Amplified detection of femtomolar DNA based on a one-to-few recognition reaction between DNA-Au conjugate and target DNA

Ultrasensitive Electrochemical DNA Biosensor Based on a Label-Free Assembling Strategy Using a Triblock polyA DNA Probe

Multiblock DNA probe attracted a large amount of scientific attention, for the development of multitarget biosensor and improved specificity/sensitivity. However, the development of multiblock DNA probes highly relied on the chemical synthesis of organic linkers or nanomaterials, which limited their practicability and biological compatibility. In this work, we developed a label-free assembling strategy using a triblock DNA capture probe, which connects two DNA probes with its intrinsic polyA fragment (probe-PolyA-probe, PAP). The middle polyA segment has a high affinity to the gold electrode surface, leading to excellent reproducibility, stability, and regeneration of our biosensor. Two flanking capture probes were tandemly co-assembled on the electrode surface with consistent spatial relationship and exactly the same amount. When combined with the target DNA, the hybridization stability was improved, because of the strong base stacking effect of two capture probes. The sensitivity of our biosensor was proved to be 10 fM, with a wide analysis range between 10 fM to 1 nM. Our PAP-based biosensor showed excellent specificity when facing mismatched DNA sequences. Even single nucleotide polymorphisms can be distinguished by each probe. The excellent practicability of our biosensor was demonstrated by analyzing genomic DNA both with and without PCR amplification.

Biosensing and Delivery of Nucleic Acids Involving Selected Well-Known and Rising Star Functional Nanomaterials

In the last fifteen years, the nucleic acid biosensors and delivery area has seen a breakthrough due to the interrelation between the recognition of nucleic acid's high specificity, the great sensitivity of electrochemical and optical transduction and the unprecedented opportunities imparted by nanotechnology. Advances in this area have demonstrated that the assembly of nanoscaled materials allows the performance enhancement, particularly in terms of sensitivity and response time, of functional nucleic acids' biosensing and delivery to a level suitable for the construction of point-of-care diagnostic tools. Consequently, this has propelled detection methods using nanomaterials to the vanguard of the biosensing and delivery research fields. This review overviews the striking advancement in functional nanomaterials' assisted biosensing and delivery of nucleic acids. We highlight the advantages demonstrated by selected well-known and rising star functional nanomaterials (metallic, magnetic and Janus nanomaterials) focusing on the literature produced in the past five years.

Robust and Universal SERS Sensing Platform for Multiplexed Detection of Alzheimer's Disease Core Biomarkers Using PAapt-AuNPs Conjugates

Multiplexed detection of Alzheimer's disease (AD) core biomarkers is of great significance to early diagnosis and personalized treatment of AD patients. Herein, we construct a robust and convenient surface-enhanced Raman scattering (SERS) biosensing platform for simultaneous detection of Aβ(1-42) oligomers and Tau protein using different Raman dye-coded polyA aptamer-AuNPs (PAapt-AuNPs) conjugates. This strategy relies on the specific protein-aptamer binding-mediated aggregation of AuNPs and the concomitant plasmonic coupling effect that allow us to "turn on" SERS detection of protein biomarkers. To the best of our knowledge, this is the first work in which PAapt-AuNPs conjugates are used for probing protein biomarkers, which may be enlightening for the exploitation of more extensive biological applications of aptamer-AuNPs conjugates. The results reveal that the present strategy displays excellent analytical performance. Moreover, the applicability of this strategy is demonstrated in the artificial cerebrospinal fluid (CSF) samples with satisfactory results. Except for the prominent sensitivity and practicality, our strategy offers additional advantages. The preparation of nanoconjugates is handy and easily repeated, and the synthesis cost is greatly reduced because it dispenses with the complicated labeling process. Moreover, the assay can be accomplished in 15 min, allowing rapid detection of protein biomarkers. Furthermore, simultaneous detection of Tau protein and Aβ(1-42) oligomers is realized by employing different Raman dye-coded nanoconjugates, which is valuable for accurately predicting and diagnosing AD disease. Thus, our PAapt-AuNPs conjugate-based multiplexed SERS strategy indeed creates a useful and universal platform for detecting multiple protein biomarkers and related clinical diagnosis.

Applications of Gold Nanoparticles in Non-Optical Biosensors

Due to their unique properties, such as good biocompatibility, excellent conductivity, effective catalysis, high density, and high surface-to-volume ratio, gold nanoparticles (AuNPs) are widely used in the field of bioassay. Mainly, AuNPs used in optical biosensors have been described in some reviews. In this review, we highlight recent advances in AuNP-based non-optical bioassays, including piezoelectric biosensor, electrochemical biosensor, and inductively coupled plasma mass spectrometry (ICP-MS) bio-detection. Some representative examples are presented to illustrate the effect of AuNPs in non-optical bioassay and the mechanisms of AuNPs in improving detection performances are described. Finally, the review summarizes the future prospects of AuNPs in non-optical biosensors.

Blocking probe as a potential tool for detection of single nucleotide DNA mutations: design and performance

Developing strategies to detect single nucleotide DNA mutations associated with treatment decisions in cancer patients from liquid biopsies is a rapidly emerging area of personalized medicine that requires high specificity. Here we report how to design an easy enzyme-free approach that could create a platform for detection of L858R mutation of EGFR that is a predictive biomarker of tyrosine kinase treatment in many cancers. This approach includes the addition of blocking probes with the antisense ssDNA at different blocking positions and different concentrations such as to avoid re-annealing with the respective sense ssDNA. The successful blocking strategy was corroborated by fluorescence spectroscopy in solution using two distinct FRET pairs and quartz crystal microbalance with dissipation (QCM-D) measurements under comparable experimental conditions, as the hybridization rate-limiting step in both methods is the nucleation process. The efficiency of hybridization of each blocking probe was strongly dependent on its position particularly when the analyte possesses a secondary hairpin-structure. We tested the performance of blocking probes in combination with gold nanoparticles; the obtained results were in agreement with those of QCM-D. These findings could facilitate the development of better biosensors, especially those using probes containing secondary structure.

Individual Au-Nanocube Based Plasmonic Nanoprobe for Cancer Relevant MicroRNA Biomarker Detection

MicroRNA205 (miR-205), as a significant tumor biomarker, is of vital importance for diagnosis of lung cancer and its overexpression patterns have been extensively studied. Here, we report a novel and label-free nanoprobe with high sensitivity and selectivity for miRNA biomarker detection using localized surface plasmon resonance (LSPR) technology on a single DNA modified gold nanocube (AuNC). This method allowed real-time monitoring of the subtle LSPR scattering peak position's change which was aroused by the variation of dielectric constant in the hybridization process of target miRNA with ssDNA modified on the surface of AuNCs. Notably, the limit of detection of the AuNC-ssDNA probe is up to 5 pM in serum sample, and these results showed that the square structure has more superior sensitivity for design and development of nanoprobe for trace lung cancer relevant miRNAs detection. The better sensing ability and stability of LSPR probe on a AuNC provide potential application to developing a high flux biochip in the future.

A FRET-based ratiometric fluorescent aptasensor for rapid and onsite visual detection of ochratoxin A

A color change observable by the naked eye to indicate the content of an analyte is considered to be the most conceivable way of various sensing protocols. By taking advantage of the Förster resonance energy transfer (FRET) principles, we herein designed a dual-emission ratiometric fluorescent aptasensor for ochratoxin A (OTA) detection via a dual mode of fluorescent sensing and onsite visual screening. Amino group-modified OTA's aptamer was firstly labeled with the green-emitting CdTe quantum dots (gQDs) donor. The red-emitting CdTe QDs (rQDs) which were wrapped in the silica sphere could serve as the reference signal, while the gold nanoparticle (AuNP) acceptors were attached on the silica surface to bind with the thiolated complementary DNA (cDNA). The hybridization reaction between the aptamer and the cDNA brought gQD-AuNP pair close enough, thereby making the FRET occur in the aptasensor fabrication, while the subsequent fluorescence recovery induced by OTA was obtained in the detection procedure. Based on the red background of the wrapped rQDs, the aptasensor in response to increasing OTA displayed a distinguishable color change from red to yellow-green, which could be conveniently readout in solution even by the naked eye. Since the bioconjugations used as the aptasensor can be produced at large scale, this method can be used for in situ, rapid, or high-throughput OTA detection after only an incubation step in a homogeneous mode. We believe that this novel aptasensing strategy provides not only a promising method for OTA detection but also a universal model for detecting diverse targets by changing the corresponding aptamer.

Enzyme-Free Detection of Mutations in Cancer DNA Using Synthetic Oligonucleotide Probes and Fluorescence Microscopy

Background

Rapid reliable diagnostics of DNA mutations are highly desirable in research and clinical assays. Current development in this field goes simultaneously in two directions: 1) high-throughput methods, and 2) portable assays. Non-enzymatic approaches are attractive for both types of methods since they would allow rapid and relatively inexpensive detection of nucleic acids. Modern fluorescence microscopy is having a huge impact on detection of biomolecules at previously unachievable resolution. However, no straightforward methods to detect DNA in a non-enzymatic way using fluorescence microscopy and nucleic acid analogues have been proposed so far.

Methods and Results

Here we report a novel enzyme-free approach to efficiently detect cancer mutations. This assay includes gene-specific target enrichment followed by annealing to oligonucleotides containing locked nucleic acids (LNAs) and finally, detection by fluorescence microscopy. The LNA containing probes display high binding affinity and specificity to DNA containing mutations, which allows for the detection of mutation abundance with an intercalating EvaGreen dye. We used a second probe, which increases the overall number of base pairs in order to produce a higher fluorescence signal by incorporating more dye molecules. Indeed we show here that using EvaGreen dye and LNA probes, genomic DNA containing BRAF V600E mutation could be detected by fluorescence microscopy at low femtomolar concentrations. Notably, this was at least 1000-fold above the potential detection limit.

Conclusion

Overall, the novel assay we describe could become a new approach to rapid, reliable and enzyme-free diagnostics of cancer or other associated DNA targets. Importantly, stoichiometry of wild type and mutant targets is conserved in our assay, which allows for an accurate estimation of mutant abundance when the detection limit requirement is met. Using fluorescence microscopy, this approach presents the opportunity to detect DNA at single-molecule resolution and directly in the biological sample of choice.

Polyacrylonitrile/noble metal/SiO₂ nanofibers as substrates for the amplified detection of picomolar amounts of metal ions through plasmon-enhanced fluorescence

Electrospun polymer/noble metal hybrid nanofibers have developed rapidly as surface-enhanced Raman scattering (SERS)-active substrates over the last few years. However, polymer/noble metal nanofibers with plasmon-enhanced fluorescence (PEF) activity have received no attention to date. Herein, we show a general and facile approach for the preparation of polyacrylonitrile (PAN)/noble metal/SiO2 nanofibrous mats with PEF activity for the first time by combining electrospinning and controlled silica coatings. These PEF-active nanofibrous mats can selectively improve the fluorescence intensity of conjugated polyelectrolytes (CPEs). Importantly, the CPE solution in the presence of a PAN/noble metal/SiO2 nanofibrous mat showed dramatic fluorescence quenching towards picomolar (pM) amounts of heavy metal ions, while the fluorescence of the CPE solution without the nanofibrous mat had no apparent quenching towards micromolar (μM) amounts of metal ions. The combination of the distance-dependent fluorescence enhancement performance of metal NPs and the ionic characteristics of the CPE solution makes the polymer/noble metal nanofibers promising substrates for greatly improving the detection sensitivity towards metal ions. We believe that this work provides a general strategy for preparing plasmon band-tuned PEF-active substrates with advantages including good selectivity, remarkable sensitivity and recyclability, which make them a preferable choice for practical sensing applications.

Ultrasensitive electrochemical detection of dual DNA targets based on G-quadruplex-mediated amplification

Dual DNA targets were ligated to a long strand containing a G-quadruplex forming sequence and detected on a capture probe modified electrode.

Versatile biosensing platform for DNA detection based on a DNAzyme and restriction-endonuclease-assisted recycling

On the basis of a DNAzyme and a restriction-endonuclease-assisted target recycling strategy using Pd-Au alloy nanocrystals to immobilize probe DNA on an electrode and catalyze the reduction of H2O2 which amplified signal and promoted the detection sensitivity, a versatile biosensing platform for DNA detection was proposed. Using p53 and oral cancer genes as models, hemin/G-quadruplex simultaneously acted as a reduced nicotinamide adenine dinucleotide (NADH) oxidase and a horseradish peroxidase (HRP)-mimicking DNAzyme, and a versatile DNA biosensor was designed for the first time based on the good electrocatalytic activity of Pd-Au alloy nanocrystals. Hemin/G-quadruplex catalyzed the reduction of H2O2, which was generated from NADH in the presence of O2, to produce an electrochemical signal when thionine functioned as the electron mediator. Moreover, the nicking endonuclease N.BstNB I caused the target DNA to cycle for multiple rounds and further amplified the electrochemical response. This versatile DNA biosensor exhibited linear ranges for the detection of p53 and oral cancer genes from 0.1 fmol L(-1) to 0.1 nmol L(-1) and 0.1 fmol L(-1) to 1 nmol L(-1), respectively. The detection limits, established as 3σ, were estimated to be 0.03 and 0.06 fmol L(-1) for the p53 and oral cancer genes, respectively. The as-prepared biosensor could discriminate mismatched sequences, indicating a satisfactory selectivity and validating the feasibility of the proposed strategy. More importantly, simply by changing the helper DNA, this versatile DNA biosensor could detect different target DNA species, which could create a new avenue for the potential diagnosis of cancer.