Heliscope builds world’s fastest DNA sequencer

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Technology Review reports that for just $1,350,000 USD you can have have the worlds fastest commercially available DNA sequencer, called the Heliscope. The machine developed by Helicos BioSciences takes just one hour to read 1.3 billion base pairs from a strand of DNA. Here is a picture of the beauty:

The Heliscope is being marketed as a DNA microscope. It is unique in the field of DNA sequencing because it sequences an actual DNA strand whereas most other sequencing technologies use PCR to create millions of copies of an original DNA template and then parallelize the analysis of these millions of strands. Although PCR based technologies can compete with the Heliscope on speed, only the heliscope offers analysis of an actual single strand of DNA. The millions of copies created from PCR based technologies differ slightly from the original template strand due to very rare but significant copying errors that occur during the creation of the copies and hence some of the information from the original strand is lost. From the article:

The technology is so new that it’s not yet clear what applications it will be best suited to. But some scientists believe that single-­molecule sequencing could be particularly important in understanding how genetic variations contribute to disease. After all, some rare mutations linked to disease may have been missed in previous genomic studies because they weren’t copied during the amplification process.

Both PCR and single strand based analyses have their place in genetics, but if you are doing single strand analysis then Helicos has the machine for you!

Like other DNA sequencing technologies, the Heliscope uses fluorescently tagged DNA to “see” the DNA sequence, but the Heliscope is unique in its ability to see individual fluroescence of a single base as noted in these quotes:

Once the fluorescently tagged base is incorporated into the new strand, the HeliScope’s camera can spot the light it emits. “The imager detects a plume–a 200-­nanometer cone of light–from the integration of a single [base] onto a ­single strand of DNA,

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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.

“You need to make sure no extra base molecules are sticking to the surface,” says Patrice Milos, chief scientific officer at Helicos. “This was one of the biggest early challenges.” After each cycle, the fluorescent markers are clipped from the newly incorporated bases, and remaining chemicals are washed away. The process is repeated sequentially with each of the four bases.

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