Laser Sequencer
"Solar bunnies" will help scientists from Russia to quickly find differences in DNA
Biologists from Russians have learned to decipher and quickly compare the DNA structure of different cells by shining their molecules with a laser and watching how its beam "crumbles" into many light and dark spots. A description of this technique was published in the journal Laser Physics Letters.
The image of the nucleotide sequence of chlamydia when modeling the operation of an optical processor (RNF).
"The principle of operation of our optical processor has been described for a long time, but the approach based on the recognition of images of nucleotide sequences is unique and differs in fundamental novelty. It has never been used in bioinformatics before," says Professor Sergey Ulyanov from Saratov State University, whose words are quoted by the press service of the Russian Science Foundation.
Initially, DNA sequencing technologies were expensive, available only to large laboratories and large teams of scientists. According to current estimates of economists, the first complete decoding of the human genome cost US taxpayers $ 2.7 billion.
The growth of computer power and new DNA decoding technologies that have appeared in recent years have reduced the cost of sequencing to several thousand dollars, which has allowed genomic technologies to penetrate into all areas of medicine and science.
Ulyanov and his team, like many other foreign and domestic scientists, are trying to take the next step in the development of molecular biology – they are creating methods that allow finding traces of specific fragments of DNA or genomes of specific organisms in virtually any place without first preparing a sample and knowing that they must be present there.
The development of such technologies is extremely important for doctors, as they will allow them to diagnose dangerous diseases at the earliest stages of their development, and find traces of infections, cancer cells and other "regime violators" even before they have time to take root in the body. Russian scientists have taken the first step towards creating such systems by "taming" a kind of solar bunnies.
As Ulyanov and his colleagues noticed, the collision of a laser beam with a long DNA molecule will cause it to break up into many dark and light spots. Their number, size and other properties will depend very much on how the barrier that their progenitor faces is arranged.
Thanks to this, changing even one "letter" in the DNA will greatly change the number and location of "sunbeams". Analyzing these differences, it is possible to understand what exactly has changed in the structure of the genome of a microbe or cell, and the sets of light and dark spots themselves can be used to compare a large number of genomes of different cells or bacterial strains.
According to the authors of the article, the same analysis technique can also be used for quick analysis and comparison of "ordinary" genomes decoded using classical methods of molecular biology. To do this, it is enough to convert them into a similar image using a special program, the so-called "optical processor", and then use it to compare them with each other.
Russian scientists have created the first program of this kind, paying attention to what exactly happens when a laser beam interacts with different DNA "letters", and compiling a set of formulas that makes it easy to calculate the number, position and other properties of "sunbeams" that would arise during a real experiment.
They tested the work of this technique of DNA analysis and comparison on fragments of the omp1 gene responsible for the work of the cell membrane in chlamydia cells, the pathogen microbe of one of the most common sexual lectures.
This gene, as scientists explain, is used today to search for traces of infection in the early stages of infection, and small mutations inside it can make the microbe "invisible" to doctors. Optical processors, as shown by the experiments of Ulyanov and his colleagues, can even find single mutations in omp1, which will speed up the detection of infection and help doctors correctly choose a medicine to fight it.
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