Double-hairpin molecular-beacon-based amplification detection for gene diagnosis linked to cancer

Tailed molecular beacon probes: an approach for the detection of structured DNA and RNA analytes

Molecular beacon (MB) probes have been extensively used for nucleic acid analysis. However, MB probes fail to hybridize with folded DNA or RNA. Here, we demonstrate that MB probes equipped with extra sequences complementary to the analyte, named 'tail', can increase the signal-to-background ratio by ∼40-fold and hybridization rates by ∼800-fold compared to conventional MB probes. Tailed MB probes can be used as mismatched-tolerant alternatives to traditional hairpin probes for fast assays.

Electrochemical aptamer biosensor for DNA detection based on label-free aptamers

Electrochemical aptasensor has been broadly advanced for nucleic acid detection. However, it is a long-term goal to design an aptasensor with high specificity, flexibility, and simplicity. In this work, we develop a strategy of triblock DNA probe, which consists of two DNA probes at both ends and ployA fragments in the middle as probe-polyA-probe. PolyA fragment has high affinity to the surface of gold electrode, so it can be assembled on the electrode surface via polyA instead of traditional Au-S bonds. When the target DNA is simultaneously hybridized with the two capture probes, the hybridization stability can be improved due to the strong base stacking effect. [Ru(NH₃)₆]³⁺, as signal probe, can be electrostatically adsorbed on the negatively charged DNA skeleton. A wide linear range (10 pM-10 μM) is obtained with a detection limit of 2.9 pM. Our electrochemical aptasensor has good repeatability, stability, and specificity. More importantly, the electrochemical sensor can successfully detect DNA in human serum samples, which proves its practical value and extensive applicability in complex environment.

Colorimetric ultrasensitive detection of DNA based on the intensity of gold nanoparticles with dark-field microscopy

We present an ultrasensitive colorimetric nucleic acid assay based on the intensity of gold nanoparticles (Au NPs) using dark field microscopy. In the absence of target DNA, two hairpin-like DNA strands with protruding single-stranded DNA (ssDNA) can be absorbed onto the Au NP surface via non-covalent interactions between the exposed nitrogen bases of ssDNA and Au NPs, which inhibits Au NPs from aggregating in a high concentration of salt media, while in the presence of target DNA, two hairpin DNA strands hybridize with target DNA to form double-stranded DNA (dsDNA). After hybridization chain reaction (HCR) amplification, rigid dsDNA polymers are formed, which results in serious Au NP aggregation in the salt environment. By measuring the intensity change of yellow and red dots on a dark-field image, the concentration of target DNA can be accurately quantified with a limit of detection (LOD) of 66 fM.

An ultrasensitive and simple fluorescence biosensor for detection of the Kras wild type by using the three-way DNA junction-driven catalyzed hairpin assembly strategy

A label-free platform for simple detection of the Kras gene was proposed by using the three-way DNA junction-driven catalyzed hairpin assembly strategy.

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.

Nicking-enhanced rolling circle amplification for sensitive fluorescent detection of cancer-related microRNAs

In this study, a biosensing system based on nicking-enhanced rolling circle amplification (N-RCA) was proposed for the highly sensitive detection of cancer-related let-7a microRNA (miRNA). The sensing system consists of a padlock probe (PP), which contains a target recognition sequence and two binding sites for nicking endonuclease (NEase), and molecular beacon (MB) as reporting molecule. Upon hybridization with let-7a, the PP can be circularized by ligase. Then, the miRNA acted as polymerization primer to initiate rolling circle amplification (RCA). With the assistance of NEase, RCA products can be nicked on the cyclized PP and are displaced during the subsequent duplication process, generating numerous nicked fragments (NFs). These NFs not only induce another RCA reaction but also open the molecular beacons (MBs) via hybridization, leading to significantly amplified fluorescence signal. Under the optimized conditions, this method exhibits high sensitivity toward target miRNA let-7a with a detection limit of as low as 10 pM, a dynamic range of three orders of magnitude is achieved, and its family member is easily distinguished even with only one mismatched base. Meanwhile, it displays good recovery and satisfactory reproducibility in fetal bovine serum (FBS). Therefore, these merits endow the newly proposed N-RCA strategy with powerful implications for miRNA detection. Graphical abstract A biosensing system based on nicking-enhanced rolling circle amplification (N-RCA) for the highly sensitive detection of cancer-related let-7a microRNA.