic acid as a blocking probe to stop polymerization, which is essential to analyze the heterozygous samples by sequencing. This approach provides a new platform for rapid and cost‐effective DNA length measurement for STRs and resequencing of small DNA fragments.     

Electroactive chitosan nanoparticles for the detection of single-nucleotide polymorphisms using peptide nucleic acids

Here we report an electrochemical biosensor that would allow for simple and rapid analysis of nucleic acids in combination with nuclease activity on nucleic acids and electroactive bionanoparticles. The detection of single-nucleotide polymorphisms (SNPs) using PNA probes takes advantage of the significant structural and physicochemical differences between the full hybrids and SNPs in PNA/DNA and DNA/DNA duplexes. Ferrocene-conjugated chitosan nanoparticles (Chi-Fc) were used as the electroactive indicator of hybridization. Chi-Fc had no affinity towards the neutral PNA probe immobilized on a gold electrode (AuE) surface. When the PNA probe on the electrode surface hybridized with a full-complementary target DNA, Chi-Fc electrostatically attached to the negatively-charged phosphate backbone of DNA on the surface and gave rise to a high electrochemical oxidation signal from ferrocene at ∼0.30 V. Exposing the surface to a single-stranded DNA specific nuclease, Nuclease S1, was found to be very effective for removing the nonspecifically adsorbed SNP DNA. An SNP in the target DNA to PNA made it susceptible to the enzymatic digestion. After the enzymatic digestion and subsequent exposure to Chi-Fc, the presence of SNPs was determined by monitoring the changes in the electrical current response of Chi-Fc. The method provided a detection limit of 1 fM (S/N = 3) for the target DNA oligonucleotide. Additionally, asymmetric PCR was employed to detect the presence of genetically modified organism (GMO) in standard Roundup Ready soybean samples. PNA-mediated PCR amplification of real DNA samples was performed to detect SNPs related to alcolohol dehydrogenase (ALDH). Chitosan nanoparticles are promising biometarials for various analytical and pharmaceutical applications. Figure The electrochemical method for SNP detection using PNA probes and chitosan nanoparticles takes advantage of the significant structural and physicochemical differences between PNA/DNA and DNA/DNA duplexes. Single-stranded DNA specific enzymes selectively choose these SNP sites and hydrolyze the DNA molecules on gold electrode (AuE) surface. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

New synthesis of a spin-labeled peptide nucleic acid and its interactions with nucleic acids

A new combined solid-liquid phase synthesis method for a spin labeled peptide nucleic acid (PNA) is developed. The methodology involved initial preparation of a protected PNA on solid phase, followed by efficient solution phase coupling to a spin label containing a reactive carboxylic group. This strategy allows to maintain the integrity of the nitroxide moiety during the various steps of chemical synthesis assuring in the same time the fidelity of the hybridization assay. This compound can be used as a reporter molecule to investigate the binding of peptide nucleic acids to oligonucleotide sequences (DNA or RNA) by EPR spectroscopy.     

Design of a sensitive aptasensor based on magnetic microbeads-assisted strand displacement amplification and target recycling

A cross-circular amplification system for sensitive detection of adenosine triphosphate (ATP) in cancer cells was developed based on aptamer–target interaction, magnetic microbeads (MBs)-assisted strand displacement amplification and target recycling. Here we described a new recognition probe possessing two parts, the ATP aptamer and the extension part. The recognition probe was firstly immobilized on the surface of MBs and hybridized with its complementary sequence to form a duplex. When combined with ATP, the probe changed its conformation, revealing the extension part in single-strand form, which further served as a toehold for subsequent target recycling. The released complementary sequence of the probe acted as the catalyst of the MB-assisted strand displacement reaction. Incorporated with target recycling, a large amount of biotin-tagged MB complexes were formed to stimulate the generation of chemiluminescence (CL) signal in the presence of luminol and H₂O₂ by incorporating with streptavidin-HRP, reaching a detection limit of ATP as low as 6.1 × 10⁻¹⁰ M. Moreover, sample assays of ATP in Ramos Burkitt's lymphoma B cells were performed, which confirmed the reliability and practicality of the protocol.     

Simultaneous photoelectrochemical detection of dual microRNAs by capturing CdS quantum dots and methylene blue based on target-initiated strand displaced amplification

Herein,we propose a novel photoelectrochemical(PEC) biosensor for dual microRNAs(miRNAs) highly sensitive and simultaneous biosensing based on strand displaced amplification(SDA) reaction.The recognition of H_(miR-21) and H_(let-7 a) by microRNA-21 and let-7 a leads to their change in hairpin structures,subsequently initiating the immobilization of abundant CdS quantum dots(CdS QD s) and methylene blue(MB) based on SDA reaction.The immobilized CdS QDs and MB produce both high PEC currents under430 nm light and 627 nm light illumination,respectively,and the generated PEC currents are closely relied on target miRNAs amounts.Thus,highly sensitive and simultaneous detection of microRNA-21 and let-7 a was readily achieved with detection limit at 6.6 fmol/L and 15.4 fmol/L based on 3σ,respectively.Further,this PEC biosensor was applied in simultaneous analysis of miRNA-21 and let-7 a in breast cancer patient's serum with acceptable results.We expect this biosensor will find more useful application in diagnosis of miRNA-related diseases.     

Rapid label-free visual assay for the detection and quantification of viral RNA using peptide nucleic acid (PNA) and gold nanoparticles (AuNPs)

A rapid label-free visual assay for the detection of viral RNA using peptide nucleic acid (PNA) probes and gold nanoparticles (AuNPs) is presented in this study. Diagnosis is a crucial step for the molecular surveillance of diseases, and a rapid visual test with high specificity could play a vital role in the management of viral diseases. In this assay, the specific agglomerative behavior of PNA with gold nanoparticles was manipulated by its complementation with viral RNA. The assay was able to detect 5–10 ng of viral RNA from various biological samples, such as allantoic fluids, cell culture fluids and vaccines, in 100 μl of test solution. The developed assay was more sensitive than a hemagglutination (HA) test, a routine platform test for the detection of Newcastle disease virus (NDV), and the developed assay was able to visually detect NDV with as little as 0.25 HA units of virus. In terms of the specificity, the test could discriminate single nucleotide differences in the target RNA and hence could provide visual viral genotyping/pathotyping. This observation was confirmed by pathotyping different known isolates of NDV. Further, the PNA-induced colorimetric changes in the presence of the target RNA at different RNA to PNA ratios yielded a standard curve with a linear coefficient of R² = 0.990, which was comparable to the value of R² = 0.995 from real-time PCR experiments with the same viral RNA. Therefore, the viral RNA in a given samples could be quantified using a simple visual spectrophotometer available in any clinical laboratory. This assay may find application in diagnostic assays for other RNA viruses, which are well known to undergo mutations, thus presenting challenges for their molecular surveillance, genotyping and quantification.     

Two successive reactions on a DNA template: a strategy for improving background fluorescence and specificity in nucleic acid detection

We report a new strategy for template-mediated fluorogenic chemistry that results in enhanced performance for the fluorescence detection of nucleic acids. In this approach, two successive templated reactions are required to induce a fluorescence signal, rather than only one. These novel fluorescein-labeled oligonucleotide probes, termed 2-STAR (STAR = Staudinger-triggered α-azidoether release) probes, contain two quencher groups tethered by separate reductively cleavable linkers. When a 2-STAR quenched probe successively binds adjacent to two mono-triphenylphosphine-(TPP)-DNAs or one dual-TPP-DNA, the two quenchers are released, resulting in a fluorescence signal. Because of the requirement for two consecutive reactions, 2-STAR probes display an unprecedented level of sequence specificity for template-mediated probe designs. At the same time, background emission generated by off-template reactions or incomplete quenching is among the lowest of any fluorogenic reactive probes for the detection of DNA or RNA.     

Combining G-quadruplex targeting motifs on a single peptide nucleic acid scaffold: a hybrid (3+1) PNA-DNA bimolecular quadruplex

We describe the first G-quadruplex targeting approach that combines intercalation and hybridization strategies by investigating the interaction of a G-rich peptide nucleic acid (PNA) acridone conjugate 1 with a three-repeat fragment of the human telomere G 3 to form a hybrid PNA-DNA quadruplex that mimicks the biologically relevant (3+1) pure DNA dimeric telomeric quadruplex. Using a combination of UV and fluorescence spectroscopy, circular dichroism (CD), and mass-spectrometry, we show that PNA 1 can induce the formation of a bimolecular hybrid quadruplex even at low salt concentration upon interaction with a single-stranded three-repeat fragment of telomeric DNA. However, PNA 1 cannot invade a short fragment of B-DNA even if the latter contains a CCC motif complementary to the PNA sequence. These studies could open up new possibilities for the design of a novel generation of quadruplex ligands that target not only the external features of the quadruplex but also its central core constituted by the tetrads themselves.     

Label-free and non-enzymatic detection of DNA based on hybridization chain reaction amplification and dsDNA-templated copper nanoparticles

A label-free and non-enzymatic amplification fluorescent method for detection of DNA has been developed by using hybridization chain reaction (HCR) and dsDNA-templated copper nanoparticles (CuNPs). First, the biotinylated capture DNA probes were immobilized on the streptavidin-modified beads through the interaction of biotin and streptavidin. Then, target DNA hybridized with the capture DNA probes, which formed a hybridized DNA with sticky end. The sticky end triggered the HCR process and formation of dsDNA polymers while two hairpin probes coexisted. Subsequently, the dsDNA polymers were employed as template for synthesis of CuNPs with excellent fluorescent properties, which provided a label-free, non-enzymatic signal response. Meanwhile, the fluorescence sensing depended on the target DNA triggered HCR, which render this method a high selectivity against single-base mismatch sequences. The concept and methodology developed in this work show great promise in the quantitative detection of DNA in biological and medical applications.     

Simultaneous electrochemical detection of multiple tumor markers based on dual catalysis amplification of multi-functionalized onion-like mesoporous graphene sheets

In this work, a sandwich-type electrochemical immunosensor for simultaneous sensitive detection of prostate specific antigen (PSA) and free prostate specific antigen (fPSA) is fabricated. Gold nanoparticles (AuNPs) modified Prussian blue and nickel hexacyanoferrates nanoparticles were firstly prepared, respectively, and then decorated onion-like mesoporous graphene sheets (denoted as Au@PBNPs/O-GS and Au@NiNPs/O-GS) as distinguishable signal tags to label different detection antibodies. Subsequently, streptavidin and biotinylated alkaline phosphatase (bio-AP) were employed to block the possible remaining active sites. With the employment of the as prepared nanohybrids, the dual catalysis amplification can be achieved by catalysis of the ascorbic acid 2-phosphate to in situ produce AA in the presence of bio-AP, and then AA was further catalyzed by Au@PBNPs/O-GS and Au@NiNPs/O-GS nanohybrids, respectively, to obtain the higher signal responses. The experiment results show that the linear range of the proposed immunosensor for simultaneous determination of fPSA is from 0.02 to 10 ng mL⁻¹ with a detection limit of 6.7 pg mL⁻¹ and PSA is from 0.01 to 50 ng mL⁻¹ with a detection limit of 3.4 pg mL⁻¹ (S/N = 3). Importantly, the proposed method offers promise for rapid, simple and cost-effective analysis of biological samples.     

Electrochemical biosensor for detection of BCR/ABL fusion gene based on hairpin locked nucleic acids probe

This communication reports on a novel biosensor to study the hybridization specificity by using thiolated hairpin locked nucleic acids (LNA) as the capture probe. The LNA probe was immobilized on the gold electrode through sulfur–Au interaction and could selectively hybridize with its target DNA. Differential pulse voltammetry (DPV) was used to monitor the hybridization reaction on the probe electrode. The decrease of the peak current of methylene blue, an electroactive indicator, was observed upon hybridization of the probe with the target DNA. The results indicated this new method has excellent specificity for single-base mismatch and complementary after hybridization, and a high sensitivity. This LNA probe has been used for assay of fusion gene in Chronic Myelogenous Leukemia (CML) of the real sample with satisfactory result.     

Sensitive determination of phenylarsenic compounds based on a dual preconcentration method with capillary electrophoresis/UV detection

A novel method based on off-line hollow fiber based liquid liquid liquid microextraction (HF-LLLME) combined with on-column anion selective exhaustive injection (ASEI)-capillary electrophoresis/ultraviolet (CE/UV) detection was proposed for the speciation of five phenylarsenic compounds including phenylarsonic acid (PAA), 4-aminophenylarsonic acid (4-APAA), 4-hydroxyphenylarsonic acid (4-HPAA), 4-nitrophenylarsonic acid (4-NPAA) and 3-nitro-4-hydroxyphenylarsonic acid (NHPAA) in this paper. In HF-LLLME, the target analytes were extracted from 5 mL aqueous samples (donor solution pH 2.15) through a thin phase of tributyl phosphate (TBP) inside the pores of a polypropylene hollow fiber and finally into an 18 μL 0.8 mmol/L Tris acceptor solution inside the lumen of the hollow fiber. Following HF-LLLME, the acceptor solutions were directly analyzed by ASEI-CE/UV. For ASEI, a large plug of water (91% length of total capillary) was introduced into the separation capillary before sample injection in order to prolong the sample injection time, and thus enhance the stacking efficiency. Under the optimized ASEI conditions, up to 236-fold of enrichment factor (EF) was obtained for the ASEI-CE/UV determination of target phenylarsenic compounds. By combining HF-LLLME with ASEI-CE/UV, EFs ranging from 155 to 1780-fold were achieved and the limits of detection (LODs) (at a signal-to-noise ratio of 3) were in the range of 0.68-6.90 μg/L for five phenylarsenic compounds; the relative standard deviations (RSDs) of corrected peak area were 5.6-11.8%. The proposed HF-LLLME-ASEI-CE/UV method was applied for the determination of five target phenylarsenic compounds in pig feed from a local pig farm, and storage pig litter, soil in agricultural field and lake water collected near this pig farm, the recoveries for the spiked samples were in the range of 85.7-104.5%, 66.7-96.2%, 28.9-46.9% and 86.9-107.8% for pig feed, pig litter, soil and lake water, respectively.     

Hg and Cu selective detection using a dual channel receptor based on thiopyrylium scaffoldings

2,4,6-Triphenylthiopyrylium functionalized with an aza-oxa-thia macrocycle is able to selectively recognize Hg²⁺ cation by a color change and Cu²⁺ cation by a remarkable significant emission enhancement.