March 31, 2015

Short and Sweet: Why Modern Molecular Biology Needs Oligos

oligos
DNA sequencing requires millions of short "barcode" chains to identify distinct samples. (Image: Flickr/Shaury Nash)

DNA sequencing and synthesis are two sides of the same coin, the “read” and “write” functions of genetic material. The field and its requisite technology took off in the 1990s with the Human Genome Project’s effort to sequence billions of bases and unlock a new era of genetically informed medicine. The resulting science is still a work in progress – it turns out the genetic code is more complicated than anticipated – but the technologies and companies it helped spawn are an impressive legacy.

Integrated DNA Technologies (IDT) got its start during the Human Genome Project, as it produced single nucleotides (the As, Ts, Cs, and Gs that comprise the genetic code) and short oligonucleotide chains (or “oligos”) to help facilitate a massive sequencing effort around the world. Of course, sequencing technology has advanced dramatically in the intervening decades, but “you still need oligos to do the sequencing,” explains Jerry Steele, IDT’s Director of Marketing, “especially in the next gen sequencing space. Sequencing and DNA synthesis go hand in hand.”

The current sequencing method of choice is Illumina, a process that frequently returns millions of bases of DNA sequence by reading distinct stepwise fluorescent signals associated with each base in a massively parallel array. To distinguish genetic material from different samples (a few hundred are often run on the same plate), scientists label each sample’s DNA extract with a distinct barcode. With each barcode comprised of about ten nucleotides, the demand for synthetic DNA chains in the sequencing process is substantial.

Unlike other biotech companies prioritizing longer constructs or gene variants, IDT specializes in relatively short oligos. These chains are used not only in Illumina barcoding, but also as primers – consistent patches of sequence that may border unknown regions and facilitate PCR-based amplification. Both techniques – “next gen” Illumina sequencing and primer-based amplification – are staples of any self-respecting applied or research-based microbiology laboratory, as they allow researchers to identify constituent organisms or confirm a gene’s presence.

With such short sequences, a single nucleotide discrepancy could mean the difference between two Illumina samples from opposite ends of the world, or between a gene native to the Firmicutes or the Proteobacteria. It’s a small margin for error, “so every base better be right,” explains Steele. “As we’ve grown, it’s just a matter of maintaining that consistency on a larger scale.” In the spirit of not fixing something that needs no repairs, IDT shipped an entire fabrication room from its headquarters in Coralville, Iowa to Belgium when that facility was being built.

Fundamental as they are to modern biology, oligos are used every day in thousands of laboratories around the world, often in innovative ways that the company itself may not have predicted. “The things that people are doing with DNA are really inspiring,” notes Steele. One of his favorite use cases involves low-impact prenatal tests: rather than a painful and invasive amniosyntesis, “we’ve discovered that now because of sequencing, we can see the baby’s DNA in a blood draw from the mother.” Improved sequencing fidelity and throughput are expanding the resolution of the technique, and Steele soon envisions scientists using next gen sequencing to detect cancer cells from the blood stream as an early diagnosis tool. “Biology is really leaving the lab and coming into the real world,” Steele explains, “and it’s going to improve a lot of lives.”

*This article is part of a special series on DNA synthesis that also appears on Wired.com