Easily untangling DNA

Belgian researchers have discovered a simple and effective way to untangle DNA, enabling its straightened-out structure to be studied under a microscope. Their method has been published in the journal ACS Nano.

“Deposition of linear DNA molecules is a critical step in many single-molecule genomic approaches including DNA mapping, fiber-FISH and several emerging sequencing technologies,” the researchers said. “In the ideal situation, the DNA that is deposited for these experiments is absolutely linear and uniformly stretched, thereby enabling accurate distance measurements.”

But current approaches for the linearisation of DNA are technically demanding. DNA sequencing, which involves the study of short strings of DNA to determine the exact order of nucleotides within a DNA molecule, is both time- and resource-intensive. And DNA mapping, which uses the longest possible DNA fragments to map the DNA’s ‘big picture’ structure, is only suitable for applications that do not require highly detailed genetic analysis.

The researchers from KU Leuven had previously developed a DNA mapping technique called fluorocoding, in which “the DNA is marked with a coloured dye to make it visible under a fluorescence microscope”, explained chemist Jochem Deen. “It is then inserted into a droplet of water together with a small amount of acid and placed on a glass plate. The DNA-infused water droplet evaporates, leaving behind the outstretched DNA pattern.”

But the complicated deposition technique “does not always produce the long, straightened pieces of DNA that are ideal for DNA mapping”, Deen continued. Engineer Wouters Sempels said the improved technique combines two factors: “the natural internal flow dynamics of a water droplet and a polymer called Zeonex that binds particularly well to DNA”.

The ‘rolling droplet’ technique is simple, low-cost and effective. The researchers inject genetic material into a droplet of water and use a pipette tip to drag it over a glass plate covered with a sticky polymer. The droplet rolls like a ball over the plate, sticking the DNA to the plate surface. The unravelled DNA can then be studied under a microscope.

“Our technique requires very little start-up materials and can be carried out quickly,” said Sempels. “It could be very effective in determining whether a patient is infected with a specific type of virus, for example.”

The study focused on viral DNA, but Sempels said the technique could just as easily be used with human or bacterial DNA. It could even be refined for cancer research and diagnosis, with Sempels suggesting it could be used to quickly tell the difference between healthy cells and cancer cells.

“Overall, our approach provides an accessible route to the study of genomic structural variation from samples containing no more than a handful of cells,” the researchers concluded.

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