Simultaneous detection of attomolar pathogen DNAs by Bio-MassCode mass spectrometry

Nucleic acid amplification-free detection of DNA and RNA at ultralow concentration

The broad spectrum of approaches for nucleic acid amplification-free detection of DNA and RNA at single-digit attomolar (10^-18 M) concentration and lower is reviewed. These low concentrations correspond roughly to the most clinically desirable detection range for pathogen-specific nucleic acid as well as the detection limits of commercially available, nucleic acid amplification tests based primarily on polymerase chain reaction (PCR). The need for more rapid and inexpensive, yet still highly accurate tests, has become evident during the pandemic. It is expected that publication of reports describing improved tests will accelerate soon, and this review covers the wide variety of detection methods based on both optical and electrical measurements that have been conceived over recent years, enabled generally by the advent of nanotechnology.

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.

Ultrasensitive Detection of Low-Abundance Protein Biomarkers by Mass Spectrometry Signal Amplification Assay

A mass spectrometry signal amplification method is developed for the ultrasensitive and selective detection of low-abundance protein biomarkers by utilizing tag molecules on gold nanoparticles (AuNPs). EpCAM and thrombin as model targets are captured by specific aptamers immobilized on the AuNPs. With laser desorption/ionization time-of-flight mass spectrometry (LDI-TOF MS), the mass tag molecules are detected to represent the protein biomarkers. Benefiting from the MS signal amplification, the assay can achieve a limit of detection of 100 aM. The method is further applied to detect thrombin in fetal bovine serum and EpCAM in cell lysates to demonstrate its selectivity and feasibility in complex biological samples. With the high sensitivity and specificity, the protocol shows great promise for providing a new route to single-cell analysis and early disease diagnosis.

Gold Nanoparticles for DNA/RNA-Based Diagnostics

The remarkable physicochemical properties of gold nanoparticles (AuNPs) have prompted development in exploring biomolecular interactions with AuNPs-containing systems, pursuing biomedical applications in diagnostics. Among these applications, AuNPs have been remarkably useful for the development of DNA/RNA detection and characterization systems for diagnostics, including systems suitable for point of need. Here, emphasis will be on available molecular detection schemes of relevant pathogens and their molecular characterization, genomic sequences associated with medical conditions (including cancer), mutation and polymorphism identification, and the quantification of gene expression.

A sensitive biosensing strategy for DNA detection based on graphene oxide and T7 exonuclease assisted target recycling amplification

A fluorescence biosensing strategy based on graphene oxide (GO) was reported for simple, rapid, sensitive, and selective DNA detection by T7 exonuclease assisted target recycling amplification. Due to the super fluorescence quenching efficiency of GO, the fluorescein amiditelabeled signal probe was firstly adsorbed onto the surface of GO and the fluorescence was quenched. Owing to its excellent selectivity for double-stranded DNA, T7 exonuclease was chosen as a signal-amplifying biocatalyst to improve the detection sensitivity. In the presence of target DNA, the signal probe could bind with target DNA and form a DNA duplex structure to trigger the digestion of the signal probe by T7 exonuclease, leading to the recycling of target DNA and the increasing of fluorescence intensity. Upon the recycling use of target DNA, this method achieved a high sensitivity towards target DNA with a detection limit of 0.3 pmol/L, which was lower than previously reported for GO-based DNA biosensors. Moreover, it does not require complex modifications of the molecular beacon and time-consuming thermal cycling procedures. Thus, the simple strategy provides a universal biosensing platform for DNA detection and it could find wide applications in DNA damage analysis and diagnostics.

Cysteine modified small ligament Au nanoporous film: an easy fabricating and highly efficient surface-assisted laser desorption/ionization substrate

Au nanoporous films (NPFs) with different surface modification and morphology were fabricated and utilized as substrates for the analysis of a series of compounds, including amino acids, drug, cyclodextrins, peptides, and polyethylene glycols, using surface-assisted laser desorption/ionization time-of-flight mass spectrometry (SALDI-TOF MS). It was found that the size and interconnection state of the NPF ligament as well as the surface modification are key parameters that affect the laser desorption/ionization performance. Compared with 2,5-dihydroxybenzoic acid, pristine NPF, and aminobenzenethiol or 3-mercaptopropanoic acid modified Au NPFs, cysteine modified Au NPF generated intense and background-suppressing mass spectra. Regarding the effect of Au NPF morphology, the Au NPF with nanopores in the range of 10-30 nm, ligament size of 5 nm, and electrochemistry surface area of 26.1 m(2)/g exhibited the highest performance as a substrate. This high-performance NPFs can be easily fabricated by capping agent replacement induced self-organization of ultrathin nanowires, followed by self-assembling of a monolayer (SAM) of cysteine. The good thermal/electroconductivity and uniformity of Au NPFs avoided the fragmentation of analytes, eliminated the intrinsic matrix ions interference, and provided good reproducibility (RSD ≤ 10%). Additionally, the fabricated NPFs can be easy divided into microarrays (a ~4 × 4 array from a 1 cm × 1 cm NPF). This work provides a simple and cost-effective route for acquiring an Au nanostructure as a SALDI substrate, which offers a new technique for high-speed analysis of low-molecular weight compounds.