From Dutch researchers who are combining surface plasmon resonance imaging with microfluidics to large companies pioneering ultra fast genetic analysis techniques, efforts to understand what DNA does at a molecular level have never been more intense.
The blueprint of an organism can be found in its proteome, the total apackage' of proteins being expressed. However, each cell contains about 10000 different proteins and not all are linked in a direct way to DNA. As a result, many are completely uncategorised. In an effort to overcome this problem, Richard Schasfoort of the University of Twente in the Netherlands is developing a special chip able to carry out thousands of protein analyses simultaneously.
According to Schasfoort, the tools which currently exist to do this job are very time-consuming and rely on visual recognition of proteins followed by the extraction of potentially interesting ones with achemical tweezers'.
Instead, the Dutch scientist and his new Biochip group within the faculty of Applied Physics propose to use a new approach which relies on a combination of microfluidics and a detection technique called surface plasmon resonance imaging (SPR). In this way, he wants to build a complete lab on a chip, capable of imaging of hundreds or thousands of proteins at the same time.
A separation technique on the chip splits the proteome into individual proteins. These then aland' on tiny gold surfaces, specially prepared for capturing the proteins: one protein per gold surface. The interaction between the protein and the gold causes a change in refractive index which, in turn, makes optical detection possible. A laser scans all the golden surfaces with proteins on them, while a camera takes an image of the protein pattern.
Labelling and analysis breakthrough
US Genomics, a pioneer of direct, linear DNA analysis for ultra-fast genetic analysis has been granted a new patent covering aspects of its GeneEngine platform that are related to analysing labelled tags on nucleic acid molecules.
The company's technology has the potential to analyse complex molecules such as DNA and RNA one thousand times faster than current technologies.
"Our GeneEngine technology offers the capability to analyse long contiguous strands of DNA very rapidly. This new patent specifically covers methods used to determine the order of tags placed on nucleic acid molecules. Data on the relative location of the tags allows us efficiently to create the maps of DNA, RNA, and proteins that can reveal unique characteristics of individuals,“ noted chairman and ceo Eugene Chan.
Mass custom arrays
Affeymetrix, the company that uses principles developed in the semiconductor industry to develop new life science tools, is now taking orders for its new GeneChip brand CustomSeq Resequencing Array. According to the company, this fast, highly accurate custom array can sequence 30000 bases in just two days at greater than 99.99 per cent accuracy.
The CustomSeq array offers researchers a powerful DNA analysis tool on the same proven Affymetrix platform that has become an industry standard for mRNA gene expression research. CustomSeq arrays are based on GeneChip technology that has already set a new standard in large-scale resequencing performance. Using whole wafers, Perlegen Sciences recently resequenced 50 human genomes in just 15 months.
Applications include candidate gene studies, pharmacogenetic studies of genetic variation across patients in clinical trials and pathogen subtyping to identify known and novel strains of microorganisms.
Affymetrix' new resequencing array offers researchers numerous benefits, including:
* CustomSeq arrays deliver completed sequence that is greater than 99.99 per cent accurate in just 48 hours, with minimal hand curation or sequence alignment. It can take weeks to get completed sequence using capillary sequencing methods.
* CArray content is determined by the researcher, who can choose any combination of contiguous genomic regions or dispersed sets of exons.
Affymetrix' parallel manufacturing method and stringent quality control ensures 99.9999 per cent reproducibility between CustomSeq arrays.
Proteomics research in Japan
Meanwhile in Japan the Reverse Proteomics Research Institute (REPRORI) a consortium of 11 major Japanese companies involved with pharmaceutical development has invested in Swedish company Biacore's latest technology known as BiacoreS51.
It has been developed in collaboration with industry leaders, including Millennium Pharmaceuticals, SmithKline Beecham and Pharmacia Corporation, and provides high quality, quantitative data regarding binding kinetics, affinity, concentration and specificity of biomolecular interactions.
The high sensitivity and throughput capability of BiacoreS51 will allow REPRORI to gain more detailed and fundamental understanding of how existing small molecule drug compounds interact with human proteins. This new technology platform will complement Biacore3000 technology already being used by REPRORI in its existing proteomics programme to consolidate and advance its approach to speeding up the discovery of novel targets for drug discovery.
"We have chosen Biacore technology to support this important research programme as we believe that it is one of the most advanced technologies available today for understanding molecular interactions at the detailed level we require,“ commented Renpei Nagashima, president of REPRORI and advisor at Chugai Pharmaceutical.
