PCR-Independent Detection of Bacterial Species-Specific 16S rRNA at 10 fM by a Pore-Blockage Sensor

Progress in methods for the detection of viable Escherichia coli

Escherichia coli (E. coli) is a prevalent enteric bacterium and a necessary organism to monitor for food safety and environmental purposes. Developing efficient and specific methods is critical for detecting and monitoring viable E. coli due to its high prevalence. Conventional culture methods are often laborious and time-consuming, and they offer limited capability in detecting potentially harmful viable but non-culturable E. coli in the tested sample, which highlights the need for improved approaches. Hence, there is a growing demand for accurate and sensitive methods to determine the presence of viable E. coli. This paper scrutinizes various methods for detecting viable E. coli, including culture-based methods, molecular methods that target DNAs and RNAs, bacteriophage-based methods, biosensors, and other emerging technologies. The review serves as a guide for researchers seeking additional methodological options and aiding in the development of rapid and precise assays. Moving forward, it is anticipated that methods for detecting E. coli will become more stable and robust, ultimately contributing significantly to the improvement of food safety and public health.

Construction of a point-of-care electrochemical biosensor for Escherichia coli 16S rRNA analysis based on MoS2 nanoprobes

Foodborne pathogens are harmful to human health because they can contaminate food and induce diseases. To efficiently distinguish and determine foodborne bacteria, an ultrasensitive point-of-care electrochemical biosensor was designed for 16S rRNA detection by coupling a signal amplification strategy with MoS2-based nanoprobes. Gold nanoparticles and thionine co-functionalized molybdenum disulfide (MoS2) nanocomposites (MoS2-Thi-AuNPs) were used to construct nanoprobes, which can efficiently monitor the detection process and amplify the detection signal. In the presence of Escherichia coli (E. coli) 16S rRNA, a classical sandwiched DNA structure was formed on the surface of a hierarchical flower-like gold nanostructure-decorated screen-printed carbon electrode (HFGN-SPCE), generating an obvious electrochemical signal from Thi. Under optimal conditions, this designed electrochemical biosensor showed a wide dynamic range (0-1.0 × 106 fM), low detection limit (2.8 fM), high selectivity and accepted stability for E. coli 16S rRNA detection in ideal buffers. Moreover, this biosensor can efficiently determine 16S rRNA in milk samples and 10 CFU mL-1 bacterial lysate. All experimental results suggested that this biosensor has a promising application in the detection of foodborne pathogens.

Nanoparticle-blockage-enabled rapid and reversible nanopore gating with tunable memory

Gated protein channels act as rapid, reversible, and fully-closeable nanoscale valves to gate chemical transport across the cell membrane. Replicating or outperforming such a high-performance gating and valving function in artificial solid-state nanopores is considered an important yet unsolved challenge. Here we report a bioinspired rapid and reversible nanopore gating strategy based on controlled nanoparticle blockage. By using rigid or soft nanoparticles, we respectively achieve a trapping blockage gating mode with volatile memory where gating is realized by electrokinetically trapped nanoparticles near the pore and contact blockage gating modes with nonvolatile memory where gating is realized by a nanoparticle physically blocking the pore. This gating strategy can respond to an external voltage stimulus (∼200 mV) or pressure stimulus (∼1 atm) with response time down to milliseconds. In particular, when 1,2-diphytanoyl-sn-glycero-3-phosphocholine liposomes are used as the nanoparticles, the gating efficiency, defined as the extent of nanopore closing compared to the opening state, can reach 100%. We investigate the mechanisms for this nanoparticle-blockage-enabled nanopore gating and use it to demonstrate repeatable controlled chemical releasing via single nanopores. Because of the exceptional spatial and temporal control offered by this nanopore gating strategy, we expect it to find applications for drug delivery, biotic-abiotic interfacing, and neuromorphic computing.

A rapid bioanalytical tool for detection of sequence-specific circular DNA and mitochondrial DNA point mutations

Mutations in mitochondrial DNA (mtDNA) have been an essential cause of numerous diseases, making their identification critically important. The majority of mtDNA screening techniques require polymerase chain reaction (PCR) amplification, enzymatic digestion, and denaturation procedures, which are laborious and costly. Herein, we developed a sensitive PCR-free electrokinetic-based sensor combined with a customized bis-peptide nucleic acid (bis-PNA) and gamma-PNA (γ-PNA) probes immobilized on beads, for the detection of mtDNA point mutations and sequence-specific supercoiled plasmid DNA at the picomolar range. The probes are capable of invading the double-stranded circular DNA and forming a stable triplex structure. Thus, this method can significantly reduce the sample preparation and omit the PCR amplification steps prior to sensing. Further, this bioanalytical tool can open up a new paradigm in clinical settings for the screening of double-stranded circular nucleic acids with a single-base mismatch specificity in a rapid and sensitive manner.

Amplification-free, sequence-specific 16S rRNA detection at 1 aM

A nucleic acid amplification-free, optics-free platform has been demonstrated for sequence-specific detection of Escherichia coli (E. coli) 16S rRNA at 1 aM (10-18 M) against a 106-fold (1 pM) background of Pseudomonas putida (P. putida) RNA. This work was driven by the need for simple, rapid, and low cost means for species-specific bacterial detection at low concentration. Our simple, conductometric sensing device functioned by detecting blockage of a nanopore fabricated in a sub-micron-thick glass membrane. Upon sequence-specific binding of target 16S rRNA, otherwise charge-neutral, PNA oligonucleotide probe-polystyrene bead conjugates become electrophoretically mobile and are driven to the glass nanopore of lesser diameter, which is blocked, thereby generating a large, sustained and readily observable step decrease in ionic current. No false positive signals were observed with P. putida RNA when this device was configured to detect E. coli 16S rRNA. Also, when a universal PNA probe complementary to the 16S rRNA of both E. coli and P. putida was conjugated to beads, a positive response to rRNA of both bacterial species was observed. Finally, the device readily detected E. coli at 10 CFU mL-1 in a 1 mL sample, also against a million-fold background of viable P. putida. These results suggest that this new device may serve as the basis for small, portable, low power, and low-cost systems for rapid detection of specific bacterial species in clinical samples, food, and water.