Electrochemical branched-DNA assay for polymerase chain reaction-free detection and quantification of oncogenes in messenger RNA

Adaptive chirality of achiral tetraphenylethene-based tetracationic cyclophanes with dual responses of fluorescence and circular dichroism in water

Two tetraphenylethene-based tetracationic cyclophanes 1 and 2 were synthesized via a one-step S_N2 reaction without using any template. Based on the fluorescence and rotational conformation of the tetraphenylethene units, these water-soluble cyclophanes exhibited adaptive chirality with dual responses of turn-on fluorescence and induced circular dichroism when combined with nucleotides and DNA in water.

Nucleic Acids Analysis

Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.

Oligonucleotide-based label-free detection with optical microresonators: strategies and challenges

This review targets diversified oligonucleotide-based biodetection techniques, focusing on the use of microresonators of whispering gallery mode (WGM) type as optical biosensors mostly integrated with lab-on-a-chip systems. On-chip and microfluidics combined devices along with optical microresonators provide rapid, robust, reproducible and multiplexed biodetection abilities in considerably small volumes. We present a detailed overview of the studies conducted so far, including biodetection of various oligonucleotide biomarkers as well as deoxyribonucleic acids (DNAs), ribonucleic acids (RNAs) and proteins. We particularly advert to chemical surface modifications for specific and selective biosensing.

Electrochemical detection of leukemia oncogenes using enzyme-loaded carbon nanotube labels

We describe an ultrasensitive electrochemical nucleic acid assay amplified by carbon nanotubes (CNTs)-based labels for the detection of human acute lymphocytic leukemia (ALL)-related p185 BCR-ABL fusion transcript. The carboxylated CNTs were functionalized with horseradish peroxidase (HRP) molecules and target-specific detection probes (DP) via diimide-activated amidation and used to label and amplify the target hybridization signal. The activity of captured HRP was monitored by square-wave voltammetry measuring the electroactive enzymatic product in the presence of 2-aminophenol and hydrogen peroxide substrate solution. The signal-amplified assay achieved a detection limit of 83 fM (5 × 10(-18) mol in 60 μL) targets oligonucleotides and has a 4-order-wide dynamic range of target concentration. The resulting assay allowed robust discrimination between the perfect match and a three-base mismatch sequence. When exposed to the full-length (491 bp) DNA oncogene, the approach demonstrated a detection limit of 1 × 10(-16) mol in 60 μL, corresponding to approximately 33 pg of the target gene. The high sensitivity and specificity of the assay enabled a PCR-free detection of target transcripts in as little as 65 ng of mRNA extracted from positive ALL cell lines SUP-B15 in comparison to those obtained from negative cell line HL-60. The approach enables a simple, low-cost and ultrasensitive electrochemical nucleic acid detection in portable devices, point-of-care and early disease diagnostic applications.

Modeling human nonalcoholic steatohepatitis-associated changes in drug transporter expression using experimental rodent models

Nonalcoholic fatty liver disease is a prevalent form of chronic liver disease that can progress to the more advanced stage of nonalcoholic steatohepatitis (NASH). NASH has been shown to alter drug transporter regulation and may have implications in the development of adverse drug reactions. Several experimental rodent models have been proposed for the study of NASH, but no single model fully recapitulates all aspects of the human disease. The purpose of the current study was to determine which experimental NASH model best reflects the known alterations in human drug transporter expression to enable more accurate drug disposition predictions in NASH. Both rat and mouse NASH models were used in this investigation and include the methionine and choline deficient (MCD) diet model, atherogenic diet model, ob/ob and db/db mice, and fa/fa rats. Pathologic scoring evaluations demonstrated that MCD and atherogenic rats, as well as ob/ob and db/db mice, developed NASH. Liver mRNA and protein expression analyses of drug transporters showed that in general, efflux transporters were induced and uptake transporters were repressed in the rat MCD and the mouse ob/ob and db/db models. Lastly, concordance analyses suggest that both the mouse and rat MCD models as well as mouse ob/ob and db/db NASH models show the most similarity to human transporter mRNA and protein expression. These results suggest that the MCD rat and mouse model, as well as the ob/ob and db/db mouse models, may be useful for predicting altered disposition of drugs with similar kinetics across humans and rodents.

Single-pair fluorescence resonance energy transfer analysis of mRNA transcripts for highly sensitive gene expression profiling in near real time

Expression analysis of mRNAs transcribed from certain genes can be used as important sources of biomarkers for in vitro diagnostics. While the use of reverse transcription quantitative PCR (RT-qPCR) can provide excellent analytical sensitivity for monitoring transcript numbers, more sensitive approaches for expression analysis that can report results in near real-time are needed for many critical applications. We report a novel assay that can provide exquisite limits-of-quantitation and consists of reverse transcription (RT) followed by a ligase detection reaction (LDR) with single-pair fluorescence resonance energy transfer (spFRET) to provide digital readout through molecular counting. For this assay, no PCR was employed, which enabled short assay turnaround times. To facilitate implementation of the assay, a cyclic olefin copolymer (COC) microchip, which was fabricated using hot embossing, was employed to carry out the LDR in a continuous flow format with online single-molecule detection following the LDR. As demonstrators of the assay's utility, MMP-7 mRNA was expression profiled from several colorectal cancer cell lines. It was found that the RT-LDR/spFRET assay produced highly linear calibration plots even in the low copy number regime. Comparison to RT-qPCR indicated a better linearity over the low copy number range investigated (10-10,000 copies) with an R(2) = 0.9995 for RT-LDR/spFRET and R(2) = 0.98 for RT-qPCR. In addition, differentiating between copy numbers of 10 and 50 could be performed with higher confidence using RT-LDR/spFRET. To demonstrate the short assay turnaround times obtainable using the RT-LDR/spFRET assay, a two thermal cycle LDR was carried out on amphiphysin gene transcripts that can serve as important diagnostic markers for ischemic stroke. The ability to supply diagnostic information on possible stroke events in short turnaround times using RT-LDR/spFRET will enable clinicians to treat patients effectively with appropriate time-sensitive therapeutics.

Polymerase chain reaction-free variable-number tandem repeat typing using gold nanoparticle-DNA monoconjugates

In this work, we report a novel polymerase chain reaction (PCR)-free variable-number tandem repeat (VNTR) typing method using a T-shaped gold nanoparticle-DNA monoconjugate, called the "watching-gene assay". The T-shaped DNA probe was synthesized by "click" chemistry and linked with the gold nanoparticle to form the gold nanoparticle-DNA monoconjugate (a VNTR probe). Through a simple annealing and ligation reaction of the VNTR probe on a synthetic DNA template mimicking the human D1S80 VNTR locus, the number of tandem repeat units could be deciphered by counting the self-assembled gold nanoparticles. The number of tandem repeat units could be identified with more than 50% yield if the repeat number was less than four. In the case of the real human genomic DNA, the 18 repeat unit number could be successfully revealed by observing the 18-gold-nanoparticle cluster, which exactly corresponded to the number of tandem repeats of the real sample. Our "watching-gene assay" is rapid, simple, and direct for data interpretation, thereby providing an advanced PCR-free genetic polymorphism analysis platform.

Electrochemiluminescence detection of c-Myc mRNA in breast cancer cells on a wireless bipolar electrode

Electrochemiluminescence (ECL) on bipolar electrode (BPE) is a sensitive, portable, and low-cost approach which has been employed to detect DNA and proteins. Here, we develop an ultrasensitive method for intracellular mRNA assay based on mRNA-mediated reporter DNA liberation and Ru(bpy)3(2+)-conjugated silica nanoparticles (RuSi@Ru(bpy)3(2+)) tag-based signal amplification.

Alu-based cell-free DNA: a potential complementary biomarker for diagnosis of colorectal cancer

OBJECTIVES

Many patients with colorectal cancer (CRC) present with regional or widespread metastasis, partially reflecting limitations of the current screening programs. This study was aimed to find a complementary marker that can improve the diagnostic accuracy.

DESIGN AND METHODS

Concentrations of cell-free DNA based on Alu (Alu-based CFD) in 31 unselected CRC patients, 30 intestinal polyp patients and 92 healthy individuals were detected by branch DNA (bDNA). Concentrations of carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9 (CA19-9) were detected by ARCHITECT assay.

RESULTS

There was significant difference in concentrations of CFD between CRC and intestinal polyp patients or healthy individuals (P<0.0001). There was no statistically significant difference in CFD in different subgroups of CRC patients with respect to gender, age, tumor site and pathologic stage, suggesting that CFD might be an independent marker relative to CEA and CA19-9. There was a significant correlation between pathologic stage and CEA or CA19-9. Although no significant correlation was observed between pathologic stage and CFD, CFD (the area under the receiver operating characteristic curve (AUC)=0.904) seemed to be a better indicator to distinguish CRC patients from intestinal polyp patients as compared with CEA (AUC=0.681) or CA19-9 (AUC=0.651). CFD was more accurate than CEA or CA19-9 in diagnosing CRC.

CONCLUSIONS

Combination of CFD, CEA and CA19-9 may be a better option for the diagnosis of CRC than any of them used alone. Discrimination CRC from intestinal polyp patients with CFD and staging with CEA and CA19-9 may substantially improve the accuracy CRC diagnosis.

Chaperone probes and bead-based enhancement to improve the direct detection of mRNA using silicon photonic sensor arrays

Herein, we describe the utility of chaperone probes and a bead-based signal enhancement strategy for the analysis of full length mRNA transcripts using arrays of silicon photonic microring resonators. Changes in the local refractive index near microring sensors associated with biomolecular binding events are transduced as a shift in the resonant wavelength supported by the cavity, enabling the sensitive analysis of numerous analytes of interest. We employ the sensing platform for both the direct and bead-enhanced detection of three different mRNA transcripts, achieving a dynamic range spanning over 4 orders of magnitude and demonstrating expression profiling capabilities in total RNA extracts from the HL-60 cell line. Small, dual-use DNA chaperone molecules were developed and found to both enhance the binding kinetics of mRNA transcripts by disrupting complex secondary structure and serve as sequence-specific linkers for subsequent bead amplification. Importantly, this approach does not require amplification of the mRNA transcript, thereby allowing for simplified analyses that do not require expensive enzymatic reagents or temperature ramping capabilities associated with RT-PCR-based methods.

Enzyme-based ultrasensitive electrochemical biosensors

Signal amplification in conventional enzyme-based biosensors is not high enough to achieve the ultrasensitive detection of biomolecules. In recent years, signal amplification has been improved by combining enzymatic reactions with redox cycling or employing multienzyme labels per detection probe. Electrochemical-chemical redox cycling and electrochemical-chemical-chemical redox cycling allow ultrasensitive detection simply by including one or two more chemicals in a solution without the use of an additional enzyme and/or electrode. Multiple horseradish peroxidase labels on magnetic bead carriers provide high signal enhancement along with a multiplex detection possibility. In both cases, the detection procedures are the same as those in conventional enzyme-based electrochemical sensors.

Electrochemical immunosensor of tumor necrosis factor α based on alkaline phosphatase functionalized nanospheres

A novel immunosensor for sensitive detection of tumor necrosis factor α was reported. First of all, gold nanoparticles were uniformly assembled on the surface of poly (styrene-acrylic acid) nanospheres, which was used as the matrix to conjugate alkaline phosphatase (ALP). And then, the obtained composite was used as multi-enzyme functionalized label for immunoassay. Biocompatible polyaniline doped with poly (acrylic acid) was electro-polymerized at the glass carbon electrode to construct the matrix for the immobilization of antibody TNF-α. After the sandwich immunoreaction, the labeled ALP was used to hydrolyze α-naphthyl phosphate to produce the electroactive α-naphthol, which could be amperometrically detected. The results showed that the electrochemical signals were proportional to the logarithm of the antigen concentration in the range of 0.02-200.00 ng/mL with the detection limit of 0.01 ng/mL. The developed immunoassay showed high sensitivity, acceptable stability and reproducibility, which might have potentially broad applications in protein diagnostics and bioassay.