A wine-induced breakdown

Chemically tailoring nanopores for single-molecule sensing and glycomics

A nanopore can be fairly-but uncharitably-described as simply a nanofluidic channel through a thin membrane. Even this simple structural description holds utility and underpins a range of applications. Yet significant excitement for nanopore science is more readily ignited by the role of nanopores as enabling tools for biomedical science. Nanopore techniques offer single-molecule sensing without the need for chemical labelling, since in most nanopore implementations, matter is its own label through its size, charge, and chemical functionality. Nanopores have achieved considerable prominence for single-molecule DNA sequencing. The predominance of this application, though, can overshadow their established use for nanoparticle characterization and burgeoning use for protein analysis, among other application areas. Analyte scope continues to be expanded, and with increasing analyte complexity, success will increasingly hinge on control over nanopore surface chemistry to tune the nanopore, itself, and to moderate analyte transport. Carbohydrates are emerging as the latest high-profile target of nanopore science. Their tremendous chemical and structural complexity means that they challenge conventional chemical analysis methods and thus present a compelling target for unique nanopore characterization capabilities. Furthermore, they offer molecular diversity for probing nanopore operation and sensing mechanisms. This article thus focuses on two roles of chemistry in nanopore science: its use to provide exquisite control over nanopore performance, and how analyte properties can place stringent demands on nanopore chemistry. Expanding the horizons of nanopore science requires increasing consideration of the role of chemistry and increasing sophistication in the realm of chemical control over this nanoscale milieu.

Surveying silicon nitride nanopores for glycomics and heparin quality assurance

Polysaccharides have key biological functions and can be harnessed for therapeutic roles, such as the anticoagulant heparin. Their complexity—e.g., >100 monosaccharides with variety in linkage and branching structure—significantly complicates analysis compared to other biopolymers such as DNA and proteins. More, and improved, analysis tools have been called for, and here we demonstrate that solid-state silicon nitride nanopore sensors and tuned sensing conditions can be used to reliably detect native polysaccharides and enzymatic digestion products, differentiate between different polysaccharides in straightforward assays, provide new experimental insights into nanopore electrokinetics, and uncover polysaccharide properties. We show that nanopore sensing allows us to easily differentiate between a clinical heparin sample and one spiked with the contaminant that caused deaths in 2008 when its presence went undetected by conventional assays. The work reported here lays a foundation to further explore polysaccharide characterization and develop assays using thin-film solid-state nanopore sensors.

The complexity of polysaccharides significantly complicates their analysis in comparison to other biopolymers. Here, the authors demonstrate that solid-state silicon nitride nanopore sensors can be used to reliably detect native polysaccharides and to perform a simple quality assurance assay on a polysaccharide therapeutic, heparin.

Pathways from epigenomics and glycobiology towards novel biomarkers of addiction and its radical cure

The recent demonstration that addiction-relevant neuronal ensembles defined by known master transcription factors and their connectome is networked throughout mesocorticolimbic reward circuits and resonates harmonically at known frequencies implies that single-cell pan-omics techniques can improve our understanding of Substance Use Disorders (SUD's). Application of machine learning algorithms to such data could find diagnostic utility as biomarkers both to define the presence of the disorder and to quantitate its severity and find myriad applications in a developmental pipeline towards therapeutics and cure. Recent epigenomic studies have uncovered a wealth of clinically important data relating to synapse-nucleus signalling, memory storage, lineage-fate determination and cellular control and are contributing greatly to our understanding of all SUD's. Epigenetics interacts extensively with glycobiology. Glycans decorate DNA, RNA and many circulating critical proteins particularly immunoglobulins. Glycosylation is emerging as a major information-laden post-translational protein modification with documented application for biomarker development. The integration of these two emerging cutting-edge technologies provides a powerful and fertile algorithmic-bioinformatic space for the development both of SUD biomarkers and novel cutting edge therapeutics.

HYPOTHESES

These lines of evidence provide fertile ground for hypotheses relating to both diagnosis and treatment. They suggest that biomarkers derived from epigenomics complemented by glycobiology may potentially provide a bedside diagnostic tool which could be developed into a clinically useful biomarker to gauge both the presence and the severity of SUD's. Moreover they suggest that modern information-based therapeutics acting on the epigenome, via RNA interference or by DNA antisense oligonucleotides may provide a novel 21st century therapeutic development pipeline towards the radical cure of addictive disorders. Such techniques could be focussed and potentiated by neurotrophic vectors or the application of interfering electric or magnetic fields deep in the medial temporal lobes of the brain.