Carbohydrate arrays as tools for the glycomics revolution

Nano-carbohydrates: Synthesis and application in genetics, biotechnology, and medicine

Combining nanoparticles with carbohydrate has triggered an exponential growth of research activities for the design of novel functional bionanomaterials, nano-carbohydrates. Recent advances in versatile synthesis of glycosylated nanoparticles have paved the way towards diverse biomedical applications. The accessibility of a wide variety of these structured nanosystems, in terms of shape, size, and organization around stable nanoparticles, has readily contributed to their development and application in nanomedicine. Glycosylated gold nanoparticles, glycosylated quantum dots, fullerenes, single-wall nanotubes, and self-assembled glyconanoparticles using amphiphilic glycopolymers or glycodendrimers have received considerable attention for their application in powerful imaging, therapeutic, and biodiagnostic devices. Recently, nano-carbohydrates were used for different types of microarrays to detect proteins and nucleic acids.

Applications of a catch and release electrospray ionization mass spectrometry assay for carbohydrate library screening

Applications of a catch and release electrospray ionization mass spectrometry (CaR-ESI-MS) assay for screening carbohydrate libraries against target proteins are described. Direct ESI-MS measurements were performed on solutions containing a target protein (a single chain antibody, an antigen binding fragment, or a fragment of a bacterial toxin) and a library of carbohydrates containing multiple specific ligands with affinities in the 10(3) to 10(6) M(-1) range. Ligands with moderate affinity (10(4) to 10(6) M(-1)) were successfully detected from mixtures containing >200 carbohydrates (at concentrations as low as 0.25 μM each). Additionally, the absolute affinities were estimated from the abundance of free and ligand-bound protein ions determined from the ESI mass spectrum. Multiple low affinity ligands (~10(3) M(-1)) were successfully detected in mixtures containing >20 carbohydrates (at concentrations of ~10 μM each). However, identification of specific interactions required the use of the reference protein method to correct the mass spectrum for the occurrence of nonspecific carbohydrate-protein binding during the ESI process. The release of the carbohydrate ligands, as ions, was successfully demonstrated using collision-induced dissociation performed on the deprotonated ions of the protein-carbohydrate complexes. The use of ion mobility separation, performed on deprotonated carbohydrate ions following their release from the complex, allowed for the positive identification of isomeric ligands.

Supported lipid bilayer microarrays created by non-contact printing

Arrays of supported lipid bilayers (SLBs) provide great potential for future drug development and multiplexed biological research, but are difficult to prepare due to the sensitivity of both the lipid and protein structural arrangement to air exposure. A novel way to produce arrays of SLBs is presented based on non-contact dispensing of vesicles to a substrate through a thin surface confined water film. The approach presents many degrees of freedom since it is not limited to a specific substrate, lipid composition, linker or controlled environment. The method allows adjustment of spot size (180-360 μm) by repeated dispensing as well as control over the composition of the spots and subsequent analytes. SLB formation by vesicle adsorption and rupture allows for incorporation of membrane proteins through pre-formed proteoliposomes. Dispensing through a dip-and-rinse water film avoids contamination, disruptive drying and the need for complex buffer compositions. Furthermore, no humidity control is necessary which simplifies the production step and prolongs the life-time of the spotting system. We characterize the method with respect to control over spot size, bilayer mobility and the formation process as well as demonstrate the possibility to fuse bilayer spots with subsequently added vesicles. Since complex lipid compositions and multiple spotting nozzles can be used, this novel technique is expected to be a promising platform for future applications, e.g. patterning to monitor peptide/protein-lipid interactions, for glycomics using glycolipids or lipopolysaccharides, and to study mixing of spatially confined lipid membranes.

Glycan and lectin microarrays for glycomics and medicinal applications

Three different array formats to study a challenging field of glycomics are presented here, based on the use of a panel of immobilized glycan or lectins, and on in silico computational approach. Glycan and lectin arrays are routinely used in combination with other analytical tools to decipher a complex nature of glycan-mediated recognition responsible for signal transduction of a broad range of biological processes. Fundamental aspects of the glycan and lectin array technology are discussed, with the focus on the choice and availability of the biorecognition elements, fabrication protocols, and detection platforms involved. Moreover, practical applications of both technologies especially in the field of clinical diagnostics are provided. The future potential of a complementary in silico array technology to reveal details of the protein-glycan-binding profiles is discussed here.

A functional carbohydrate chip platform for analysis of carbohydrate-protein interaction

A carbohydrate chip based on glass or other transparent surfaces has been suggested as a potential tool for high-throughput analysis of carbohydrate-protein interactions. Here we proposed a facile, efficient, and cost-effective method whereby diverse carbohydrate types are modified in a single step and directly immobilized onto a glass surface, with retention of functional orientation. We modified various types of carbohydrates by reductive amination, in which reducing sugar groups were coupled with 4-(2-aminoethyl)aniline, which has di-amine groups at both ends. The modified carbohydrates were covalently attached to an amino-reactive NHS-activated glass surface by formation of stable amide bonds. This proposed method was applied for efficient construction of a carbohydrate microarray to analyze carbohydrate-protein interactions. The carbohydrate chip prepared using our method can be successfully used in diverse biomimetic studies of carbohydrates, including carbohydrate-biomolecule interactions, and carbohydrate sensor chip or microarray development for diagnosis and screening.

Rewritable glycochips

We describe microarraying of carbohydrates for protein screening using either disulfide bridge or Schiff base imine immobilization chemistries on plasmachemical deposited functional nanolayers. The commonly observed issue of nonspecific background binding of proteins is overcome by spotting carbohydrates through a protein-resistant overlayer yielding spatially localized interaction with a reactive functional underlayer.

Trityl-derivatized carbohydrates immobilized on a polystyrene microplate

Carbohydrate biosensors, including carbohydrate arrays, are attracting increased attention for the comprehensive and high-throughput investigation of protein-carbohydrate interactions. Here, we describe an effective approach to fabricating a robust microplate-based carbohydrate array capable of probing protein binding and screening for inhibitors in a high-throughout manner. This approach involves the derivatization of carbohydrates with a trityl group through an alkyl linker and the immobilization of the trityl-derivatized carbohydrates (mannose and maltose) onto microplates noncovalently to construct carbohydrate arrays. The trityl carbohydrate derivative has very good immobilization efficiency for polystyrene microplates and strong resistance to aqueous washing. The carbohydrate arrays can probe the interactions with the lectin Concanavalin A and screen this protein for the well-known inhibitors methyl alpha-D-mannopyranoside and methyl alpha-D-glucopyranoside in a high-throughput manner. The method described in this paper represents a convenient way of fabricating robust noncovalent carbohydrate arrays on microplates and offers a convenient platform for high-throughput drug screening.

Recent applications of the Cu(I)-catalysed Huisgen azide-alkyne 1,3-dipolar cycloaddition reaction in carbohydrate chemistry

This article surveys recent applications of Cu(I)-catalysed 1,3-dipolar cycloaddition of azides and alkynes in carbohydrate chemistry, highlighting developments in the preparation of simple glycoside and oligosaccharide mimetics, glyco-macrocycles, glycopeptides, glyco-clusters and carbohydrate arrays.

Merging Organic and Polymer Chemistries to Create Glycomaterials for Glycomics Applications

[Image: see text] Oligosaccharides at cell surfaces are known to play a critical role in many biological processes such as biorecognition, interactions between cells and with artificial surfaces, immune response, infection and inflammation. In order to facilitate studies of the role of sugars, an increasing number of novel tools are becoming available. New synthetic strategies now provide much more efficient access to complex carbohydrates or glycoconjugates. Branched carbohydrates and hybrids of carbohydrates conjugated to polymers have been prepared using solution and/or solid-phase synthesis and advanced methods of polymerization. These materials are essential for the development of methodologies to study and map the molecular structure-function relationship at interfaces. This article highlights recent advances in the synthesis of carbohydrates and polymer hybrids mimicking the properties and functionalities of the natural oligosaccharides, as well as selected applications in biology, biotechnology and diagnostics.

Survey of the year 2004 commercial optical biosensor literature

The year 2004 represents a milestone for the biosensor research community: in this year, over 1000 articles were published describing experiments performed using commercially available systems. The 1038 papers we found represent an approximately 10% increase over the past year and demonstrate that the implementation of biosensors continues to expand at a healthy pace. We evaluated the data presented in each paper and compiled a 'top 10' list. These 10 articles, which we recommend every biosensor user reads, describe well-performed kinetic, equilibrium and qualitative/screening studies, provide comparisons between binding parameters obtained from different biosensor users, as well as from biosensor- and solution-based interaction analyses, and summarize the cutting-edge applications of the technology. We also re-iterate some of the experimental pitfalls that lead to sub-optimal data and over-interpreted results. We are hopeful that the biosensor community, by applying the hints we outline, will obtain data on a par with that presented in the 10 spotlighted articles. This will ensure that the scientific community at large can be confident in the data we report from optical biosensors.