14 April 2021

DNA Pipette

Updated method of extracellular DNA capture from biological samples

XX2 century

Although DNA sequencing is becoming an increasingly common procedure, extracting even a single DNA molecule from a biological sample is not an easy task.

The development of the staff of the University of California at Riverside makes it relatively easy to detect and capture DNA from liquid samples (this may be, in particular, blood) using a tiny glass tube and an electric current. The method is described in an article published in Nanoscale journal (Farajpour et al., Measuring trapped DNA at the liquid-air interface for enhanced single molecule sensing).

DNA is a double–stranded, electrically charged molecule that stores all the information an organism needs for life. Its usual "workplace" is inside the cell nucleus, where it is in a collapsed state. Extracting DNA from a cell is impractical for many scientific and medical tasks, since it takes a lot of time.

But the body is being renewed – and this means that some of the cells die, their membranes are destroyed and release the contents, which includes DNA. In practice, this means that every blood sample, for example, includes several strands of free-floating DNA, which theoretically can be detected and extracted.

In practice, most of the extracellular DNA is destroyed by scavenger cells, macrophages that purify the body of waste. As a result, there is not too much DNA in the blood.

Most methods of capturing and studying extracellular DNA are expensive. First, a concentrate is obtained, then fluorescent dyes are used for DNA visualization.

Kevin Freedman led a scientific group whose goal was to improve the method of DNA detection and analysis, known as nanopore sequencing.

The essence of the approach is the use of an electric charge to direct a DNA sample directly into a glass tube with a small hole, a nanopore; that is, in this case we are talking about a so–called solid-state nanopore made of borosilicate glass. This is a "nanopipette" with a hole with a diameter of 20 nm (slightly wider than the thickness of the DNA helix), inside which there is a positive electrode.


In the illustration: (a) – a glass tube with a tiny hole and an electrode inserted into a liquid sample to collect DNA floating in the sample; (b) photo of a borosilicate glass nanopipette.

DNA has a negative electric charge because it has many polar molecules (molecules with an unevenly distributed charge).

DNA moves towards the electrode and passes through the nanopore, at the time of passage the current changes, it can be measured and so DNA can be determined. The researchers found that the number of DNA fragments captured depends on how deeply the nanopipette is immersed in the liquid. It works most effectively near the surface – that's where the most fragments accumulate. It is also shown that DNA concentration occurs in the cooled liquid layer. Researchers believe that the effect is due precisely to temperature – evaporation occurs at the air-liquid boundary and a noticeable temperature gradient is observed.

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