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Technological Landscapes: Accelerated Synthetic DNA Replication for Cancer Research

Lexington-based Raindance Technologies provides innovative microdroplet-based solutions that accelerate research and development for human healthcare and industrial markets.

 

That living forms reproduce themselves is a wonder. That we understand the process of cell replication borders on the incredulous.

The first level of understanding began in 1870 when the biochemist Friedrich Miescher discovered that, in addition to protein, there was an acid contained within the nucleus of living cells. In early 1900, this nucleic acid was determined to be DNA (deoxyribonucleic acid). This discovery raised the question as to whether-or-not it is the proteins in living cells or the DNA that is the molecule of heredity.

It was not until 1944 that DNA was declared the genetic material. In 1952, Maurice Wilkins and Rosalind Franklin used X-ray diffraction to discover that the DNA structure was in the form of a helix. Then on April 25, 1953 James D. Watson and Francis Crick announced that the DNA structure was actually a double helix. The two strands of the helix could probably be separated and that separation was probably the mechanism for replication.They were awarded a 1962 Nobel Prize.

It would take until 1968 before the genetic code, contained within the DNA in the form of genes, would be deciphered. The ability to rapidly synthesize DNA became the dominant theme in the rapidly growing field of molecular genetics.

The critical issue for the biochemists concerned how to synthesize the complex replication process so that enough material could be created for use in practical applications. Specifically, cloning not only requires undamaged DNA material but a team of assisting molecules. The molecules behave like dress designers. They unstitch the double helix and connect the appropriate parent chemicals to the daughter chemicals to create segments of the six-foot long thread. The segments are then stitched together and proofread to ensure that the combinations of chemicals are in the correct positions within the strands. It is a dance of living links.

The major breakthrough in cloning occurred in 1977 when Frederick Sanger discovered a technique to synthetically sequence the gene structure of the DNA in such a way that all of the necessary molecular functions were activated. This catalyst for cloning is called a “polymerace”. He was awarded the Nobel Prize in 1980.

In 1983 Kary Mullis built upon Sanger’s work. His enhanced method resulted in a breakthrough chain reaction in replication. This method became known as the polymerase-chain-reaction (PCR). For this work Mullis received the Nobel Prize in 1986. By 1983 all of the ingredients were available to produce practical, low-cost DNA replicators that could generate millions of copies of targeted DNA segments in a few hours instead of days.

And that is exactly what Lexington-based Raindance Technologies accomplished in 2011 with the introduction of the ThunderStorm technology.

The instrument (see photo) created millions of discrete droplets that can encapsulate a single molecule, cell or chemical reaction. The information is then individually sorted, digitized and analyzed. ThunderStorm is uniquely designed for rapid DNA sequencing using PCR. For example, the digital PCR method has been used to accurately determine cancer cells from normal cells by the encapsulation of individual DNA molecules. The molecular data is subsequently digitally analyzed within the system. Digitized PCR technology is useful in the diagnosis of diseases, human gene therapy, pharmaceutical products, forensics, control of environmental problems, animal husbandry and genetic engineering in plants.

To design a product that rapidly evaluates single cells and preserves the sample’s structural integrity without contamination is a remarkable technological achievement. The droplet size is in the range of 5 to 25 pico-liters (about ten-billionths of a cubic centimeter) and each droplet must not vary by more than one-percent from each other. Microfluidic electronic processers are required combined with uniquely designed high-precision pumps. The flow-rate is 3,000 droplets per second. Only 250 nanograms (9 billionths of an ounce) of sample DNA is required to initiate the process.

On April 2 of this year, RainDance introduced a more advanced version of the RainStorm instrument called the “RainDrop Digital PCR System” that is capable of generating greater than a billion reactions in a day. The new product offers enhanced methods of analysis that increases the analytical power of the PCR method by at least ten times.

On that occasion, Roopom Banerjee, president and CEO of RainDance, said “Two years ago RainDance embarked on an ambitious goal when it set out to develop a digital PCR technology platform that would fundamentally transform cancer research, and open the door to new ways that cancers may be detected, monitored and treated in the future. With the introduction of our RainDance System at AACR (American Association for Cancer Research) we have realized this vision and officially ushered in the next generation of PCR.”

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