The utility of carbohydrate microarrays in glycomics

Tellurium in carbohydrate synthesis

In this article, we discuss about the influence of tellurium in carbohydrate synthesis. Mainly the chapter focuses on the importance of the tellurium during the synthesis of glycosides and during the oxidation of glucose.

Small molecule microarrays: the first decade and beyond

Molecular Bits and Chips: Profiling and discovering the next generation of small molecule ligands.

Lectin microarrays for glycomic analysis

Glycomics is the study of comprehensive structural elucidation and characterization of all glycoforms found in nature and their dynamic spatiotemporal changes that are associated with biological processes. Glycocalyx of mammalian cells actively participate in cell-cell, cell-matrix, and cell-pathogen interactions, which impact embryogenesis, growth and development, homeostasis, infection and immunity, signaling, malignancy, and metabolic disorders. Relative to genomics and proteomics, glycomics is just growing out of infancy with great potential in biomedicine for biomarker discovery, diagnosis, and treatment. However, the immense diversity and complexity of glycan structures and their multiple modes of interactions with proteins pose great challenges for development of analytical tools for delineating structure function relationships and understanding glyco-code. Several tools are being developed for glycan profiling based on chromatography, mass spectrometry, glycan microarrays, and glyco-informatics. Lectins, which have long been used in glyco-immunology, printed on a microarray provide a versatile platform for rapid high throughput analysis of glycoforms of biological samples. Herein, we summarize technological advances in lectin microarrays and critically review their impact on glycomics analysis. Challenges remain in terms of expansion to include nonplant derived lectins, standardization for routine clinical use, development of recombinant lectins, and exploration of plant kingdom for discovery of novel lectins.

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.

Carbohydrate cluster microarrays fabricated on three-dimensional dendrimeric platforms for functional glycomics exploration

We reported here a novel, ready-to-use bioarray platform and methodology for construction of sensitive carbohydrate cluster microarrays. This technology utilizes a three-dimensional (3-D) poly(amidoamine) starburst dendrimer monolayer assembled on glass surface, which is functionalized with terminal aminooxy and hydrazide groups for site-specific coupling of carbohydrates. A wide range of saccharides, including monosaccharides, oligosaccharides and polysaccharides of diverse structures, are applicable for the 3-D bioarray platform without prior chemical derivatization. The process of carbohydrate coupling is effectively accelerated by microwave radiation energy. The carbohydrate concentration required for microarray fabrication is substantially reduced using this technology. Importantly, this bioarray platform presents sugar chains in defined orientation and cluster configurations. It is, thus, uniquely useful for exploration of the structural and conformational diversities of glyco-epitope and their functional properties.

Fabrication and characterization of a sialoside-based carbohydrate microarray biointerface for protein binding analysis with surface plasmon resonance imaging

Monitoring multiple biological interactions in a multiplexed array format has numerous advantages. However, converting well-developed surface chemistry for spectroscopic measurements to array-based high-throughput screening is not a trivial process and often proves to be the bottleneck in method development. This paper reports the fabrication and characterization of a new carbohydrate microarray with synthetic sialosides for surface plasmon resonance imaging (SPRi) analysis of lectin-carbohydrate interactions. Contact printing of functional sialosides on neutravidin-coated surfaces was carried out and the properties of the resulting elements were characterized by fluorescence microscopy and atomic force microscopy (AFM). Sambucus nigra agglutinin (SNA) was deposited on four different carbohydrate functionalized surfaces and differential binding was analyzed to reveal affinity variation as a function of headgroup sialic acid structures and linking bonds. SPRi studies indicated that this immobilization method could result in high quality arrays with RSD < 5% from array element to array element, superior to the conventional covalent linkage used for protein cholera toxin (CT) in a comparison experiment, which yields nonuniform array elements with RSD > 15%. Multiplexed detection of SNA/biotinylated sialoside interactions on arrays up to 400 elements has been performed with good data correlation, demonstrating the effectiveness of the biotin-neutravidin-based biointerface to control probe orientation for reproducible and efficient protein binding to take place. Additionally, the regeneration of the array surface was demonstrated with a glycine stripping buffer, rendering this interface reusable. This in-depth study of array surface chemistry offers useful insight into experimental conditions that can be optimized for better performance, allowing many different protein-based biointeractions to be monitored in a similar manner.

Introduction to microarray technology

DNA microarrays can be used for large number of application where high-throughput is needed. The ability to probe a sample for hundred to million different molecules at once has made DNA microarray one of the fastest growing techniques since its introduction about 15 years ago. Microarray technology can be used for large scale genotyping, gene expression profiling, comparative genomic hybridization and resequencing among other applications. Microarray technology is a complex mixture of numerous technology and research fields such as mechanics, microfabrication, chemistry, DNA behaviour, microfluidics, enzymology, optics and bioinformatics. This chapter will give an introduction to each five basic steps in microarray technology that includes fabrication, target preparation, hybridization, detection and data analysis. Basic concepts and nomenclature used in the field of microarray technology and their relationships will also be explained.

An array of possibilities for pectin

Pectins are a major component of plant cell walls and have numerous roles in plant growth and development. Extracted pectins are widely used as functional food ingredients in products including ice creams, jams, jellies and milk drinks. Although all are based on a galacturonan-rich backbone, pectins are an immensely diverse family of polysaccharides, the functional properties of which are dictated by their fine structures. Understanding the biological roles of pectins and optimizing their industrial usage requires a detailed knowledge of their diversity and spatial and temporal distributions, and microarray technology is a promising tool for high throughput pectin analysis. This article discusses the technical aspects of the production of pectin microarrays and explores their current and potential future uses in the context of recent work in the field.

The prospects of glycan biomarkers for the diagnosis of diseases

Over 40 years of literature shows that glycosylation is greatly affected by diseases such as cancer. This opinion article argues the intrinsic advantages of using glycans as disease markers over other biomolecules and the potential of glycan profiling for diagnosing and determining the progression of disease.

Carbohydrate Moieties as Vaccine Candidates: meeting summary

In September 2007, a meeting entitled 'Carbohydrate Moieties as Vaccine Candidates' was held at the National Institutes of Health (Bethesda, MD). This meeting brought together scientists from a number of disciplines to address issues concerning carbohydrate moieties as targets for vaccines for a variety of pathogens and tumors. In addition, the meeting participants addressed fundamental topics of glycoimmunology including the recognition of glycotopes by B and T lymphocytes, the ontogeny of anti-carbohydrate immune responses, peptide mimicry, carbohydrate antigen processing pathways and adjuvants. One session reported progress in the development of new tools such as computational algorithms, glycan arrays and oligosaccharide synthesis and their application to carbohydrate vaccine research. The session titles were: (1) immune response to bacterial carbohydrate antigens; (2) immune response to glycolipids; (3) immune response to carbohydrate antigens on other microbes and on tumors; (4) novel vaccine approaches; (5) novel tools in carbohydrate vaccine research; (6) bench to bedside: carbohydrate moieties as vaccine immunopotentiators.

Carbohydrate arrays as tools for research and diagnostics

In a very short time, carbohydrate microarrays have become important tools to investigate binding events that involve sugars. High throughput analysis of carbohydrate interactions with a wide range of binding partners, including proteins, RNA, whole cells and viruses, can be performed. Questions ranging from simple binding events to in-depth kinetic analysis can be addressed. This tutorial review summarizes methods to produce carbohydrate microarrays as well as their use. Some selected examples illustrate applications and the potential that these tools hold.

Small-molecule microarrays as tools in ligand discovery

Small molecules that bind and modulate specific protein targets are increasingly used as tools to decipher protein function in a cellular context. Identifying specific small-molecule probes for each protein in the proteome will require miniaturized assays that permit screening of large collections of compounds against large numbers of proteins in a highly parallel fashion. Simple and general binding assays involving small-molecule microarrays can be used to identify probes for nearly any protein in the proteome. The assay may be used to identify ligands for proteins in the absence of knowledge about structure or function. In this tutorial review, we introduce small-molecule microarrays (SMMs) as tools for ligand discovery; discuss methods for manufacturing SMMs, including both non-covalent and covalent attachment strategies; and provide examples of ligand discovery involving SMMs.

Identification of N-glycan of alpha-fetoprotein by lectin affinity microarray

PURPOSE

The occurrence of cancer accompanies with changes in glycosylation of related proteins. A simple, rapid and high-throughput manner analyzing the N-glycan moiety is needed in the cancer glycoproteome study.

METHODS

Gel-slide was used as solid support of lectin microarray. We fabricated the lectin microarray with selected lectins to identify the N-glycan compositions of glycoproteins, to determine the individual N-glycan pattern of several glycoproteins and to compare the N-glycan compositions of alpha-fetoproteins (AFPs) from different sources.

RESULTS

It is feasible to analyze N-glycan pattern of glycoproteins with the lectin affinity microarray. The optimum loading concentration of lectins in this array is 1 mg/ml. The lectin microarray is sensitive, and it can even detect tested glycoprotein less than 1 pg. There is a linear relationship between the fluorescence intensity and the cy3 concentration of glycoprotein at the range from 10 to 1,000 nM.

CONCLUSION

The lectin microarray could give a panel of lectin affinity patterns of individual glycoproteins, and it could indicate the minimal differences of N-glycan compositions between AFPs from different sources. The developed lectin affinity microarray may contribute to the research of glycoproteomics associated with cancer and other diseases.