Synthesis and oligodeoxynucleotide binding properties of pyrrolidinyl peptide nucleic acids bearing prolyl-2-aminocyclopentanecarboxylic acid (ACPC) backbones

A series of novel conformationally rigid pyrrolidinyl peptide nucleic acids (PNA) based on d-prolyl-2-aminocyclopentanecarboxylic acid (ACPC) backbones has been synthesized. Investigation of the binding properties of four stereoisomeric PNAs possessing different stereochemistry at the ACPC part with DNA revealed that a precise stereochemistry of the backbone is very important in determining the binding properties. Only the PNA containing (1S,2S)-ACPC can form a very stable 1:1 complex with the complementary DNA in a sequence-specific manner.     

Cyanuryl peptide nucleic acid: synthesis and DNA complexation properties

The synthesis of cyanuryl PNA monomer (CyaPNA) 6 was achieved by direct N-monoalkylation of cyanuric acid with N-(2-Boc-aminoethyl)-N′-(bromoacetyl)glycyl ethyl ester 4. Compound 6 was incorporated as a T-mimic into PNA oligomers and biophysical studies on their triplexes/duplex complexes with complementary DNA oligomers indicated unusual stabilization of PNA:DNA hybrids when the cyanuryl unit was located in the middle of the PNA oligomer.     

Synthesis and nucleic acid binding studies of novel pyrrolidinyl PNA carrying an N-amino-N-methylglycine spacer

Two novel pyrrolidinyl peptide nucleic acids comprising alternating sequences of thymine-modified d- or l-proline and an N-amino-N-methylglycine spacer were synthesized using solid-phase methodology. UV and CD titrations together with a gel-binding shift assay revealed that neither of the homothymine PNA decamers bind to their complementary DNA or RNA. This was considered to be due to an unfavorable secondary structure which could not be alleviated by the presence of the positively charged protonated amine in the PNA backbone.     

A novel approach for the detection of DNA using immobilized peptide nucleic acid (PNA) probes and signal enhancement by real-time immuno-polymerase chain reaction (RT-iPCR)

A new approach for the detection of DNA target molecules is described, using capture probes and subsequent signal enhancement by a uniform polymerase chain reaction (PCR). Peptide nucleic acid probes were immobilized in real-time PCR-compatible microtiter plates. After hybridization of biotinylated DNA targets, detection was performed by real-time immuno-PCR, a method formerly used for protein detection. We demonstrate the feasibility of this strategy for the qualitative detection of DNA oligonucleotides with a detection limit (LOD) of 6 attomol. Furthermore, the method was applied to PCR-amplified samples from genetically modified maize DNA (Mon810). A 483-bp DNA fragment was detected in mixture with 99.9% of noncomplementary DNA with a sensitivity down to the level of attomole. Figure       

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.     

Poly(o-phenylenediamine) colloid-quenched fluorescent oligonucleotide as a probe for fluorescence-enhanced nucleic acid detection

In this Letter, we demonstrate that chemical oxidation polymerization of o-phenylenediamine (OPD) by potassium bichromate at room temperature results in the formation of submicrometer-scale poly(o-phenylenediamine) (POPD) colloids. Such colloids can absorb and quench dye-labeled single-stranded DNA (ssDNA) very effectively. In the presence of a target, a hybridization event occurs, which produces a double-stranded DNA (dsDNA) that detaches from the POPD surface, leading to recovery of dye fluorescence. With the use of an oligonucleotide (OND) sequence associated with human immunodeficiency virus (HIV) as a model system, we demonstrate the proof of concept that POPD colloid-quenched fluorescent OND can be used as a probe for fluorescence-enhanced nucleic acid detection with selectivity down to single-base mismatch.     

A novel sandwich assay with molecular beacon as report probe for nucleic acids detection on one-dimensional microfluidic beads array

A novel sandwich assay with molecular beacons as report probes has been developed and integrated into one-dimensional microfluidic beads array (1-D chip) to pursue a label-free and elution-free detection of DNA/mRNA targets. In contrast with the immobilized molecular beacons, this sandwich assay can offer lower fluorescence background and correspondingly higher sensitivity. Furthermore, this sandwich assay on 1-D chip operating in conjunction with molecular beacon technique allows multiple targets detection without the need of laborious and time-consuming elution, which makes the experiment process simple, easy to handle, and reproducible results. In the experiment, the synthesized DNA targets with different concentrations were detected with a detection limit of ∼0.05 nM. Moreover, the mRNA expression changes in A549 cells before and after anticancer drug 5-flouorouracil treatments were detected and the results were validated by the conventional RT-PCR method.     

A new cyano-substituted fluorescamine superior to its original form as a fluorescent probe for amino acid detection

Synthesis and spectral study of two new cyano-substituted fluorescamine as the fluorescent probes for amino acid detection have been carried out comparing with the original fluorescamine. Of the three compounds, the derivative with a cyano group at the meta-position on the 4-phenyl group was found to be superior to the original one in the reactivity toward some amino acids as well as the fluorescence intensity of the adducts. The fluorescent amino acid adducts were also applied to the peroxyoxalate chemiluminescence system as the fluorophores, in which the derivative described above was found to be more effective also in chemiluminescence than the original one.     

Terbium fluorescence as a sensitive,inexpensive probe for UV-induced damage in nucleic acids

Much effort has been focused on developing methods for detecting damaged nucleic acids. However, almost all of the proposed methods consist of multi-step procedures, are limited, require expensive instruments, or suffer from a high level of interferences. In this paper, we present a novel simple, inexpensive, mix-and-read assay that is generally applicable to nucleic acid damage and uses the enhanced luminescence due to energy transfer from nucleic acids to terbium(III) (Tb³⁺). Single-stranded oligonucleotides greatly enhance the Tb³⁺ emission, but duplex DNA does not. With the use of a DNA hairpin probe complementary to the oligonucleotide of interest, the Tb³⁺/hairpin probe is applied to detect ultraviolet (UV)-induced DNA damage. The hairpin probe hybridizes only with the undamaged DNA. However, the damaged DNA remains single-stranded and enhances the intrinsic fluorescence of Tb³⁺, producing a detectable signal directly proportional to the amount of DNA damage. This allows the Tb³⁺/hairpin probe to be used for sensitive quantification of UV-induced DNA damage. The Tb³⁺/hairpin probe showed superior selectivity to DNA damage compared to conventional molecular beacons probes (MBs) and its sensitivity is more than 2.5 times higher than MBs with a limit of detection of 4.36 ± 1.2 nM. In addition, this probe is easier to synthesize and more than eight times cheaper than MBs, which makes its use recommended for high-throughput, quantitative analysis of DNA damage.     

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.     

Fluorescent detection of single nucleotide polymorphism utilizing a hairpin DNA containing a nucleotide base analog pyrrolo-deoxycytidine as a fluorescent probe

A novel fluorescent method for the detection of single nucleotide polymorphism (SNP) was developed using a hairpin DNA containing nucleotide base analog pyrrolo-deoxycytidine (P-dC) as a fluorescent probe. This fluorescent probe was designed by incorporating a fluorescent P-dC into a stem of the hairpin DNA, whose sequence of the loop moiety complemented the target single strand DNA (ss-DNA). In the absence of the target ss-DNA, the fluorescent probe stays a closed configuration in which the P-dC is located in the double strand stem of the fluorescent probe, such that there is weak fluorescence, attributed to a more efficient stacking and collisional quenching of neighboring bases. In the presence of target ss-DNA, upon hybridizing the ss-DNA to the loop moiety, a stem-loop of the fluorescent probe is opened and the P-dC is located in the ss-DNA, thus resulting in strong fluorescence. The effective discrimination of the SNP, including single base mismatch ss-DNA (A, T, G) and double mismatch DNA (C, C), against perfect complementary ss-DNA was achieved by increased fluorescence intensity, and verified by thermal denaturation and circular dichroism spectroscopy. Relative fluorescence intensity had a linear relationship with the concentration of perfect complementary ss-DNA and ranged from 50 nM to 3.0 μM. The linear regression equation was F/F₀ = 2.73 C (μM) + 1.14 (R = 0.9961) and the detection limit of perfect complementary ss-DNA was 16 nM (S/N = 3). This study demonstrates that a hairpin DNA containing nucleotide base analog P-dC is a promising fluorescent probe for the effective discrimination of SNP and for highly sensitive detection of perfect complementary DNA.     

DNA-, RNA- and self-pairing properties of a pyrrolidinyl peptide nucleic acid with a (2′R,4′S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbone

A new pyrrolidinyl peptide nucleic acid (PNA) comprising of an alternate sequence of 4′-nucleobase-modified proline with (2′R,4′S) configuration and a (1S,2S)-2-aminocyclopentanecarboxylic acid [(2′R,4′S)-acpcPNA] backbone was synthesized and its DNA-, RNA- and self-pairing properties studied. T_m and CD studies suggested that the (2′R,4′S)-acpcPNA forms antiparallel hybrids to DNA and RNA with high sequence and direction specificity. The stability of these hybrids is comparable to those of the (2′R,4′R)-acpcPNA hybrids previously reported by our group. On the other hand, experiments with a self-complementary sequence indicated that the new (2′R,4′S)-acpcPNA forms a more stable antiparallel self-hybrid than (2′R,4′R)-acpcPNA.     

A TCF-based colorimetric and fluorescent probe for palladium detection in an aqueous solution

A new fluorescent probe (TCF-AC) that contains 2-dicyanomethylene-3-cyano-4,5,5-trimethyl-2,5-dihydrofuran (TCF) skeleton has been developed. Probe TCF-AC exhibits highly selective and sensitive detection toward Pd⁰ in EtOH/H₂O (1:1, v/v, PBS 20?mM, pH?=?7.4) solution with fluorescence “turn on” and colorimetric changes. The Pd⁰ detection by TCF-AC holds some advantages including good anti-interference ability, a relative large Stokes shift (>100?nm), and a low detection limit (7.05?×?10^?7?M). Cell imaging studies demonstrate that TCF-AC is applicable to detect Pd⁰ in living HeLa cells.     

Non-covalent anionic porphyrin functionalized multi-walled carbon nanotubes as an optical probe for specific DNA detection

With water-soluble anionic tetra (p-carboxyphenyl) porphyrin (TCPP) to solubilize multi-walled carbon nanotubes (MCNTs), we obtained a suspension that could be stable more than 1 week. With this TCPP/MCNTs suspension, we propose a spectrofluorometric method of DNA hybridization in this contribution. Our basic finding for this work is that the fluorescence from a dye-tagged single stranded DNA (ssDNA), which was directly added to the TCPP/MCNTs suspension, gets quenched, and the fluorescence could be remained if the dye-tagged single stranded DNA is first to be hybridized with its complementary target DNA to form a double stranded DNA (dsDNA) hybrid and added into the TCPP/MCNTs suspension. Mechanism investigations showed that the reason for the former is due to the adsorption of ssDNA on the surfaces of MCNTs, and that for the latter is due to the strong electrostatic repulsion force between the negative charge TCPP/MCNTs complexes and dsDNA. Thus, target DNA in a DNA sample and single-base mismatch in DNA sequences could be easily detected.     

Determination of DNA using sodium 9,10-anthraquinone-2-sulfonate as an in situ photochemical fluorescence probe

An in situ photochemical fluorescence probe method for the determination of DNA with sodium 9,10-anthraquinone-2-sulfonate (AQS) as a photochemical fluorescence probe was developed. It was based on the conversion of AQS into an intensively fluorescent product by irradiating with UV radiation. The photochemical reaction is retarded by DNA. The determination can be carried out by measuring the fluorescence intensity at a fixed time. The calibration graph was linear in the range 0–80 ng ml⁻¹ calf thymus (CT) DNA (r = 0.9991), the limit of detection was 3.2 ng ml⁻¹ CT DNA (n = 9). The kinetic behaviour of the photochemical reaction and the effects of experimental conditions were investigated and discussed in detail. The results of absorption spectra and competitive binding experiments suggested the interaction between AQS and DNA to be intercalative.     

Innovative approach for the electrochemical detection of non-electroactive organophosphorus pesticides using oxime as electroactive probe

An innovative approach for sensitive and simple electrochemical detection of non-electroactive organophosphorus pesticides (OPs) was described in this report. The novel strategy emphasized the fabrication of an oxime-based sensor via attaching pralidoxime (PAM) on graphene quantum dots (GQDs) modified glassy carbon electrode. The introduction of GQDs significantly increased the effective electrode area, and then enlarged the immobilization quantity of PAM. Thus, the oxidation current of PAM was obviously increased. Relying on the nucleophilic substitution reaction between oxime and OPs, fenthion was detected using PAM as the electroactive probe. Under optimum conditions, the difference of oxidation current of PAM was proportional to fenthion concentration over the range from 1.0 × 10⁻¹¹ M to 5.0 × 10⁻⁷ M with a detection limit of 6.8 × 10⁻¹² M (S/N = 3). Moreover, the favorable detection performance in water and soil samples heralded the promising applications in on-site OPs detection.     

Synthesis and DNA binding behavior of a naphthalene diimide derivative carrying two dicobalt hexacarbonyl complexes as an infrared DNA probe

Naphthalene diimide having two dicobalt hexacarbonyl complexes at its substituent termini 1 was designed and synthesized as an infrared probe for double stranded DNA. Spectrophotometric and viscometric DNA binding studies of 1 and naphthalene diimide having two acetylene moieties 2 as its precursor were carried out to prove their threading intercalation binding modes. Fourier Transform Infrared Reflection-Absorption Spectroscopy (FT-IR RAS) measurements were achieved for DNA-immobilized on a gold surface before and after hybridization with complementary DNA strand. Distinguished absorption peaks assigned to the dicobalt hexacarbonyl complexes were obtained in the case of the formation of double stranded DNA after treatment with 1. This result revealed that 1 can be used as an infrared probe for monitoring double stranded DNA.     

A pinacol boronate caged NIAD-4 derivative as a near-infrared fluorescent probe for fast and selective detection of hypochlorous acid

A pinacol boronate caged NIAD-4 derivative was demonstrated to be a near-infrared fluorescent probe for fast and selective detection of hypochlorite over other ROS species.     

CdTe quantum dots as a highly selective probe for prion protein detection: colorimetric qualitative, semi-quantitative and quantitative detection

CdTe quantum dots (QDs) were used as a highly selective probe for the detection of prion protein. Orange-emitting precipitates appeared within 30 s of the addition of recombination prion protein (rPrP) to a solution of green-emitting CdTe QDs. This allowed colorimetric qualitative and semi-quantitative detection of rPrP. The decrease in fluorescence intensity of the supernatant could be used for quantitative detection of rPrP. The fluorescence intensity of the supernatant was inversely proportional to the rPrP concentration from 8 to 200 nmol L⁻¹ (R² = 0.9897). Transmission electron microscopy results showed that fibrils existed in the precipitates and these were partly transformed to amyloid plaques after the addition of rPrP.