New Methods for the Generation of Carbohydrate Arrays on Glass Slides and Their Evaluation

Identification of Nanomolar Lectin Ligands by a Glycodendrimer Microarray

Carbohydrate-protein interactions play key roles in a wide variety of biological processes. These interactions are usually weak, with dissociation constants in the low millimolar to high micromolar range. Nature uses multivalency to reach high avidities via the glycoside cluster effect. Capitalizing on this effect, numerous synthetic multivalent glycoconjugates have been described and used as ligands for carbohydrate-binding proteins. However, valency is only one of the several parameters governing the binding mechanisms that are different for every biological receptor, making it almost impossible to predict. In this context, ligand optimization requires the screening of a large number of structures with different valencies, rigidities/flexibilities, and architectures. In this article, we describe a screening platform based on a glycodendrimer array and its use to determine the key parameters for high-affinity ligands of lectin. Several glycoclusters and glycodendrimers displaying varying numbers of α-N-acetylgalactosamine residues were covalently attached on glass slides, and their bindings were studied with the fluorophore-functionalized Helix pomatia agglutinin (HPA) used as a lectin model. This technique requires minimal quantities of glycoconjugate compared to those for other techniques and affords useful information on the binding strength. Building of the glycodendrimer array and quantification of the interactions with HPA are described.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for the period 2005-2006

This review is the fourth update of the original review, 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 2006. The review covers fundamental studies, fragmentation of carbohydrate ions, method developments, and applications of the technique to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, glycated proteins, glycolipids from bacteria, glycosides, and various other natural products. There is a short section on the use of MALDI-TOF mass spectrometry for the study of enzymes involved in glycan processing, a section on industrial processes, particularly the development of biopharmaceuticals and a section on the use of MALDI-MS to monitor products of chemical synthesis of carbohydrates. Large carbohydrate-protein complexes and glycodendrimers are highlighted in this final section.

Specific recognition of lectins by oligonucleotide glycoconjugates and sorting on a DNA microarray

Two glycoconjugates bearing different DNA tags are mixed in solution with lectins; both interact with their specific lectin and the resulting complexes are sorted, according to their DNA sequences, at the surface of micro-reactors bearing the immobilised complementary DNA sequences.

DNA-directed immobilisation of glycomimetics for glycoarrays application: comparison with covalent immobilisation, and development of an on-chip IC50 measurement assay

Glycoarrays are powerful tools for the understanding of protein/carbohydrate interactions and should find applications in the diagnosis of diseases involving these interactions. Immobilisation of the carbohydrate probe is a key issue in the elaboration of high performance devices. In the present study, we have compared the fluorescent signal intensity and determined the lower detection limit of glycoconjugates immobilised at two concentrations (0.5 and 25 microM) by DNA-directed immobilisation (DDI), to glycoconjugates covalently immobilised on the solid support (borosilicate glass slide). At 0.5 microM, DDI led to a stronger fluorescence signal (by a factor of 4.5) and to a lower detection limit (20 nM) than covalent immobilisation (higher than 200 nM). We also report the development of an IC(50) measurement assay of DDI immobilised glycoconjugates. We found that the relative affinity per galactose residue of RCA 120 for glycoconjugates bearing one or three galactose residues was different by a factor of 23 when measured under IC(50) conditions or by direct fluorescence reading.

Glycoarrays--tools for determining protein-carbohydrate interactions and glycoenzyme specificity

Carbohydrate arrays (glycoarrays) have recently emerged as a high-throughput tool for studying carbohydrate-binding proteins and carbohydrate-processing enzymes. A number of sophisticated array platforms that allow for qualitative and quantitative analysis of carbohydrate binding and modification on the array surface have been developed, including analysis by fluorescence spectroscopy, mass spectrometry and surface plasmon resonance spectroscopy. These platforms, together with examples of biologically-relevant applications are reviewed in this Feature Article.

ChipCheckII - predicting binding curves for multiple analyte strands on small DNA microarrays

Incomplete binding, saturation, and cross-hybridization between partially complementary strands complicate the parallel detection of nucleic acids via DNA microarrays. Treating the competing equilibria governing binding to microarrays requires computational tools. We have developed the web-based program ChipCheckII that calculates total hybridization matrices for target strands interacting with probes on small DNA microarrays. The program can be used to compute the extent of cross-hybridization and other phenomena affecting fidelity of detection based on sequences, quantities of strands, and hybridization conditions as inputs. Enthalpy and entropy of duplex formation are generated locally with UNAfold, including those for complexes that are partially matched. Simulated binding versus temperature curves for portions of a commercial genome chip demonstrate the extent to which cross-hybridization can complicate DNA detection. ChipCheckII is expected to aid nucleic acid chemists in developing high fidelity DNA microarrays.

Application of carbohydrate array technology to antigen discovery and vaccine development

Carbohydrate arrays are a new technology developed for high-throughput evaluation of interactions between carbohydrates and proteins, cells or viruses. Carbohydrate arrays contain many different carbohydrate structures on a solid support. The format allows one to probe hundreds or thousands of potential receptor-ligand interactions while using only tiny amounts of material. Recently, carbohydrate arrays have been applied to vaccine development in several ways. First, carbohydrate arrays have been utilized for the discovery and characterization of carbohydrate antigens. Second, they have been used to evaluate immune responses to vaccine candidates. Third, carbohydrate arrays have been used to identify and characterize reagents necessary for vaccine development. Although still at an early stage, carbohydrate array technology has tremendous potential for accelerating vaccine development.

Surface plasmon resonance study of protein-carbohydrate interactions using biotinylated sialosides

Lectins are carbohydrate binding proteins found in plants, animals, and microorganisms. They serve as important models for understanding protein-carbohydrate interactions at the molecular level. We report here the fabrication of a novel sensing interface of biotinylated sialosides to probe lectin-carbohydrate interactions using surface plasmon resonance spectroscopy (SPR). The attachment of carbohydrates to the surface using biotin-NeutrAvidin interactions and the implementation of an inert hydrophilic hexaethylene glycol spacer (HEG) between the biotin and the carbohydrate result in a well-defined interface, enabling desired orientational flexibility and enhanced access of binding partners. The specificity and sensitivity of lectin binding were characterized using Sambucus nigra agglutinin (SNA) and other lectins including Maackia amurensis lectin (MAL), concanavalin A (Con A), and wheat germ agglutinin (WGA). The results indicate that alpha2,6-linked sialosides exhibit high binding affinity to SNA, while alteration in sialyl linkage and terminal sialic acid structure compromises the affinity by a varied degree. Quantitative analysis yields an equilibrium dissociation constant (KD) of 777 +/- 93 nM for SNA binding to Neu5Ac alpha2,6-LHEB. Transient SPR kinetics confirms the K D value from the equilibrium binding studies. A linear relationship was obtained in the 10-100 microg/mL range with limit of detection of approximately 50 nM. Weak interactions with MAL, Con A, and WGA were also quantified. The control experiment with bovine serum albumin indicates that nonspecific interaction on this surface is insignificant over the concentration range studied. Multiple experiments can be performed on the same substrate using a glycine stripping buffer, which selectively regenerates the surface without damaging the sialoside or the biotin-NeutrAvidin interface. This surface design retains a high degree of native affinity for the carbohydrate motifs, allowing distinction of sialyl linkages and investigation pertaining to the effect of functional group on binding efficiency. It could be easily modified to identify and quantify binding patterns of any low-affinity biologically relevant systems, opening new avenues for probing carbohydrate-protein interactions in real time.

Carbohydrate Microarray on Glass: A Tool for Carbohydrate-Lectin Interactions

A simple method to immobilize carbohydrates on a glass surface to obtain a carbohydrate microarray is described. The array was used to study carbohydrate-lectin interactions. The glass surface was modified with aldehyde terminated linker groups of various chain lengths. Coupling of carbohydrates with an amino terminated alkyl spacer to the aldehyde terminated glass followed by reductive amination resulted in carbohydrate microarrays. Fluorescently labeled (FI-TC) lectins (concanavalin A and Arachis hypogaea) were used to study specific carbohydrate-lectin interactions. contact angle, atomic force microscopy (AFM) and confocal laser fluorescence microscopy (CLFM) techniques were used in this study to monitor the modification of the glass and the successful selective binding of lectins to the carbohydrate microarray.

Recent trends in the synthesis of O-glycosides of 2-amino-2-deoxysugars

The discovery of new methods for stereoselective glycoside synthesis and convergent oligosaccharide assembly has been critical for the area of glycosciences. At the heart of this account is the discussion of the approaches for stereoselective synthesis of glycosides of 2-amino-2-deoxysugars that have emerged during the past two decades. The introductory part provides general background information and describes the key features and challenges for the synthesis of this class of compounds. Subsequently, major approaches to the synthesis of 2-amino-2-deoxyglycosides are categorized and discussed. Each subsection elaborates on the introduction (or protection) of the amino functionality, synthesis of glycosyl donors by introduction of a suitable leaving group, and glycosidation. Wherever applicable, the deprotection of a temporary amino group substituent and the conversion onto the natural acetamido functionality is described. The conclusions part evaluates the current standing in the field and provides a perspective for future developments.

Microarrays of heparin oligosaccharides obtained by nitrous acid depolymerization of isolated heparin

Heparin oligosaccharides derived by nitrous acid depolymerization of heparin have been immobilized on amine-coated glass slides. The formation of a Schiff base creates heparin chips that are a suitable platform for the high-throughput analysis of carbohydrate-protein interactions.

Fluorous-based carbohydrate microarrays

The success of microarrays, such as DNA chips, for biosample screening with minimal sample usage has led to a variety of technologies for assays on glass slides. Unfortunately, for small molecules, such as carbohydrates, these methods usually rely on covalent bond formation, which requires unique functional handles and multiple chemical steps. A new simpler concept in microarray formation is based on noncovalent fluorous-based interactions. A fluorous tail is designed not only to aid in saccharide purification but also to allow direct formation of carbohydrate microarrays on fluorous-derivatized glass slides for biological screening with lectins, such as concanavalin A. The noncovalent interactions in the fluorous-based array are even strong enough to withstand the detergents used in assays with the Erythrina crystagalli lectin. Additionally, the utility of benzyl carbonate protecting groups on fucose building blocks for the formation of alpha-linkages is demonstrated.