Secondary Ions Mass Spectrometric Signal Enhancement of Peptides on Enlarged-Gold Nanoparticle Surfaces

Utilization of chromogenic enzyme substrates for signal amplification in multiplexed detection of biomolecules using surface mass spectrometry

MicroRNAs (miRNAs) are important post-transcriptional gene regulators and can serve as potential biomarkers for many diseases. Most of the current miRNA detection techniques require purification from biological samples, amplification, labeling, or tagging, which makes quantitative analysis of clinically relevant samples challenging. Here we present a new strategy for the detection of miRNAs with uniformity over a large area based on signal amplification using enzymatic reactions and measurements using time-of-flight secondary ion mass spectrometry (ToF-SIMS), a sensitive surface analysis tool. This technique has high sequence specificity through hybridization with a hairpin DNA probe and allows the identification of single-base mismatches that are difficult to distinguish by conventional mass spectrometry. We successfully detected target miRNAs in biological samples without purification, amplification, or labeling of target molecules. In addition, by adopting a well-known chromogenic enzymatic reaction from the field of biotechnology, we extended the use of enzyme-amplified signal enhancement ToF (EASE-ToF) to protein detection. Our strategy has advantages with respect to scope, quantification, and throughput over the currently available methods, and is amenable to multiplexing based on the outstanding molecular specificity of mass spectrometry (MS). Therefore, our technique not only has the potential for use in clinical diagnosis, but also provides evidence that MS can serve as a useful readout for biosensing to perform multiplexed analysis extending beyond the limitations of existing technology.

TOF-SIMS analysis of an isocitrate dehydrogenase 1 mutation-associated oncometabolite in cancer cells

The development of analytical tools for accurate and sensitive detection of intracellular metabolites associated with mutated metabolic enzymes is important in cancer diagnosis and staging. The gene encoding the metabolic enzyme isocitrate dehydrogenase 1 (IDH1) is mutated in various cancers, and mutant IDH1 could represent a good biomarker and potent target for cancer therapy. Owing to a mutation in an important arginine residue in the catalytic pocket, mutant IDH1 catalyzes the production of 2-hydroxyglutarate (2-HG) instead of its wild type product α-ketoglutarate (α-KG), which is involved in multiple cellular pathways involving the hydroxylation of proteins, ribonucleic acid, and deoxyribose nucleic acid (DNA). Since 2-HG is an α-KG antagonist, inhibiting normal α-KG-dependent metabolism, high intracellular levels of 2-HG result in abnormal histone and DNA methylation. Therefore, accurate and sensitive analytical tools for the direct detection of 2-HG in cancer cells expressing mutant IDH1 would benefit this field, as it would minimize the need both for complicated experimental procedures and for large amounts of biological samples. Here, the authors describe a useful analytical method for the direct detection of 2-HG in lysates from a mutant IDH1-expressing cell line by time-of-flight secondary ion mass spectrometry (TOF-SIMS) analysis, a powerful surface analysis tool. In addition, the authors verified the efficacy of the specific mutant IDH1 inhibitor AGI-5198 by tracking the intracellular 2-HG concentration, which decreased in a dose-dependent manner. Our results demonstrate the large potential of TOF-SIMS as an analytical tool for the simple, direct detection of oncometabolites during cancer diagnosis, and for verifying the efficiency of the targeted cancer drugs.

Correlating microscopy techniques and ToF-SIMS analysis of fully grown mammalian oocytes

An innovative protocol for the 2D-molecular thin film analysis applying ToF-SIMS, SEM, AFM and optical microscopy imaging of fully grown mice oocytes is described.

Mass Spectrometry of Nanoparticles is Different

Secondary ion mass spectrometry, SIMS, is a method of choice for the characterization of nanoparticles, NPs. For NPs with large surface-to-volume ratios, heterogeneity is a concern. Assays should thus be on individual nano-objects rather than an ensemble of NPs; however, this may be difficult or impossible. This limitation can be side-stepped by probing a large number of dispersed NPs one-by-one and recording the emission from each NP separately. A large collection of NPs will likely contain subsets of like-NPs. The experimental approach is to disperse the NPs and hit an individual NP with a single massive cluster (e.g., C-60, Au-400). At impact energies of ~1 keV/atom, they generate notable secondary ion (SI) emission. Examination of small NPs (≤20 nm in diameter) shows that the SI emission is size-dependent and impacts are not all equivalent. Accurate identification of the type of impact is key for qualitative assays of core or outer shell composition. For quantitative assays, the concept of effective impacts is introduced. Selection of co-emitted ejecta combined with rejection (anticoincidence) of substrate ions allows refining chemical information within the projectile interaction volume. Last, to maximize the SI signal, small NPs (≤5 nm in diameter) can be examined in the transmission mode where the SI yields are enhanced ~10-fold over those in the (conventional) reflection direction. Future endeavors should focus on schemes acquiring SIs, electrons, and photons concurrently.

Guided formation of sub-5 nm interstitial gaps between plasmonic nanodisks

To achieve a reliable formation of a surface-enhanced Raman scattering (SERS) sensor with evenly distributed hot spots on a wafer scale substrate, we propose a hybrid approach combining physical nanolithography for preparing Au nanodisks and chemical Au reduction for growing them. During the chemical growth, the interstitial distance between the nanodisks decreased from 60 nm to sub-5 nm. The resulting patterns of the nanogap-rich Au nanodisks successfully enhance the SERS signal, and its intensity map shows only a 5% or less signal variation on the entire sample.

Probing nanoparticles and nanoparticle-conjugated biomolecules using time-of-flight secondary ion mass spectrometry

Bio-conjugated nanoparticles have emerged as novel molecular probes in nano-biotechnology and nanomedicine and chemical analyses of their surfaces have become challenges. The time-of-flight (TOF) secondary ion mass spectrometry (SIMS) has been one of the most powerful surface characterization techniques for both nanoparticles and biomolecules. When combined with various nanoparticle-based signal enhancing strategies, TOF-SIMS can probe the functionalization of nanoparticles as well as their locations and interactions in biological systems. Especially, nanoparticle-based SIMS is an attractive approach for label-free drug screening because signal-enhancing nanoparticles can be designed to directly measure the enzyme activity. The chemical-specific imaging analysis using SIMS is also well suited to screen nanoparticles and nanoparticle-biomolecule conjugates in complex environments. This review presents some recent applications of nanoparticle-based TOF-SIMS to the chemical analysis of complex biological systems.

An ultra-sensitive detection of a whole virus using dual aptamers developed by immobilization-free screening

In this study, we successfully developed a ssDNA aptamer pairs by using an advanced immobilization-free SELEX method with affinity-based selection and counter-screening process at every round. By implementing this method, two different aptamers specifically binding to bovine viral diarrhea virus type 1(BVDV type 1) with high affinity were successfully screened. This aptamer pair was applied to ultrasensitive detection platform for BVDV type 1 in a sandwich manner. The ultrasensitive detection of BVDV type 1 using one of aptamers conjugated with gold nanoparticles was obtained in aptamer-aptamer sandwich type sensing format, with the limit of detection of 800 copies/ml, which is comparable to a real-time PCR method.