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Each channel is capable of holding and sequencing a separate DNA sample. Sequencing the samples in parallel, the machine takes just one hour to read 1. Called the HeliScope, it is the first commercial instrument that can directly read the sequence of a single such strand, a capability that gives it the potential for unprecedented speed.
The HeliScope, introduced earlier this year, is joining an intense race for faster and cheaper sequencing technologies. The applications of cheap sequencing are almost limitless, from disease diagnostics to research that could yield microbes engineered to produce biofuels or medicines.
In other advanced sequencing technologies currently in use, including those from Illumina, Applied Biosystems, and Life Sciences which was acquired by Roche last year , the DNA to be sequenced must be amplified, or copied many times; the copies are then read simultaneously to make it easier to detect fluorescent signals that indicate the position of each DNA letter. In addition, single-molecule sequencing may be able to generate a more complete picture of the genome. Awake at Night With the Helicos technology, the DNA to be sequenced is first chopped into short pieces about bases long and injected into a flow cell, a specialized glass slide.
The flow cell is coated with tiny snippets of DNA that are designed to snag the fragments as they float by, anchoring them in place. The immobilized pieces of DNA are fluorescently labeled so that their position under a fluorescence microscope can be recorded by a camera.
Nearly a billion pieces of DNA can be analyzed in a single sequencing experiment, compared with about , to 50 million for other technologies. The added weight stops any vibrations from interfering with the signals the device must detect. A complex optical system and a tangle of tubing surround the microscope, connecting it to what looks like a miniature fridge filled with bottles of specially made chemicals.
When a scientist activates the machine, a precisely choreographed dance of fluids begins. An enzyme called DNA polymerase and a single type of fluorescently labeled base—say, A—flow into the cell. The enzyme causes those As to take their places in growing strands of DNA that complement the strands in the samples. Each of the four bases can pair with only one other base, so an added A must line up opposite an existing T, and a C against a G.
Other advanced sequencing methods use a similar approach, known as sequencing by synthesis. But unlike those technologies, the HeliScope can distinguish the unamplified fluorescent signal of a single base taking its place on a growing DNA strand. One key to that ability is a nonstick material that the company developed, which coats the surface of the flow cell and allows it to be washed clean between reactions: residual fluorescent bases would make it more difficult to accurately detect individual sequencing reactions.
The process is repeated sequentially with each of the four bases. The HeliScope generates a massive amount of raw data every second. Scientists load the machine, press a button on its face, and leave. Once the HeliScope creates its series of fluorescence photographs, an accompanying data-processing center converts them into strings of letters.
Software pastes these pieces together to form a longer sequence. Skip to Content. The HeliScope is the first commercial machine to sequence a single piece of DNA rather than one copied many times. A coating on the surface of the cell allows it to be washed clean between reactions. Stephen Quake, cofounder of Helicos Biosciences, talks about sequencing. Latest content Load more.
Single Molecule Sequencing with a HeliScope Genetic Analysis System
Metrics details. Single-molecule sequencing enables DNA or RNA to be sequenced directly from biological samples, making it well-suited for diagnostic and clinical applications. Here we review the properties and applications of this rapidly evolving and promising technology. Classical DNA sequencing sometimes referred to as first generation sequencing was developed in the late s and evolved from a low-throughput, almost 'artisan' approach, in which the same radiolabeled DNA sample was run on a gel with one lane for each nucleotide [ 1 , 2 ], to an automated method in which all four fluorescently labeled dye terminators for a single sample [ 3 ] were loaded onto individual capillaries.
Sample preparation does not require ligation or PCR amplification, avoiding the GC-content and size biases observed in other technologies. DNA is simply sheared, tailed with poly A, and hybridized to a flow cell surface containing oligo-dT for sequencing-by-synthesis of billions of molecules in parallel. This process also requires far less material than other technologies. Gene expression measurements can be done using 1 st -strand cDNA-based methods RNA- Seq or using a novel approach that allows direct hybridization and sequencing of cellular RNA for the most direct quantitation possible.
Helicos single molecule fluorescent sequencing
A new gene expression technique adapted for single molecule sequencing to accurately and quantitatively measure gene expression levels using only nanograms of total RNA. In recent years, next-generation DNA sequencers have produced an increasingly detailed picture of how genes are expressed at the molecular level. The transcriptional output of these genes - the RNA copies produced from DNA - has revealed a richness of complexity in transcript structure and function, providing insights into the molecular-level properties of cancers and other diseases. A unique approach, CAGE enables not only high-throughput gene expression profiling, but also simultaneous identification of transcriptional start sites TSS specific to each tissue, cell or condition.