Expanding the repertoire of pyrrolidyl PNA analogues for DNA/RNA hybridization selectivity: aminoethylpyrrolidinone PNA (aepone-PNA)

New PNA analogues derived from aminoethylpyrrolidin-5-one backbone show stabilization of aepone-PNA:DNA hybrids and destabilization of the corresponding RNA hybrids compared to unmodified PNA.     

Enzyme-assisted binary probe for sensitive detection of RNA and DNA

The new enzyme-assisted assay for DNA/RNA detection provides real-time fluorescent signal readout along with low limit of detection and high discrimination power toward a single-base substitution. Requiring only two new unmodified DNA oligonucleotides for the detection of each new analyte, the assay is an efficient tool for low-cost analysis of multiple analytes.     

cis-Cyclopentyl PNA (cpPNA) as constrained chiral PNA analogues: stereochemical dependence of DNA/RNA hybridization

DNA/RNA hybridization studies of PNA-T oligomers with cis-(1S,2R/1R,2S)-cyclopentyl units in the backbone show stereochemistry dependent binding with RNA/DNA discrimination.     

Washing-free electrochemical DNA detection using double-stranded probes and competitive hybridization reaction

A new electrochemical DNA detection method using double-stranded probes and competitive hybridization reaction offers highly selective discrimination of single base mismatch without post-hybridization washing.     

Dual-amplified sensitive DNA detection based on conjugated polymers and recyclable autocatalytic hybridization of DNA

A simple and extremely sensitive dual-amplification platform for the detection of DNA was developed combining signal amplification of conjugated polymers and recyclable autocatalytic hybridization of DNA.     

A thermodynamic investigation into the binding properties of DNA functionalized gold nanoparticle probes and molecular fluorophore probes

We report the first quantitative analysis of the oligonucleotide binding thermodynamics for DNA functionalized gold nanoparticle probes and compare our findings to molecular fluorophore probes on a sequence-for-sequence basis. With proper design, nanoparticle probes show significantly increased binding over molecular fluorophore probes under identical conditions. This is significant because probe binding strength directly influences detection sensitivity limits.     

Impedimetric genosensors for the detection of DNA hybridization

Impedance spectroscopy is proposed as the transduction principle for detecting the hybridization of DNA complementary strands. In our experiments, different DNA oligonucleotides were used as model gene substances. The gene probe is first immobilized on a graphite-epoxy composite working electrode based genosensor. Detection principle is based on changes of impedance spectra of a redox marker, the ferro/ferricyanide couple, after hybridization with target DNA. Resistance offered to the electrochemical reaction serves as the working signal, allowing for an unlabelled gene assay.      

Carbon dots-based fluorescent probes for sensitive and selective detection of iodide

We report on a simple method for the determination of iodide in aqueous solution by exploiting the fluorescence enhancement that is observed if the complex formed between carbon dots and mercury ion is exposed to iodide. Fluorescent carbon dots (C-dots) were treated with Hg(II) ion which causes quenching of the emission of the C-dots. On addition of iodide, the Hg(II) ions are removed from the complex due to the strong interaction between Hg(II) and iodide. This causes the fluorescence to be restored and enables iodide to be determined in the 0.5 to 20 μM concentration range and with a detection limit of ~430 nM. The test is highly selective for iodide (over common other anions) and was used for the determination of iodide in urine.

Cyclopentane-modified PNA improves the sensitivity of nanoparticle-based scanometric DNA detection

trans-Cyclopentane-modified PNA has been successfully utilized as a target capture strand to improve the detection limit of a known DNA detection assay, and provide high levels of mismatch discrimination.     

Junction probes - sequence specific detection of nucleic acids via template enhanced hybridization processes

Junction probe nucleic acid detection technology allows the amplified sensing of analytes at isothermal conditions. The addition of a second dimension to detection probes permits the use of cheap commercially available DNA processing enzymes such as restriction endonucleases to detect single nucleotide polymorphisms, SNPs.     

Polymer-DNA hybrids as electrochemical probes for the detection of DNA

The syntheses of several norbornene block copolymers containing oligonucleotide and ferrocenyl side chains and their use in the electrochemical detection of DNA are described. Two kinds of DNA-containing block copolymers with either ferrocenyl or dibromoferrocenyl groups were prepared via ring-opening metathesis polymerization (ROMP). Based on these two distinct ferrocene derivatives, a triblock copolymer labeling strategy was developed. With this strategy, the identity of DNA target can be determined by the E1/2s of the ferrocenyl moieties and the ratio of peak currents. These polymers exhibit predictable and tailorable electrochemical properties, high DNA duplex stability, and unusually sharp melting transitions, which are highly desirable characteristics for DNA detection applications. Significantly, single-base mismatches could be easily detected using two distinct block copolymers as dual-channel detection probes in an electrochemical DNA detection format.     

Molecular beacon probes for the detection of cisplatin-induced DNA damage

Cisplatin (cis-diamminedichloroplatinum(II)) causes crosslinking of DNA at AG and GG sites in cellular DNA, inhibiting replication, and making it a useful anti-cancer drug. Several techniques have been used previously to detect nucleic acid damage but most of these tools are labour-intensive, time-consuming, and/or expensive. Here, we describe a sensitive, robust, and quantitative tool for detecting cisplatin-induced DNA damage by using fluorescent molecular beacon probes (MB). Our results show a decrease of fluorescence in the presence of cisplatin-induced DNA damage, confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The decrease in fluorescence upon damage scales with the number of AG and GG sites, indicating the ability of MB to quantitatively detect DNA damage by cisplatin.     

Dendrimer-based biosensor for chemiluminescent detection of DNA hybridization

We report on a highly sensitive chemiluminescent (CL) biosensor for the sequenc-specific detection of DNA using a novel bio barcode DNA probe modified with gold nanoparticles that were covered with a dendrimer. The modified probe is composed of gold nanoparticles, a dendrimer, the CL reagent, and the DNA. The capture probe DNA was immobilized on magnetic beads covered with gold. It first hybridizes with the target DNA and then with one terminal end of the signal DNA on the barcoded DNA probe. CL was generated by adding H₂O₂ and Co(II) ions as the catalyst. The immobilization of dendrimer onto the gold nanoparticles can significantly enhance sensitivity and gives a detection limit of 6 fmol L^-1 of target DNA.

DNA hybridization chain reaction and DNA supersandwich self-assembly for ultrasensitive detection

The fabrication of sensitive sensors with high selectivity is highly desirable for the detection of some important biomarkers,such as nucleic acids,proteins,small molecules and ions.DNA hybridization chain reaction(HCR) and DNA supersandwich self-assembly(SSA) are two prevalent enzyme-free signal amplification strategies to improve sensitivity of the sensors.In this review,we firstly describe the characteristics about DNA HCR and DNA SSA,and then summarize the advances in the one-dimensional DNA nanostructures assisted by HCR and SSA.This review has been divided into three parts according to the two signal amplification methods and highlights recent progress in these two strategies to improve the detection sensitivity of proteins,nucleic acids,small molecules and ions.     

A visible light responsive molecularly imprinted photoelectrochemical sensor for the sensitive detection of BSA

Journal of Solid State Electrochemistry - A molecularly imprinted photoelectrochemical (PEC) cathodic sensor was developed for the detection of bovine serum albumin (BSA). The PEC sensor was...     

Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins.

The binding of a series of PNA and DNA probes to a group of unusually stable DNA hairpins of the tetraloop motif has been observed using absorbance hypochromicity (ABS), circular dichroism (CD), and a colorimetric assay for PNA/DNA duplex detection. These results indicate that both stable PNA-DNA and DNA-DNA duplexes can be formed with these target hairpins, even when the melting temperatures for the resulting duplexes are up to 50 degrees C lower than that of the hairpin target. Both hairpin/single-stranded and hairpin/hairpin interactions are considered in the scope of these studies. Secondary structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic obstacles to hybridization imposed by both target and probe secondary structure are significant concerns for the continued development of antisense agents and especially diagnostic probes.