New rapid technique to map DNA by melting base pairs

26 July 2010

A new method for rapidly mapping the base pairs of a DNA molecule has been developed by researchers in Sweden and Denmark. The technique could be used to find out more easily whether someone is carrying a genetic predisposition to certain diseases.

The aim is that the new technique could be used to diagnose and characterise diseases that are caused by significant changes and mutations in the genetic make-up, known as structural variations, that are associated with, for example, cancer, autism and several hereditary diseases.

In addition, the method could be of use in criminal investigations, because it might speed up identification of evidence.

The results are published in the latest issue of the journal Proceedings of the National Academy of Sciences of the USA (PNAS).

The technique, which has recently been patented, uses the fact that different parts of the DNA molecule melt at different temperatures. A central component of the DNA molecule is the nucleobase pairs. These are found in two pair varieties: AT, which stands for adenine and thymine; and GC, which stands for guanine and cytosine. The GC pair is more firmly bound and requires a higher temperature to melt.

By first stretching out the tightly twisted DNA molecule in a nanochannel and then heating it up so that only the AT pair melt, it is possible to obtain a ‘barcode' of the person's 46 chromosomes. In order to make certain parts darker than others, the DNA molecule must be stained. The parts that melt — the AT parts — emit less fluorescence and become dark fields in the barcode.

The image produced shows the rough composition of the DNA molecule, and thus that of the chromosome. Such barcodes are nothing new, but this approach to creating the barcodes is completely new. With this method, the DNA analysis process becomes significantly shorter, from 24 hours to around one or two hours.

"The technique is quicker, easier and cheaper than existing methods. Therefore we hope that it can be used in hospitals in the future. Mapping a person's genome, or genetic make-up, is currently an expensive and complicated process", said Jonas Tegenfeldt, researcher in Solid State Physics at Lund University and one of the senior authors of the article.

"The barcode technique could be a simple way to identify what types of virus and bacteria we are dealing with. We can also find out whether something has gone wrong in the human genome, because it is possible to see if any part of the chromosome has moved for any reason. This is what happens in certain diseases", explains Jonas Tegenfeldt, adding that beyond all the applications an important motivation for the research is still ‘just' basic scientific curiosity.

A further advantage of this barcode technique over other techniques is that only one DNA molecule is required. The fact that the DNA does not have to be amplified also means that it is easy to compare a number of cells and thereby discover any differences between them.

The method provides a rough image of the genome, but compared to other similar methods, such as chromosome banding, the image is still a thousand times sharper. The fact that the measurements must be performed on each molecule individually could also pose a limitation; it is not easy to obtain an average from a large number of molecules.

Reference

1. Walter Reisner, Niels B. Larsen, Asli Silahtaroglu, Anders Kristensen, Niels Tommerup, Jonas O. Tegenfeldt, and Henrik Flyvbjerg. Single-molecule denaturation mapping of DNA in nanofluidic channels,  Proceedings of the National Academy of Sciences of the USA (PNAS). Published online before print July 7, 2010.
doi: 10.1073/pnas.1007081107
www.pnas.org/content/early/2010/06/15/1007081107