Electronic single-molecule identification of carbohydrate isomers by recognition tunnelling

Abstract

Carbohydrates are one of the four main building blocks of life, and are categorized as monosaccharides (sugars), oligosaccharides and polysaccharides. Each sugar can exist in two alternative anomers (in which a hydroxy group at C-1 takes different orientations) and each pair of sugars can form different epimers (isomers around the stereocentres connecting the sugars). This leads to a vast combinatorial complexity, intractable to mass spectrometry and requiring large amounts of sample for NMR characterization. Combining measurements of collision cross section with mass spectrometry (IM–MS) helps, but many isomers are still difficult to separate. Here, we show that recognition tunnelling (RT) can classify many anomers and epimers via the current fluctuations they produce when captured in a tunnel junction functionalized with recognition molecules. Most importantly, RT is a nanoscale technique utilizing sub-picomole quantities of analyte. If integrated into a nanopore, RT would provide a unique approach to sequencing linear polysaccharides.

Controlling DNA Tug‐of‐War in a Dual Nanopore Device

“…Voltage field‐force balancing would be facilitated by the atomic level precision of the biopore structures. Solid‐state based alternatives include patterning recognition tunneling electrodes on a surface between the controlling pores or as part of a multilayered membrane, which have sensing potential beyond nucleic acids . Beyond sequencing, the device could enable genome mapping, or detecting the presence/absence of base modifications along with the sequence context (via PNA‐PEG labeling) that is needed for clinical relevance.…”

Observation of giant conductance fluctuations in a protein

“…[25] Before use, the probes were tested in 1 mM phosphate buffer (pH=7.4) at 0.5 V bias to ensure that the leakage current was <1 pA. For functionalization, the probe was gently cleaned using ethanol and water, respectively, and then dried in a flow of nitrogen. The probe was immersed in a 0.5 mg/mL peptide solution for ~20 h. After that, the probe was taken out, rinsed with water, dried with nitrogen gas, and used immediately.…”

“…A Pd wire probe, etched to a sharp point and insulated to within a few tens of nm of its apex, was used in an Agilent PicoSPM together with a Pd-coated substrate as described elsewhere. [25] Pd, rather than Au was used because tunneling devices made with Pd are more stable. [26] Probes and substrates were functionalized with cyclic RGD peptide (inset Figure 1B) as described in Methods.…”

Surveying silicon nitride nanopores for glycomics and heparin quality assurance

“…The potential for integration of additional instrumentation components, such as control and readout electrodes, around the thin-film SiN x nanopore core, is especially compelling 28 , 45 , 46 . Recent (nanopore-free) work on recognition electron tunneling measurements on polysaccharides, for example, has reaffirmed the importance of a nanopore development path that values augmented nanopore sensing capabilities 47 . A key question concerning the use of SiN x nanopores for polysaccharide sensing is whether this fabrication material is compatible with sensing glycans, which can exhibit a wide range of chemical and physical properties.…”

“…Variability in polysaccharide electrokinetic mobility arising from differences in molecular structures may exacerbate the effect of these interactions. These issues become particularly important when analyte translocation through a constricted pore is required, such as in transverse electron tunneling measurements 28 , 47 .…”