DNA sewing machine

DNA sewing machine created by Kyohei Terao from Kyoto University and colleagues. They designed laser-directed microdevices to pick up and manoeuvre giant individual molecules of DNA. The technology will also be useful for a number of other applications including DNA sequencing and molecular electronic. This should help enable the goals of $10-1000 whole genome sequencing and help with DNA manufacturing (using DNA as a structural material). There is a lot of further potential for more specially designed microtools and structures for improving the manipulation of DNA and other molecules.

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In conclusion, we have demonstrated the method and device for on-site single-molecule manipulation of giant DNA molecules, using optically driven microstructures for picking up and separating a DNA fibers from a bundle. We used a microfabricated hook together with winding/unwinding of the DNA fiber onto microfabricated bobbins. This method enables the manipulation of DNA molecules in the order of mega base pairs under a microscope without fragmentation. The method is purely mechanical, and requires no chemical modifications; moreover, it can manipulate any desired part of the targeted DNA in the microscope view. This method will create avenues for space-resolved single molecule assays of large chromosomal DNA, along with its applications in gene location and epigenetic studies.

Single molecule analysis of DNA is limited by the difficulty of stretching out and handling these long molecules – eukaryotic DNA can range from millimetres to centimetres. A giant DNA molecule is very fragile, explains Terao, so to catch it and manipulate it without breaking it is a challenge.

Thinking of a strand of DNA as a piece of sewing thread, Terao developed microhooks to pick up the DNA, just like we would use our fingers to pick up thread. When thread is very long it becomes tiresome to manipulate it just with our fingers and instead we wind it around bobbins to make it compact. This is what inspired us to use microbobbins, says Terao.

Optical tweezers – where tightly focused laser beams trap and hold tiny objects – are used to catch and move these microdevices. The z-shaped microhook is directed by the tweezers to pick up a single strand of DNA, and barbs in the openings of the hook prevent the caught DNA unhooking. In the case of bobbins, two focused laser beams are used to revolve one bobbin around the other. The revolving motion winds the DNA molecule between the two bobbins.

This DNA manipulation technique should prove useful in applications such as fluorescence in situ hybridisation (FISH), says Terao.