Signal amplification by glyco-qPCR for ultrasensitive detection of carbohydrates: applications in glycobiology

Functional nucleic acids in glycobiology: A versatile tool in the analysis of disease-related carbohydrates and glycoconjugates

As significant components of the organism, carbohydrates and glycoconjugates play indispensable roles in energy supply, cell signaling, immune modulation, and tumor cell invasion, and function as biomarkers since aberrance of them has been proved to be associated with the emergence and development of certain diseases. Functional nucleic acids (FNAs) have properties including easy-to-synthesize, good stability, good biocompatibility, low cost, and high programmability, they have attracted significant research attention and been incorporated into biosensors for detecting disease-related carbohydrates and glycoconjugates. This review summarizes the construction strategies and biosensing applications of FNAs-based biosensors in glycobiology in terms of target recognition and signal transduction. By illustrating the mechanisms and comparing the performances, the challenges and development opportunities in this area have been critically elaborated. We believe that this review will provide a better understanding of the role of FNAs in the analysis of disease-related carbohydrates and glycoconjugates, and inspire further discovery in fields that include glycobiology, chemical biology, clinical diagnosis, and drug development.

Genetically encoded multivalent liquid glycan array displayed on M13 bacteriophage

The central dogma of biology does not allow for the study of glycans using DNA sequencing. We report a liquid glycan array (LiGA) platform comprising a library of DNA 'barcoded' M13 virions that display 30-1,500 copies of glycans per phage. A LiGA is synthesized by acylation of the phage pVIII protein with a dibenzocyclooctyne, followed by ligation of azido-modified glycans. Pulldown of the LiGA with lectins followed by deep sequencing of the barcodes in the bound phage decodes the optimal structure and density of the recognized glycans. The LiGA is target agnostic and can measure the glycan-binding profile of lectins, such as CD22, on cells in vitro and immune cells in a live mouse. From a mixture of multivalent glycan probes, LiGAs identify the glycoconjugates with optimal avidity necessary for binding to lectins on living cells in vitro and in vivo.

Synthetic heparan sulfate standards and machine learning facilitate the development of solid-state nanopore analysis

The application of solid-state (SS) nanopore devices to single-molecule nucleic acid sequencing has been challenging. Thus, the early successes in applying SS nanopore devices to the more difficult class of biopolymer, glycosaminoglycans (GAGs), have been surprising, motivating us to examine the potential use of an SS nanopore to analyze synthetic heparan sulfate GAG chains of controlled composition and sequence prepared through a promising, recently developed chemoenzymatic route. A minimal representation of the nanopore data, using only signal magnitude and duration, revealed, by eye and image recognition algorithms, clear differences between the signals generated by four synthetic GAGs. By subsequent machine learning, it was possible to determine disaccharide and even monosaccharide composition of these four synthetic GAGs using as few as 500 events, corresponding to a zeptomole of sample. These data suggest that ultrasensitive GAG analysis may be possible using SS nanopore detection and well-characterized molecular training sets.

Recent advances in biotechnology for heparin and heparan sulfate analysis

Heparan sulfate (HS) is a class of linear, sulfated, anionic polysaccharides, called glycosaminoglycans (GAGs), which present on the mammalian cell surfaces and extracellular matrix. HS GAGs display a wide range of critical biological functions, particularly in cell signaling. HS is composed of repeating units of 1 → 4 glucosidically linked uronic acid and glucosamine residues. Heparin, a pharmacologically important version of HS, having higher sulfation and a higher content of iduronic acid than HS, is a widely used clinical anticoagulant. However, due to their heterogeneity and complex structure, HS and heparin are very challenging to analyze, limiting biological studies and even resulting in safety concerns in their therapeutic application. Therefore, reliable methods of structural analysis of HS and heparin are critically needed. In addition to the structural analysis of heparin, its concentration in blood needs to be closely monitored to avoid complications such as thrombocytopenia or hemorrhage caused by heparin overdose. This review summarizes the progress in biotechnological approaches in the structural characterization of HS and heparin over the past decade and includes the development of the ultrasensitive approaches for detection and measurement in biological samples.

Generation of Glycosyl Radicals from Glycosyl Sulfoxides and Its Use in the Synthesis of C-linked Glycoconjugates

We here report glycosyl sulfoxides appended with an aryl iodide moiety as readily available, air and moisture stable precursors to glycosyl radicals. These glycosyl sulfoxides could be converted to glycosyl radicals by way of a rapid and efficient intramolecular radical substitution event. The use of this type of precursors enabled the synthesis of various complex C-linked glycoconjugates under mild conditions. This reaction could be performed in aqueous media and is amenable to the synthesis of glycopeptidomimetics and carbohydrate-DNA conjugates.

Enhanced visualization of cell surface glycans via a hybridization chain reaction

We apply a DNA hybridization chain reaction (HCR) to achieve sensitively amplified imaging of cell surface glycosylation.

Sensitive multiplex detection of whole bacteria using self-assembled cell binding domain complexes

Detecting bacterial cells at low levels is critical in public health, the food industry and first response. Current processes typically involve laborious cell lysis and genomic DNA extraction to achieve 100-1000 CFU mL^-1 levels for detecting gram-positive bacteria. As an alternative to DNA-based methods, cell wall binding domains (CBDs) derived from lysins having a modular structure with an N-terminal catalytic domain and a C-terminal CBD, can be used to detect bacterial pathogens as a result of their exceptionally specific binding to target bacteria with great avidity. We have developed a highly sensitive method for multiplex detection of whole bacterial cells using self-assembled CBD complexes. Self-assembled CBD-SA-reporter complexes were generated using streptavidin (SA), biotin-CBDs, and biotinylated reporters, such as glucose oxidase (GOx) and specific DNA sequences. The simultaneous detection of three test bacteria, Staphylococcus aureus, Bacillus anthracis-Sterne, and Listeria innocua cells in PBS could be accomplished with a 96-well plate-based sandwich method using CBD-SA-GOx complex-coupled spectrophotometric assay to achieve a detection limit of >100 CFU mL^-1. To achieve greater detection sensitivity, we used CBD-SA-DNA complexes and qPCR of specific DNA barcodes selectively bound to the surface of target bacterial cells, which resulted in a detection sensitivity as low as 1-10 CFU mL^-1 without cross-reactivity. This sensitive multiplex detection of bacterial pathogens using both CBD-SA-GOx and CBD-SA-DNA complexes has the potential to be quickly combined with point-of-care compatible diagnostics for the rapid detection of pathogens in test samples.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012

This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.

Double-Enzymes-Mediated Bioluminescent Sensor for Quantitative and Ultrasensitive Point-of-Care Testing

We report an ultrasensitive, quantitative, and rapid bioluminescent immunosensor (ABS) for point-of-care testing (POCT) of the disease biomarker in clinical samples using double enzymes including alkaline phosphatase (ALP) and luciferase. In the presence of the biomarker, the ALP attached on the surface of immuno-nanocomplex dephosphorylates adenine triphosphate (ATP), subsequently inhibiting the ATP-luciferin-luciferase bioluminescent reaction. The highly sensitive response of ATP (picomolar level) allows for ultrasensitive detection of biomarker via the effective change of the bioluminescence intensity through ALP- and luciferase-catalyzed reactions, which can be quantitatively determined by a portable ATP detector. This ABS fulfills the criteria for POCT that performs sensitive (femtomolar level of biomarkers) and quantitative measurement quickly (less than 1 h) with minimal equipment (portable detector).

Applying DNA rolling circle amplification in fluorescence imaging of cell surface glycans labeled by a metabolic method

Glycans on the cell surfaces are essential for cellular communication. Metabolically labeling glycans can introduce unnatural sugars into cellular glycans, which can facilitate further labeling. We report herein imaging cell surface glycosylation by using click chemistry and DNA rolling circle amplification (RCA) to improve detection sensitivity. Through the RCA amplification, the image resolution of a cell was significantly improved and much fewer unnatural sugars were used than required previously. The advantage of this method is that it avoids introducing too much unnatural sugar, which can interfere with normal, physiological cell function. Simultaneously, the enhanced fluorescence intensity conveniently facilitates the detection of cells' own biosynthetic glycans by simply using a microplate reader. The results indicate that the metabolically labelling ability is different for different carbohydrates and different cells. Next, the RCA technique was adopted in a fluorescence resonance energy transfer (FRET)-based methodology that facilitated the glycan imaging of specific proteins on the cell surface. This method is broadly applicable to imaging the glycosylation of cellular proteins. Our results highlight the applications of RCA in metabolic glycan labeling, which can be used to monitor the glycosylation status on cells, and study the means by which glycosylation regulates cell function.

Sequential glycan profiling at single cell level with the microfluidic lab-in-a-trench platform: a new era in experimental cell biology

It is now widely recognised that the earliest changes that occur on a cell when it is stressed or becoming diseased are alterations in its surface glycosylation. Current state-of-the-art technologies in glycoanalysis include mass spectrometry, protein microarray formats, techniques in cytometry and more recently, glyco-quantitative polymerase chain reaction (Glyco-qPCR). Techniques for the glycoprofiling of the surfaces of single cells are either limited to the analysis of large cell populations or are unable to handle multiple and/or sequential probing. Here, we report a novel approach of single live cell glycoprofiling enabled by the microfluidic "Lab-in-a-Trench" (LiaT) platform for performing capture and retention of cells, along with shear-free reagent loading and washing. The significant technical improvement on state-of-the-art is the demonstration of consecutive, spatio-temporally profiling of glycans on a single cell by sequential elution of the previous lectin probe using their corresponding free sugar. We have qualitatively analysed glycan density on the surface of individual cells. This has allowed us to qualitatively co-localise the observed glycans. This approach enables exhaustive glycoprofiling and glycan mapping on the surface of individual live cells with multiple lectins. The possibility of sequentially profiling glycans on cells will be a powerful new tool to add to current glycoanalytical techniques. The LiaT platform will enable cell biologists to perform many high sensitivity assays and also will also make a significant impact on biomarker research.

High sensitivity detection of active botulinum neurotoxin by glyco-quantitative polymerase chain-reaction

The sensitive detection of highly toxic botulinum neurotoxin (BoNT) from Clostridium botulinum is of critical importance because it causes human illnesses if foodborne or introduced in wounds and as an iatrogenic substance. Moreover, it has been recently considered a possible biological warfare agent. Over the past decade, significant progress has been made in BoNT detection technologies, including mouse lethality assays, enzyme-linked immunosorbent assays, and endopeptidase assays and by mass spectrometry. Critical assay requirements, including rapid assay, active toxin detection, sensitive and accurate detection, still remain challenging. Here, we present a novel method to detect active BoNTs using a Glyco-quantitative polymerase chain-reaction (qPCR) approach. Sialyllactose, which interacts with the binding-domain of BoNTs, is incorporated into a sialyllactose-DNA conjugate as a binding-probe for active BoNT and recovered through BoNT-immunoprecipitation. Glyco-qPCR analysis of the bound sialyllactose-DNA is then used to detect low attomolar concentrations of BoNT and attomolar to femtomolar concentrations of BoNT in honey, the most common foodborne source of infant botulism.

Ultrasensitive detection and quantification of acidic disaccharides using capillary electrophoresis and quantum dot-based fluorescence resonance energy transfer

Rapid and highly sensitive detection of the carbohydrate components of glycoconjugates is critical for advancing glycobiology. Fluorescence (or Förster) resonance energy transfer (FRET) is commonly used in detection of DNA, in protein structural biology, and in protease assays but is less frequently applied to glycan analysis due to difficulties in inserting two fluorescent tags into small glycan structures. We report an ultrasensitive method for the detection and quantification of a chondroitin sulfate disaccharide based on FRET, involving a CdSe-ZnS core-shell nanocrystal quantum dot (QD) streptavidin conjugate donor and a Cy5 acceptor. The disaccharide was doubly labeled with biotin and Cy5. QDs then served to concentrate the target disaccharide, enhancing the overall energy transfer efficiency, with unlinked QDs and Cy5 hydrazide producing nearly zero background signal in capillary electrophoresis using laser-induced fluorescence detection with two different band-pass filters. This method is generally applicable to the ultrasensitive analysis of acidic glycans and offers promise for the high-throughput disaccharide analysis of glycosaminoglycans.

Chemoenzymatic synthesis of glycosaminoglycans: re-creating, re-modeling and re-designing nature's longest or most complex carbohydrate chains

Glycosaminoglycans (GAGs) are complex polysaccharides composed of hexosamine-containing disaccharide repeating units. The three most studied classes of GAGs, heparin/heparan sulfate, hyaluronan and chondroitin/dermatan sulfate, are essential macromolecules. GAGs isolated from animal and microbial sources have been utilized therapeutically, but naturally occurring GAGs are extremely heterogeneous limiting further development of these agents. These molecules pose difficult targets to construct by classical organic syntheses due to the long chain lengths and complex patterns of modification by sulfation and epimerization. Chemoenzymatic synthesis, a process that employs exquisite enzyme catalysts and various defined precursors (e.g. uridine 5'-diphosphosphate-sugar donors, sulfate donors, acceptors and oxazoline precursors), promises to deliver homogeneous GAGs. This review covers both theoretical and practical issues of GAG oligosaccharide and polysaccharide preparation as single molecular entities and in library formats. Even at this early stage of technology development, nearly monodisperse GAGs can be made with either natural or artificial structures.