Typing of multiple single-nucleotide polymorphisms by a microsphere-based rolling circle amplification assay

A novel and cost-efficient allele-specific PCR method for multiple SNP genotyping in a single run

Cost-effective methods for DNA genotyping were needed because single nucleotide polymorphisms (SNPs) were essential biomarkers associated with many diseases. Allele-specific PCR (AS-PCR) has the advantages of mature instruments and high sensitivity. But conventional AS-PCR needs to multiply the number of reactions or primers for multiple targets, which complicates the operation and increases the cost. Herein, we proposed a novel AS-PCR method for multiple SNP genotyping in a single run. Wild-type allele-specific primer (WT primer) was designed for each target gene. The sample and WT primers only needed to undergo multiplexed AS-PCR once simultaneously. After AS-PCR, the concentration of remaining primers varied among the samples of each genotype combination, due to the different matching performance between template and WT primers. The remaining primers then triggered multiplexed molecular beacon-rolling circle amplification, and the molecular beacons labelled with different fluorescent dyes corresponded to different targets. The fluorescence ratios of the sample to the positive control were used as the genotyping indexes. This method was able to detect samples with concentrations as low as 10 fM. We successfully applied the method to the multiple genotyping of 23 hair root samples for ADH1B and ALDH2 genes, obtaining completely consistent results with sequencing. The reagent cost was 0.6 dollar for one sample, showing a good cost performance. This proposed approach had a great application prospect in simultaneously rapid and accurate genotyping of multi-SNPs, and provided a new method for personalized health management.

Nicking-assisted on-loop and off-loop enzymatic cascade amplification for optomagnetic detection of a highly conserved dengue virus sequence

Applications of conventional linear ligation-rolling circle amplification (RCA) are restricted by the sophisticated operation steps and unsatisfactory picomolar-level detection limits. We herein demonstrate an RCA-based cascade amplification reaction that converts a side-reaction to secondary amplification, which improves the detection limit and simplifies the operation compared to linear ligation-RCA assays. The proposed nicking-assisted enzymatic cascade amplification (NECA) comprises an on-loop amplification reaction using circular templates to generate intermediate amplicons, and an off-loop amplification reaction using intermediate amplicons as primers for end amplicons. The whole NECA reaction is homogeneous and isothermal. Amplicons anneal to detection probes that are grafted onto magnetic nanoparticles (MNPs), such that MNP clusters form and can be detected in real-time using optomagnetic measurements. The optomagnetic sensor detects the presence and size increase of MNP clusters by optical transmission measurements in an oscillating magnetic field. A detection limit of 2 fM was achieved with a total assay time of ca. 70 min. By combining optomagnetic readouts of signal phase lag and hydrodynamic size increase of MNPs, NECA-based target quantification provided a wide dynamic detection range of ca. 4.5 orders of magnitude. Moreover, the specificity and the serum detection capability of the proposed method were investigated.

Improving the sensitivity and selectivity of a DNA probe using graphene oxide-protected and T7 exonuclease-assisted signal amplification

The accurate analysis of single-nucleotide polymorphisms is of great significance for clinical detection and diagnosis. Based on the hybridization hindrance caused by graphene oxide (GO) and hairpin probe, we report a T7 Exo-assisted cyclic amplification technique to distinguish single-base mismatch for highly sensitive and selective detection of mutant-type DNA. When the mutant-type target is completely complementary to the probe, the T7 Exo hydrolyzes the probe and releases the fluorescent molecule from the GO surface, resulting in a fluorescence signal. Conversely, when the wild-type mismatch target is present, the weak hybridization prevents the release of FAM-labeled probe from the GO surface. Therefore, the FAM-labeled probe cannot be degraded efficiently by T7 Exo, and the fluorescence is still quenched by GO. The detection limit of the proposed method can be as low as 34 fM due to the cyclic signal amplification. The experimental results showed that the established method could be used to detect single-nucleotide polymorphisms accurately and sensitively at low cost.

Hyperbranched rolling circle amplification (HRCA)-based fluorescence biosensor for ultrasensitive and specific detection of single-nucleotide polymorphism genotyping associated with the therapy of chronic hepatitis B virus infection

Detection of specific genes related to drug action can provide scientific guidance for personalized medicine. Taking the detection of a single-nucleotide polymorphism (SNP) genotyping related to the chronic hepatitis B virus (HBV) therapy as an example, a novel biosensor with high sensitivity and selectivity was developed based on the hyperbranched rolling circle amplification (HRCA) in this work. The single-base mutant DNA (mutDNA) sequence can perfectly hybridize with the specially designed discrimination padlock probe and initiate the HRCA reaction. Subsequently, a great abundant of double-strand DNA sequences were released and a strong fluorescence signal can be detected after adding SYBR Green I. In particular, the enhanced fluorescence intensity exhibits a linear relationship with the logarithm of mutDNA concentration ranging from 0.1 nM to 40 nM with a low detection limit of 0.05 nM. However, when there was even a single base mismatch in the target DNA, the HRCA was suppressed and fluorescence response process could not occur, resulting in a high selectivity of this biosensor. Moreover, this detection strategy also performs well in human serums, demonstrating its potential application in detecting SNPs in real biological samples.

Extending Circulating Tumor DNA Analysis to Ultralow Abundance Mutations: Techniques and Challenges

Liquid biopsies that analyze circulating tumor DNA (ctDNA) hold great promise in the guidance of clinical treatment for various cancers. However, the innate characteristics of ctDNA make it a difficult target: ctDNA is highly fragmented, and found at very low concentrations, both in absolute terms and relative to wildtype species. Clinically relevant target sequences often differ from the wildtype species by a single DNA base pair. These characteristics make analyzing mutant ctDNA a uniquely difficult process. Despite this, techniques have recently emerged for analyzing ctDNA, and have been used in pilot studies that showed promising results. These techniques each have various drawbacks, either in their analytical capabilities or in practical considerations, which restrict their application to many clinical situations. Many of the most promising potential applications of ctDNA require assay characteristics that are not currently available, and new techniques with these properties could have benefits in companion diagnostics, monitoring response to treatment and early detection. Here we review the current state of the art in ctDNA detection, with critical comparison of the analytical techniques themselves. We also examine the improvements required to expand ctDNA diagnostics to more advanced applications and discuss the most likely pathways for these improvements.

Isothermal Amplification of Nucleic Acids

Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.

Scaling up an electrochemical signal with a catalytic hairpin assembly coupling nanocatalyst label for DNA detection

A new strategy for the electrochemical detection of DNA based on catalytic hairpin assembly combined with nanocatalyst label-based redox cycling reaction signal amplification. A superior detection limit of 0.3 aM toward DNA was achieved.

A novel electrochemical aptasensor for highly sensitive detection of thrombin based on the autonomous assembly of hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme nanowires

In this work, a new signal amplified strategy was constructed based on isothermal exponential amplification reaction (EXPAR) and hybridization chain reaction (HCR) generating the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme (HRP-mimicking DNAzyme) nanowires as signal output component for the sensitive detection of thrombin (TB). We employed EXPAR's ultra-high amplification efficiency to produce a large amount of two hairpin helper DNAs within a minutes. And then the resultant two hairpin helper DNAs could autonomously assemble the hemin/G-quadruplex HRP-mimicking DNAzymes nanowires as the redox-active reporter units on the electrode surface via hybridization chain reaction (HCR). The hemin/G-quadruplex structures simultaneously served as electron transfer medium and electrocatalyst to amplify the signal in the presence of H2O2. Specifically, only when the EXPAR reaction process has occurred, the HCR could be achieved and the hemin/G-quadruplex complexes could be formed on the surface of an electrode to give a detectable signal. The proposed strategy combines the amplification power of the EXPAR, HCR, and the inherent high sensitivity of the electrochemical detection. With such design, the proposed assay showed a good linear relationship within the range of 0.1 pM-50 nM with a detection limit of 33 fM (defined as S/N=3) for TB.

Detection of single-nucleotide polymorphisms using an ON-OFF switching of regenerated biosensor based on a locked nucleic acid-integrated and toehold-mediated strand displacement reaction

Although various strategies have been reported for single-nucleotide polymorphisms (SNPs) detection, development of a time-saving, specific, and regenerated electrochemical sensing platform still remains a realistic goal. In this study, an ON-OFF switching of a regenerated biosensor based on a locked nucleic acid (LNA)-integrated and toehold-mediated strand displacement reaction technique is constructed for detection of SNPs. The LNA-integrated and methylene blue-labeled capture probe with an external toehold is designed to switch on the sensing system. The mutant-type DNA probe completes complementary with the capture probe to trigger the strand displacement reaction, which switches off the sensing system. However, when the single-base mismatched wild-type DNA probe is presented, the strand displacement reaction cannot be achieved; therefore, the sensing system still keeps the ON state. This DNA sensor is stable over five reuses. We further testify that the LNA-integrated sequence has better recognition ability for SNPs detection compared to the DNA-integrated sequence. Moreover, this DNA senor exhibits a remarkable discrimination capability of SNPs among abundant wild-type targets and 6000-fold (m/m) excess of genomic DNA. In addition, it is selective enough in complex and contaminant-ridden samples, such as human urine, soil, saliva, and beer. Overall, these results demonstrate that this reliable DNA sensor is easy to be fabricated, simple to operate, and stable enough to be readily regenerated.

Development of an electrochemical method for Ochratoxin A detection based on aptamer and loop-mediated isothermal amplification

Loop-mediated isothermal amplification (LAMP) is an outstanding DNA amplification procedure, in which the reaction can accumulate 10(9) copies from less than 10 copies of input template within an hour. While the amplification reaction is extremely powerful, the quantitative detection of LAMP products is still analytically difficult. Besides, the type of targets that LAMP can detect is also less, which to some extent limited the application of LAMP. In this study, we are reporting for the first time an efficient and accurate detection system which employs the integration of LAMP, aptamer and the electrochemical method for the sensitive detection of Ochratoxin A (OTA). Aptamers were designed as the forward outer primer to trigger the LAMP reaction, and then the LAMP amplification products were combined with a redox active molecule methylene blue (MB) and analyzed by an electrode using differential pulse voltammograms (DPV). As the reaction progresses, the MB intercalated into double-stranded regions of LAMP amplicons reduces the free MB concentration. Hence, the peak current of reaction mixture decreased with the amplification because of the slow diffusion of MB-amplified DNA complex to the electrode surface. The peak height of the current was related to the input amount of the aptamers, providing a ready means to detection the concentration of OTA. With such design, the proposed assay showed a good linear relationship within the range of 0.001-50 nM with a detection limit of 0.3 pM (defined as S/N = 3) for OTA.

Signal-to-noise ratio enhancement of silicon nanowires biosensor with rolling circle amplification

Herein, we describe a novel approach for rapid, label-free and specific DNA detection by applying rolling circle amplification (RCA) based on silicon nanowire field-effect transistor (SiNW-FET) for the first time. Highly responsive SiNWs were fabricated with a complementary metal oxide semiconductor (CMOS) compatible anisotropic self-stop etching technique which eliminated the need for hybrid method. The probe DNA was immobilized on the surface of SiNW, followed by sandwich hybridization with the perfectly matched target DNA and RCA primer that acted as a primer to hybridize the RCA template. The RCA reaction created a long single-stranded DNA (ssDNA) product and thus enhanced the electronic responses of SiNW significantly. The signal-to-noise ratio (SNR) as a figure-of-merit was analyzed to estimate the signal enhancement and possible detection limit. The nanosensor showed highly sensitive concentration-dependent conductance change in response to specific target DNA sequences. Because of the binding of an abundance of repeated sequences of RCA products, the SNR of >20 for 1 fM DNA detection was achieved, implying a detection floor of 50 aM. This RCA-based SiNW biosensor also discriminated perfectly matched target DNA from one-base mismatched DNA with high selectivity due to the substantially reduced nonspecific binding onto the SiNW surface through RCA. The combination of SiNW FET sensor with RCA will increase diagnostic capacity and the ability of laboratories to detect unexpected viruses, making it a potential tool for early diagnosis of gene-related diseases.

Ultrasensitive single-nucleotide polymorphism detection using target-recycled ligation, strand displacement and enzymatic amplification

We report herein the development of a highly sensitive and selective approach for label-free DNA detection by combining target-recycled ligation (TRL), magnetic nanoparticle assisted target capture/separation, and efficient enzymatic amplification. We show that our approach can detect as little as 30 amol (600 fM in 50 μL) of unlabelled single-stranded DNA targets and offer an exquisitely high discrimination ratio (up to >380 fold with background correction) between a perfect-match cancer mutant and its single-base mismatch (wild-type) DNA target. Furthermore, it can quantitate the rare cancer mutant (KRAS codon 12) in a large excess of coexisting wild-type DNAs down to 0.75%. This sensor appears to be well-suited for sensitive SNP detection and a wide range of DNA mutation based diagnostic applications.

Detection of metal ions (Cu2+, Hg2+) and cocaine by using ligation DNAzyme machinery

The Cu(2+)-dependent ligation DNAzyme is implemented as a biocatalyst for the colorimetric or chemiluminescence detection of Cu(2+) ions, Hg(2+) ions, or cocaine. These sensing platforms are based on the structural tailoring of the sequence of the Cu(2+)-dependent ligation DNAzyme for specific analytes. The tethering of a subunit of the hemin/G-quadruplex DNAzyme to the ligation DNAzyme sequence, and the incorporation of an imidazole-functionalized nucleic-acid sequence, which acts as a co-substrate for the ligation DNAzyme that is tethered to the complementary hemin/G-quadruplex subunit. In the presence of different analytes, Cu(2+) ions, Hg(2+) ions, or cocaine, the pretailored Cu(2+)-dependent ligation DNAzyme sequence stimulates the respective ligation process by combining the imidazole-functionalized co-substrate with the ligation DNAzyme sequence. These reactions lead to the self-assembly of stable hemin/G-quadruplex DNAzyme nanostructures that enable the colorimetric analysis of the substrate through the DNAzyme-catalyzed oxidation of 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid), ABTS(2-), by H(2)O(2) into the colored product ABTS(·-), or the chemiluminescence detection of the substrate through the DNAzyme-catalyzed oxidation of luminol by H(2)O(2). The detection limits for the sensing of Cu(2+) ions, Hg(2+) ions, and cocaine correspond to 1 nM, 10 nM and 2.5 μM, respectively. These different sensing platforms also reveal impressive selectivities.

Signal amplified strategy based on target-induced strand release coupling cleavage of nicking endonuclease for the ultrasensitive detection of ochratoxin A

In this work, a new signal amplified strategy based on target-induced strand release coupling cleavage of nicking endonuclease for the ultrasensitive detection of ochratoxin A (OTA) is reported. OTA aptamer (DNA1) and OTA aptamer complementary (DNA2) were immobilized onto a magnetic bead (MB). In the presence of OTA, DNA2 was dissociated and released from the MB. The released DNA2 then hybridized with DNA3, which was linked at the 5' terminus of the amplification template and can extend along the template in the presence of Phi 29 DNA polymerase. The formed double-stranded DNA was cleaved by nicking endonuclease Nb.BbvCI and produced a short single-stranded DNA. The cleaved DNA strand generated a new site by Phi 29 DNA polymerase and the process of extension and cleavage was cyclical. Thus, a amount of the short single-stranded DNA were produced. Using DNA and ABEI labeled carboxylic silica nanoparticles chemiluminescence (CL) probe, the short single-stranded DNA could be sensitively detected. The CL intensity (ΔI) versus the concentration of OTA was linear in the range from 1.0×10(-12) to 5.0×10(-8)g mL(-1). The detection limit was 3.0×10(-13)g mL(-1), and the RSD was 3.4% at 1.0×10(-10)g mL(-1) (n=7). The developed method has been applied to detect OTA in naturally contaminated wheat samples. Due to its simplicity, sensitivity and no need of specific recognition of aptamer for cleavage, this CL bioassay offers a promising approach for the detection of OTA and other biomolecules.

Fluorescence and visual detection of single nucleotide polymorphism using cationic conjugated polyelectrolyte

We report a simple assay for visual detection of single nucleotide polymorphisms (SNPs) with good sensitivity and selectivity. The selectivity is determined by Escherichia coli (E. coli) DNA ligase mediated circular formation upon recognition of the point mutation on DNA targets. Rolling cycle amplification (RCA) of the perfect-matched DNA target is then initiated using the in situ formed circular template in the presence of Phi29 enzyme. Due to amplification of the DNA target, the RCA product has a tandem-repeated sequence, which is significantly longer than that for the SNP strand. Direct addition of a cationic conjugated polymer of poly[9,9'-bis(6'-(N,N,N-trimethylammonium)hexyl)fluorene-co-9,9'-bis(2-(2-(2-(N,N,N-trimethylammonium)ethoxyl)-ethoxy)-ethyl)fluorene tetrabromide] containing 20 mol% 2,1,3-benzothiadiazole (PFBT(20)) into the RCA solution leads to blue-whitish fluorescent color for SNP strand and yellowish fluorescent color for amplified DNA, due to PFBT(20)/DNA complexation induced intrachain/interchain energy transfer. To further improve the contrast for visual detection, FAM-labeled peptide nucleic acid (PNA) was hybridized to each amplified sequence, which is followed by the addition of poly{2,7-[9,9-bis(6'-N,N,N-trimethylammoniumhexyl)]fluorene-co-2,5-difluoro-1,4-phenylene dibromide} (PFP). The PNA/DNA hybridization brings PFP and FAM-PNA into close proximity for energy transfer, and the solution fluorescent color appears green in the presence of target DNA with a detection limit of 1 nM, which is significantly improved as compared to that for most reported visual SNP assay.

Particles and microfluidics merged: perspectives of highly sensitive diagnostic detection

There is a growing need for diagnostic technologies that provide laboratories with solutions that improve quality, enhance laboratory system productivity, and provide accurate detection of a broad range of infectious diseases and cancers. Recent advances in micro- and nanoscience and engineering, in particular in the areas of particles and microfluidic technologies, have advanced the "lab-on-a-chip" concept towards the development of a new generation of point-of-care diagnostic devices that could significantly enhance test sensitivity and speed. In this review, we will discuss many of the recent advances in microfluidics and particle technologies with an eye towards merging these two technologies for application in medical diagnostics. Although the potential diagnostic applications are virtually unlimited, the most important applications are foreseen in the areas of biomarker research, cancer diagnosis, and detection of infectious microorganisms.

Triggered polycatenated DNA scaffolds for DNA sensors and aptasensors by a combination of rolling circle amplification and DNAzyme amplification

The concept of triggered polycatenated DNA scaffolds has been elegantly introduced into ultrasensitive biosensing applications by a combination of rolling circle amplification (RCA) and DNAzyme amplification. As compared to traditional methods in which one target could only initiate the formation of one circular template for RCA reaction, in the present study two species of linear single-stranded DNA (ssDNA) monomers are self-assembled into mechanically interlocked polycatenated nanostructures on capture probe-tagged magnetic nanoparticles (MNPs) only upon the introduction of one base mutant DNA sequence as initiator for single-nucleotide polymorphisms (SNPs) analysis. The resultant topologically polycatenated DNA ladder is further available for RCA process by using the serially ligated circular DNA as template for the synthesis of hemin/G-quadruplex HRP-mimicking DNAzyme chains, which act as biocatalytic labels for the luminol-H(2)O(2) chemiluminescence (CL) system. Notably, the problem of high background induced by excess hemin itself is circumvented by immobilizing the biotinylated RCA products on streptavidin-modified MNPs via biotin-streptavidin interaction. Similarly, a universal strategy is contrived by substitutedly employing aptamer as initiator for the construction of polycatenated DNA scaffolds to accomplish ultrasensitive detection of proteins based on structure-switching of aptamer upon target binding, which is demonstrated by using thrombin as a model analyte in this study. Overall, with two successive amplification steps and one magnetic separation procedure, this flexible biosensing system exhibits not only high sensitivity and specificity with the detection limits of SNPs and thrombin as low as 71 aM and 6.6 pM, respectively, but also excellent performance in real human serum assay with no PCR preamplification for SNPs assay. Given the unique and attractive characteristics, this study illustrates the potential of DNA nanotechnology in bioanalytical applications for both fundamental and practical research.

Rolling circle amplification combined with gold nanoparticle aggregates for highly sensitive identification of single-nucleotide polymorphisms

A highly sensitive and specific colorimetry-based rolling circle amplification (RCA) assay method for single-nucleotide polymorphism genotyping has been developed. A circular template is generated by ligation upon the recognition of a point mutation on DNA targets. An RCA amplification is then initiated using the circular template in the presence of Phi29 polymerase. The RCA product can be digested by a restricting endonuclease, and the cleaved DNA fragments can mediate the aggregation of gold nanoparticle-tagged DNA probes. This causes a colorimetric change of the solution as the indicator of the mutation occurrence, which can be detected using UV-vis spectroscopy or viewed by naked eyes. On the basis of the high amplification efficiency of Phi29 polymerase, a mutated target of approximately 70 fM can be detected in this assay. In addition, the protection of the circle template using phosphorothioated nucleotides allows the digestion reaction to be performed simultaneously in RCA. Moreover, DNA ligase offers high fidelity in distinguishing the mismatched bases at the ligation site, resulting in positive detection of mutant targets even when the ratio of the wild-type to the mutant is 10,000:1. The developed RCA-based colorimetric detection scheme was demonstrated for SNP typing of beta-thalassemia gene at position -28 in genomic DNA.

Fluorescence aptameric sensor for strand displacement amplification detection of cocaine

A new fluorescence method based on aptamer-target interactions has been developed for cocaine detection with target-induced strand displacement. Here we describe new probes, the hairpin-probe and the single strand-probe (ss-probe), that possess two recognition sequences of cocaine aptamer. In the presence of cocaine, both probes would associate with the target to form a tripartite complex. The conformational change in the hairpin-probe causes the opening of a hairpin structure and the hybridization to primer. With polymerase and the dNTPs, the replication of the single-stranded domain of hairpin-probe triggers the process of primer extension. When the hairpin-probe is converted into a fully double-stranded form, the ss-probe and cocaine are displaced to bind another hairpin-probe and initiate new amplification cycles. Fluorescence signal generation would be observed upon SYBR Green I intercalating into the new DNA double helix. The new protocol design permits detection of as low as 2 nM cocaine in a closed tube, offering a convenient approach for a homogeneous assay. Compared with previously reported cocaine aptameric sensors, our new method is highly sensitive, selective, and economical.

Microsphere-based rolling circle amplification microarray for the detection of DNA and proteins in a single assay

We describe a high-density microarray for simultaneous detection of proteins and DNA in a single test. In this system, Rolling Circle Amplification (RCA) was used as a signal amplification method for both protein and nucleic acid detection. The microsphere sensors were tested with synthetic DNA and purified recombinant protein analytes. The target DNA sequence was designed from a highly conserved gene that encodes the outer membrane protein P6 (OMP-P6) of both typeable and nontypeable strains of Haemophilus influenzae. The proinflammatory mediators IL-6 and IL-8 were selected as target proteins. Capture antibodies were first immobilized on fluorescently encoded microspheres. The microspheres were then loaded into the etched microwells of an imaging optical fiber bundle. A sandwich assay was performed for target proteins IL-6 and IL-8 using biotin-labeled secondary antibodies. Biotinylated capture DNA probes were then attached to the detection antibodies via an avidin bridge. A padlock probe, complementary to the target sequence, was subsequently hybridized to the capture probe. In the presence of the target sequence, the padlock probe was ligated, and this circular sequence was used for RCA. Following RCA, multiple fluorescently labeled signal probes were hybridized to each amplified sequence, and the microarray was imaged using an epi-fluorescence microscope. With this assay, detection limits down to 10 fM and 1 pM were achieved for proteins and target DNA, respectively. In addition to this new approach for detecting both protein and DNA in a single test using RCA, the limit of detection for IL-8 and IL-6 was improved by 3 orders of magnitude compared to similar microsphere-based assays.

Split hybridisation probes for electrochemical typing of single-nucleotide polymorphisms

This paper describes the development of a highly selective single-nucleotide polymorphisms (SNPs) typing method based on the use of split hybridisation probes and demonstrates the concept through the electrochemical analysis of single-base mutations in actual patient samples. The requirement that two probes hybridised adjacent to one another to allow for stabilisation (via base-stacking) and binding of the allele-specific oligonucleotide (ASO), imparted highly stringent selectivity criteria to the assay. Simple rules for tuning the characteristics of such stacking/ASO probe pairs and achieve full mismatch discrimination at ambient conditions (with no need to strictly control the temperature) are provided. All genotyping experiments were indeed performed at room temperature, using the planar surface of disposable probe-modified gold electrodes as the genosensing platform. The ability to detect nanomolar amounts of a synthetic target even within a vast excess of single-base substituted sequences gave strong evidence of the specificity of the split probes assay. Proving the general validity of this genotyping approach, application of the analytical pathway was further demonstrated for clinical targets (amplified from the human TP53 gene) whose mutational site was poorly accessible, being part of a thermodynamically stable hairpin. In combination with use of auxiliary oligonucleotides (which restored the availability of each pre-defined hybridisation site), the assay demonstrated the ability to fully discriminate single-base mutations with detection limits in the high picomolar range (total analysis time: 60 min). Our specific probe design, hybridisation and signal transduction paths make the analytical process remarkably simple, relatively low cost and, thus, well suited for low throughput analysis of clinically relevant samples.

Rolling circle amplification: applications in nanotechnology and biodetection with functional nucleic acids

Rolling circle amplification (RCA) is an isothermal, enzymatic process mediated by certain DNA polymerases in which long single-stranded (ss) DNA molecules are synthesized on a short circular ssDNA template by using a single DNA primer. A method traditionally used for ultrasensitive DNA detection in areas of genomics and diagnostics, RCA has been used more recently to generate large-scale DNA templates for the creation of periodic nanoassemblies. Various RCA strategies have also been developed for the production of repetitive sequences of DNA aptamers and DNAzymes as detection platforms for small molecules and proteins. In this way, RCA is rapidly becoming a highly versatile DNA amplification tool with wide-ranging applications in genomics, proteomics, diagnosis, biosensing, drug discovery, and nanotechnology.

KRAS mutation testing for predicting response to anti-EGFR therapy for colorectal carcinoma: proposal for an European quality assurance program

Novel therapeutic agents targeting the epidermal growth factor receptor (EGFR) have improved outcomes for patients with colorectal carcinoma. However, these therapies are effective only in a subset of patients. Activating mutations in the KRAS gene are found in 30-40% of colorectal tumors and are associated with poor response to anti-EGFR therapies. Thus, KRAS mutation status can predict which patient may or may not benefit from anti-EGFR therapy. Although many diagnostic tools have been developed for KRAS mutation analysis, validated methods and standardized testing procedures are lacking. This poses a challenge for the optimal use of anti-EGFR therapies in the management of colorectal carcinoma. Here we review the molecular basis of EGFR-targeted therapies and the resistance to treatment conferred by KRAS mutations. We also present guideline recommendations and a proposal for a European quality assurance program to help ensure accuracy and proficiency in KRAS mutation testing across the European Union.

A two-dimensional suspension array system by coupling field flow fractionation to flow cytometry

Flow field flow fractionation (Fl-FFF) was coupled to flow cytometry to improve the performance of suspension arrays. Size-based separation of the protein-conjugated microspheres by Fl-FFF was performed and the results demonstrated that, the separation could tolerate a wide range of carrier fluid conditions (pH values, salt concentrations, and buffer compositions) favorable for immunoassays. The immuno-complex remained intact during Fl-FFF, as revealed by fluorescence measurements before and after the Fl-FFF separation, and SDS-PAGE of the eluted proteins. The sample throughput of the suspension array can be increased several folds by using particles of different sizes and separating them with Fl-FFF before flow cytometric measurement. Moreover, the gel result hinted that the continuous wash inside the Fl-FFF system may lower the assay background, another possible advantage of the two-dimensional suspension array system.