Thursday, July 22, 2010

Melting DNA Into Barcode Drives Speedy Genome Mapping

A team of EU-funded researchers has created a cheap, easy method to 'melt' DNA (deoxyribonucleic acid) molecules into a barcode in 1 or 2 hours - instead of the usual 24. This new technique, described in the Proceedings of the National Academy of Sciences USA, could be used for rapid genetic mapping and medical diagnosis.

The READNA ('Revolutionary approaches and devices for nucleic acid analysis') project received close to EUR 12 million from the Health Theme of the Seventh Framework Programme (FP7), which funds groundbreaking techniques for DNA sequencing and genotyping to revolutionise nucleic acid analysis methods.

'Mapping a person's genome is currently an expensive and complicated process,' explained Jonas Tegenfeldt of Lund University in Sweden. The new technique could overcome both drawbacks. First, it requires only one molecule of DNA for analysis, so the DNA does not have to be amplified beforehand. Also, it neither requires pre-treatment nor fragmentation of the DNA molecule, so it can detect variations along the DNA sequence without affecting the overall organisation of the genome.

The process is therefore faster and cheaper. It also enables comparisons between cells without having to average out the results over a group of amplified molecules. These qualities make it a perfect candidate for routine hospital analysis, for instance to find out if a patient carries a genetic predisposition to a disease.

DNA barcodes are not new but this method introduces a novel way of obtaining them. The technique is based on the fact that different parts of the DNA molecule melt at different temperatures.

The DNA molecule is made up of two strands that can be separated in the lab for analysis. Each DNA strand has a distinctive sequence, i.e. a characteristic succession of nucleobases called adenine, thymine, guanine and cytosine (A, T, G and C). The two strands are held together by bounds between the nucleobases: 'A' can only pair with 'T', and 'G' always pairs with 'C'. The 'G-C' pair is bound more firmly than the 'A-T' pair, so it requires a higher temperature to melt.

The researchers first stretched the DNA in a nanochannel before heating it up to the temperature where only the 'A-T' bond melts. The DNA is previously stained with a special fluorescent substance to get an image of the melted molecule. The pattern of partial melting reveals the underlying sequence in a coarse-grained manner: the 'A-T'-rich parts that melt emit less fluorescence and become dark fields in the barcode. This barcode is unique to the specific sequence of each DNA molecule analysed.

The READNA consortium comprises researchers from 12 academic institutions and 6 private companies across Europe. The group is applying the advantages of nanofabrication technology - developed originally for the integrated circuit industry - to the assembly of small-scale 'nanofluidic' devices for the manipulation and analysis of single molecules.

The barcode technique is now patented and could have important medical applications, for instance to identify virus and bacteria in a patient. According to Dr Tegenfeldt, '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.'

Source: Cordis News Release
For more information, please visit:
Proceedings of the National Academy of Sciences (PNAS):
Lund University:
Please contact Jonas Tegenfeldt, researcher at the Division of Solid State Physics at the Faculty of Engineering, Lund University
Read the PNAS article Single-molecule denaturation mapping of DNA in nanofluidic channels 

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