Personal genome in half an hour

American scientists have demonstrated the possibility of real-time observation of individual polymerase proteins as they complete single-stranded DNA to double-stranded. The new method should significantly reduce the cost and speed up the procedure for sequencing the personal genome.

In 2000, after 10 years of work, the first stage of the Human Genome project was completed. The cost of the project was about $3,000,000. Since then, the development of sequencing methods has made it possible to significantly reduce the cost of the procedure: for example, genome sequencing for $60,000 was reported this spring, and several companies have already announced their readiness to market equipment that reduces the cost of full sequencing to $ 5,000. Now a California company is introducing equipment that makes it possible to fully sequence the human genome in half an hour at a cost of only about $ 1,000.

Until now, sequencing (determining the sequence of nucleotides in DNA) was possible only for short sections of DNA several bases long, which required "cutting" DNA into short fragments, determining the sequence of nucleotides in each of them, and then combining the data for a complete reconstruction of the genome. This process must be repeated many times with overlapping turns on top of each other, which is necessary to get an accurate picture, which is why it takes so much time.

A more promising approach is to observe the process of recreating double-stranded DNA from a single strand in real time. The problem lies in the difficulty of observing this process due to the too small size of the molecules. However, scientists from Pacific BioSciences (Menlo Park, California) have developed a method by which this problem can be solved (Science, DOI:10.1126/science.1162986).

DNA synthesis is carried out by enzymes called DNA polymerases. Polymerase attaches to single-stranded DNA and, step by step, completes a second chain of nucleotides complementary to the existing nucleotides. The essence of the new method is to attach fluorescent labels of different colors to each of the four types of nucleotides and observe flashes as the second DNA chain is completed from the labeled nucleotides. The sequence of colored flashes at the same time shows the sequence of addition of nucleotides.

The method is based on two important achievements.

First, scientists have developed a mode-free waveguide (zero-mode waveguide), which is a hollow metal cylinder with a diameter of 20 nm, in which single-stranded DNA and protein polymerase are located.

Inside it, it is possible to directly observe fluorescence flashes from individual polymerization acts, since the small size of the waveguide significantly weakens the background lighting that overlaps the observed flashes otherwise.

The second component is a new method of attaching fluorescent labels to nucleotides in the process of DNA synthesis from nucleotide triphosphates. Instead of attaching them to the part that is included in DNA, as is currently done, the tags are attached to the part of the nucleotide that goes into the environment during the reaction (the phosphate "tail"). This avoids the addition of a huge number of fluorescent labels during DNA synthesis.

To date, chips containing 3,000 waveguides have been created, and the company hopes to release them to the market by 2010. By 2013, it is planned to place up to a million waveguides on one chip and simultaneously monitor DNA synthesis in each of them. The founder of the company, Stefan Turner, assumes that such a chip will be able to completely sequence the human genome in half an hour with an accuracy of 99.999 percent, and the full cost of the procedure will be $ 1,000.
 
Anna Chvyreva, EternalMind.ru , according to New Scientist: Molecular fireworks could produce '30 minute genomes' 

Portal "Eternal youth" www.vechnayamolodost.ru05.12.2008