Electrogenerated chemiluminescence detection of adenosine based on triplex DNA biosensor

Lateral flow DNA biosensor for visual detection of nucleic acid with triple-helix DNA functionalized carbon nanotube

We describe a novel lateral flow DNA biosensor (LFDB) based on carbon nanotube (CNT) and triple helix DNA (THD). The carboxylated CNT was first conjugated with amine-modified auxiliary single-stranded DNA probe (P1) by dehydration reaction and used as signal probe. A main DNA probe (P0) was introduced to react with the P1 and formed the THD on the CNT surface. Because of the large spatial effect, P1 was in an inactive state and cannot hybridize with the capture DNA probe (P2) fixed on the LFDB test area. When the target DNA was present, P0 in the triple helix DNA hybridized with the target DNA due to the stronger base action, and the decomposition of the triple helix structure exposed P1. Therefore, P1 on CNT surface was activated to hybridize with P2. The CNT along with P1 was thus captured at the test area and accumulated to show a black line, which can be observed by naked eye for qualitative analysis and recorded with a portable grayscale reader for quantitative analysis. Single-stranded DNA was used as a target to prove the feasibility of the model. Under the best experimental conditions, the THD-CNT based LFDB was able to detect the lowest DNA concentration of 15 pM, which is 2.67 times better than that of the traditional duplex CNT-based LFDB. It should be noted that the LFDB based on THD functionalized CNT can differentiate between one-base-mismatched DNA and the complementary target DNA, can detected target DNA in 10% human serum, and can be employed as a versatile platform to detect various target (proteins, small molecular) by changing the sequence of P0. This biosensor platform has enormous potential in the point-of-care detection of a rich diversity of analytes for clinical diagnosis and biomedical research.

Three's a crowd - stabilisation, structure, and applications of DNA triplexes

DNA is a strikingly flexible molecule and can form a variety of secondary structures, including the triple helix, which is the subject of this review. The DNA triplex may be formed naturally, during homologous recombination, or can be formed by the introduction of a synthetic triplex forming oligonucleotide (TFO) to a DNA duplex. As the TFO will bind to the duplex with sequence specificity, there is significant interest in developing TFOs with potential therapeutic applications, including using TFOs as a delivery mechanism for compounds able to modify or damage DNA. However, to combine triplexes with functionalised compounds, a full understanding of triplex structure and chemical modification strategies, which may increase triplex stability or in vivo degradation, is essential - these areas will be discussed in this review. Ruthenium polypyridyl complexes, which are able to photooxidise DNA and act as luminescent DNA probes, may serve as a suitable photophysical payload for a TFO system and the developments in this area in the context of DNA triplexes will also be reviewed.

Functionalized MOF PCN-222-loaded quantum dots as an electrochemiluminescence sensing platform for the sensitive detection of p-nitrophenol

The composite PCN-222@CdSe was used to detect PNP.

Colorimetric adenosine aptasensor based on DNA cycling amplification and salt-induced aggregation of gold nanoparticles

An aptamer based assay is described for the colorimetric detection of adenosine. The presence of adenosine triggers the deformation of hairpin DNA oligonucleotide (HP1) containing adenosine aptamer and then hybridizes another unlabeled hairpin DNA oligonucleotide (HP2). This leads to the formation of a double strand with a blunt 3' terminal. After exonuclease III (Exo III)-assisted degradation, the guanine-rich strand (GRS) is released from HP2. Hence, the adenosine-HP1 complex is released to the solution where it can hybridize another HP2 and initiate many cycles of the digestion reaction with the assistance of Exo III. This leads to the generation of a large number of GRS strands after multiple cycles. The GRS stabilize the red AuNPs against aggregation in the presence of potassium ions. If, however, GRS forms a G-quadruplex, it loses its ability to protect gold nanoparticles (AuNPs) from salt-induced AuNP aggregation. Therefore, the color of the solution changes from red to blue which can be visually observed. This colorimetric assay has a 0.13 nM detection limit and a wide linear range that extends from 5 nM to 1 μM. Graphical abstract Schematic presentation of a colorimetric aptamer biosensor for adenosine detection based on DNA cycling amplification and salt-induced aggregation of gold nanoparticles.

Triplex DNA Nanostructures: From Basic Properties to Applications

Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-organic frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.

Development of a luminescent G-quadruplex-selective iridium(III) complex for the label-free detection of adenosine

A panel of six luminescent iridium(III) complexes were synthesized and evaluated for their ability to act as G-quadruplex-selective probes. The novel iridium(III) complex 1 was found to be highly selective for G-quadruplex DNA, and was employed for the construction of a label-free G-quadruplex-based adenosine detection assay in aqueous solution. Two different detection strategies were investigated for adenosine detection, and the results showed that initial addition of adenosine to the adenosine aptamer gave superior results. The assay exhibited a linear response for adenosine in the concentration range of 5 to 120 μM (R(2) = 0.992), and the limit of detection for adenosine was 5 μM. Moreover, this assay was highly selective for adenosine over other nucleosides, and exhibited potential use for biological sample analysis.

A universal label-free fluorescent aptasensor based on Ru complex and quantum dots for adenosine, dopamine and 17β-estradiol detection

Based on specific aptamer binding properties, a strategy for adenosine, dopamine and 17β-estradiol detection was realised by employing Ru complex and quantum dots (QDs) as fluorescence probes. Ru complex, which could quench the fluorescence of QDs, preferred to bind with aptamer DNA and resulted in the fluorescence rise of QDs. When the aptamer DNA was incubated with the target first, it could not bind with Ru complex and the fluorescence of QDs was quenched. Under the optimal condition, the fluorescence intensity was linearly proportional to the concentration of adenosine, dopamine and 17β-estradiol with a limit of detection (LOD) of 101 nM, 19 nM and 37 nM, respectively. The experiments in fetal bovine serum were also carried out with good results. This universal method was rapid, label-free, low-cost, easy-operating and highly repeatable for the detection of adenosine, dopamine and 17β-estradiol. Qualitative detection by naked eyes was also available without complex instruments. It could also be extended to detect various analytes, such as metal ions, proteins and small molecules by using appropriate aptamers.

Ruthenium polypyridine complexes combined with oligonucleotides for bioanalysis: a review

Ruthenium complexes are among the most interesting coordination complexes and they have attracted great attention over the past decades due to their appealing biological, catalytic, electronic and optical properties. Ruthenium complexes have found a unique niche in bioanalysis, as demonstrated by the substantial progress made in the field. In this review, the applications of ruthenium complexes coordinated with polypyridine ligands (and analogues) in bioanalysis are discussed. Three main detection methods based on electrochemistry, electrochemiluminescence, and photoluminscence are covered. The important targets, including DNA and other biologically important targets, are detected by specific biorecognition with the corresponding oligonucleotides as the biorecognition elements (i.e., DNA is probed by its complementary strand and other targets are detected by functional nucleic acids, respectively). Selected examples are provided and thoroughly discussed to highlight the substantial progress made so far. Finally, a brief summary with perspectives is included.

Electrochemical impedance spectroscopy aptasensor for ultrasensitive detection of adenosine with dual backfillers

A highly sensitive and label-free electrochemical impedance spectroscopy (EIS) aptasensor for the detection of adenosine was fabricated by co-assembling thiolated aptamer, dithiothreitol (DTT) and 6-mercaptohexanol (MCH) on gold electrode surface, forming Au/aptamer-DTT/MCH. The interfacial electron transfer resistance (Ret) of the aptasensor using [Fe(CN)6](3-/4-) as the probe increased with adenosine concentration, and the change in Ret (∆Ret) against the logarithm of adenosine concentration was linear over the range from 0.05 pM to 17 pM with a detection limit of 0.02 pM. Compared to that of aptasensors fabricated with MCH or DTT alone as the backfiller, the detection limit was improved dramatically (LOD was 0.03 nM and 0.2 pM for Au/aptamer/MCH and Au/aptamer-DTT, respectively), which was attributed primarily to the coupling of the cyclic- and linear -configuration backfillers. The coupling showed remarkably higher resistance to nonspecific adsorption, leading to low background noise and high response signal. The aptasensor reported herein is applicable for the detection of other kinds of aptamer-binding chemicals and biomolecules.

Electrochemiluminescence aptasensor based on bipolar electrode for detection of adenosine in cancer cells

Here we report a novel approach for the detection of adenosine in cancer cells by electrochemiluminescence (ECL) on a wireless indium tin oxide bipolar electrode (BPE). In this approach, ferrocene (Fc) which is labeled on adenosine aptamer is enriched on one pole of the BPE by hybridization with its complementary DNA (ssDNA) and oxidized to Fc(+) under an external voltage of 5.0V at the two ends of BPE. Then, a reversed external voltage was added on the BPE, making Fc(+) enriched pole as cathode. The presence of Fc(+) promotes the oxidation reaction on the anodic pole of the BPE, resulting in a significant increase of ECL intensity using Ru(bpy)3(2+)/tripropylamine (TPA) system as test solution. The presence of target adenosine was reflected by the ECL signal decrease on the anodic pole caused by the target-induced removal of ferrocene-aptamer on the cathodic pole. The decrease of ECL signal was logarithmically linear with the concentration of ATP in a wide range from 1.0 fM to 0.10 μM. This ECL biosensing system could accurately detect the level of adenosine released from cancer cells.

Facile electrochemical biosensor based on a new bifunctional probe for label-free detection of CGG trinucleotide repeat

We have developed a simple and label-free electrochemical assay to detect CGG trinucleotide repeat. For this purpose, a new bifunctional probe (FecNCD2) was developed, in which a recognition part (naphthyridine carbamate dimmer, NCD) was connected with an electro-active part (ferrocenyl group) using a chain of -CO-NH-CH2-CH2-. The results of circular dichroismic measurements indicated that FecNCD2 exhibited a superior performance for selective binding to CGG trinucleotide repeats compared to a previous bifunctional electrochemical probe connected with shorter linker -CH2- (FecNCD1). Then, the electrochemical properties of FecNCD2 were evaluated and were found to show a good redox response due to the ferrocene moiety. Owing to the high performances of FecNCD2, the label-free electrochemical biosensor for CGG repeats was constructed by immobilizing them onto gold disk electrode and by using FecNCD2 as an electrochemical probe in solution. Further CGG repeats in solution were confirmed to be detectable using the CGG modified biosensor in competitive experiments, i.e., by treating it in test solutions containing FecNCD2 and d(CGG)10 or others. No interference of ct-DNA on the CGG detection was also confirmed with this approach. The strategy should have significant potential for the development of versatile and low-cost biosensor for early diagnosis and treatment of neurodegenerative diseases associated with trinucleotide repeats.

Ultrasensitive electrogenerated chemiluminescent DNA-based biosensing switch for the determination of bleomycin

An ultrasensitive electrogenerated chemiluminescent (ECL) DNA-based biosensing switch for the determination of bleomycin (BLM) was developed based on Fe(II) · BLM-mediated hairpin DNA strand cleavage and a structure-switching ECL-dequenching mechanism. A thiolated ss-DNA was used as a substrate for BLMs: one terminus was tethered onto an electrode surface, and the other terminus was labelled with the ECL quencher ferrocene to form a hairpin structure. This thiolated ss-DNA self-assembled on to the tris(2,2'-bipyridine)ruthenium-gold nanoparticle composite modified gold electrode. In the presence of Fe(II) · BLM, the ECL DNA biosensing switch undergoes an irreversible cleavage event that can trigger a significant increase in ECL intensity. The relationship of ECL intensity and the concentration of BLMs was found to be linear in the range of 5 fM - 5000 fM with a detection limit of 2 fM. This work demonstrates that the design of a highly sensitive ECL DNA-based biosensing switch that uses the sequence selectivity of DNA cleavage mediated by the antitumor drug BLM in combination with a chemical quencher, such as ferrocene, to quench ECL signal(s), offers a promising approach for the determination of ultratrace amounts of antitumor drugs.

Simple chemiluminescence aptasensors based on resonance energy transfer

In the present work, two aptamer-based probes and related sensor systems were developed with chemiluminescence signaling. The detection was based on "turning-on" chemiluminescence with switching "off" of the resonance energy transfer after the aptamer's recognition of the target molecule. In this design, a DNA/aptamer duplex linked a chemiluminescence group and a gold nanoparticle together. Only low-intensity chemiluminescence was obtained due to the highly efficient resonance energy transfer. After introducting the target molecule, structure-switching took place with turning off the energy transfer; thus, a restoration and turning on of the chemiluminescence was obtained. The two designs differed in the chemiluminescence groups, since one was a covalently linked luminol molecule, while the other was a conjugated horseradish peroxidase for the catalysis of further chemiluminescence reactions. These schemes provided simple and effective sensing toward a model analyte, adenosine.