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BioArray Briefs: Mar 8, 2002


Protein Chip Update: Peptide Chips in Nature Biotech, Zyomyx Hooks Up with Specialty Labs


The challenge of getting the right formula for surface chemistry on a chip has frustrated many would-be array makers in the protein arena. How do you immobilize the ligands without allowing nonspecific binding of proteins to the chip? Now a group of University of Chicago researchers has detailed, in an article in the March 2002 issue of Nature Biotechnology, a method for producing peptide chips that they claim overcomes these problems.

They used a clean gold substrate, which is immersed in alkanethiols 1 and 2 to make a monolayer. The glycol groups on this monolayer act to prevent nonspecific protein and radioisotope interactions, and the hydroquinone groups in the monolayer act as a “chemical handle” to selectively immobilize ligands, the researchers wrote.

The researchers tested this surface chemistry on a chip where they selectively immobilized a peptide-cyclopentadine conjugate of the peptide AclYGEFKKKC-NH2 on the monolayer, then used these chips to characterize the phosphorylation of the peptide by c-Src kinase. First they just used one type of peptide and one concentration of the kinase to test out the basic chemistry, and then they adapted the chip to characterize multiple kinase reactions, arraying mixtures of the c-SrC kinase with two kinase inhibitors, querceten and tyrphostin A47, at a range of concentrations.

For detection, the researchers tried out all of the three major techniques — radioactivity, fluorescence, and surface plasmon resonance spectroscopy, and found that the arrays worked with all three.

The group said it is now working on preparing arrays to identify protein-ligand complexes, to evaluate enzymatic activities such as protease and phosphate activities, and to “determine flanking sequences for enzyme substrates.” They also suggested their chips could be useful for other small-molecule arrays.


Zyomyx, of Hayward, Calif., has granted clinical testing company Specialty Laboratories early access to its protein profiling biochip platform. Under the agreement, the two will work to discover multi-analyte diagnostic markers using Zyomyx’s protein chips and Specialty’s archive of biological samples. The two will also work together to design assay standards and controls, and Specialty will evaluate any assay the two companies develop. If Specialty does use a test, Zyomyx will retain exclusive rights to in-house testing services and will provide royalties to Zyomyx. Zyomyx will retain the right to develop and sell diagnostic test kits and therapeutic applications of these biomarker assays, and will pay royalties to Specialty, the companies said.


Carb Chips Aren’t Just For Snacking: Columbia Group Develops Carbohydrate Array


A study published in Nature Biotechnology this month describes one of the first examples of a carbohydrate microarray. Researchers at Columbia University spotted 48 different carbohydrate antigens — including polysaccharides, glycosaminoglycans, glycoproteins, and semisynthetic glycoconjugates — onto glass slides coated with nitrocellulose, and air-dried them. To create the 150-micron-sized spots, 20,000 of which fit on a single microscope slide, they used a standard cDNA spot-arrayer. They found the arrays were very sensitive, enabling detection of sugar-binding antibodies in small samples of human serum. The scientists also used the glyco-chips to determine the specificities of known carbohydrate-binding antibodies and discovered unexpected crossreactivity, pointing to new epitopes for these antibodies in vivo.

In a preliminary experiment to test the binding of the carbohydrates — which does not involve chemical conjugation — to the surface, the scientists noticed that larger polysaccharides bound more efficiently than smaller ones, which limits the technology somewhat. Carbohydrates, which mediate molecular recognition between cells, have important roles in fertilization, development, cancer, and infection. Carbohydrate- or glyco-arrays may find widespread applications in these areas of research.


BioDiscovery and Genops Enter Integration Partnership


BioDiscovery, based in Marina Del Ray, Calif., and Genops Bioinformatics of Vancouver, Canada, said last week that they had entered a strategic collaboration to merge their microarray- and sequence-based analysis platforms.

Under the terms of the agreement, BioDiscovery’s GeneDirector, CloneTracker, ImaGene, and GeneSight data analysis products will be integrated with Genops’ Ngene sequence analysis platform.

Financial terms of the agreement were not disclosed.

The Scan

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.