Glass nanopore pulls DNA like spaghetti through a needle
The purely electrical technique captures cell-free DNA from the surface
of a sample

Date:
April 6, 2021
Source:
University of California - Riverside
Summary:
Nanopore sensing can extract cell-free DNA from a liquid sample.

Researchers used electric current to direct free-floating DNA into
the 20 nanometer opening of a glass tube. The DNA concentrated near
the surface, making it relatively easy to collect numerous samples.



FULL STORY ==========================================================================
DNA sequencing has become so common, few realize how hard it is to even
extract a single molecule of DNA from a biological sample.


========================================================================== Research led by UC Riverside is making it easier to detect and capture
DNA from fluid samples such as blood using a tiny glass tube and electric current. The technique, described in the journal, Nanoscale, can also
improve cancer diagnosis in the future.

DNA, a double-stranded, electrically charged molecule that contains all
the information an organism needs to create and organize the building
blocks of life, is tightly folded within the cell nucleus. Extracting
the DNA from a single cell is time consuming and impractical for many
medical and scientific purposes. Fortunately, as cells die naturally,
their membranes burst, releasing the contents, including DNA. This means
that a blood sample, for example, contains many strands of free-floating
DNA that should, in theory, be easier to identify and extract in quantity.

However, scavenger cells called macrophages that clean up cellular
waste destroy most cell-free DNA, leaving it at low concentrations in
the blood. Most approaches to capturing cell-free DNA require expensive techniques that first concentrate the molecules before using fluorescent
dyes to help see the DNA.

Corresponding author Kevin Freedman, an assistant professor of
bioengineering at UC Riverside's Marlan and Rosemary Bourns College of Engineering, led an effort to improve detection and capture of DNA at
lower concentrations by using an electric charge to direct a DNA sample directly into a glass tube with a tiny opening called a nanopore. Nanopore sensing has emerged as a fast, reliable, and cost-effective diagnosis
tool in different medical and clinical applications.

"We know that if you apply voltage across a cell membrane, ions will move through pores in the cell membrane," Freedman said. "DNA also travels with
the electric field, and we can use it to move the DNA." The researchers
put a positive electrode inside a glass tube with an opening, or pore,
20 nanometers wide -- a bit bigger than a DNA molecule but too small
to admit cells. They applied an electrical potential to the nanopore,
which was dipped into a vial containing a DNA sample and a negative
electrode. The cell- free DNA moved into the pore and blocked it. The
change in electrical current as the DNA traveled through the pore allowed
the researchers to detect it.

"It's like trying to pull spaghetti through a needle," Freedman said. "To
go through the pore it has to be almost perfectly linear." The closer
to the liquid surface the researchers held the pore, the more DNA it
picked up.

"Amazingly, we found that DNA accumulates at the liquid-air interfaces. If there is a cooling layer, the DNA will try to go to the cooler location," Freedman said. "We hope the same is true for a blood sample, so the same mechanism can be used to concentrate DNA near the surface. Not only
is this beneficial, but this nanopore-sensing strategy demonstrated a
higher signal-to- noise ratio near the surface as well. It is really
a win-win situation." With some refinements, the authors think their
purely electric technique could help diagnose some kinds of cancer from
a single blood sample. In addition to DNA, as tumors grow, vesicles are released into the blood stream. These mini lipid-based droplets can be
thought of as mini-cells that are identical to the original cancer cells
and could also be detected by nanopore sensing.

Considering all the unique features of this purely electrical technique,
the nanopore-sensing system has the potential to be utilized as a
point-of-care diagnostic test evaluation in the future.

========================================================================== Story Source: Materials provided by
University_of_California_-_Riverside. Original written by Holly
Ober. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Nasim Farajpour, Lauren S. Lastra, Vinay Sharma, Kevin J. Freedman.

Measuring trapped DNA at the liquid-air interface for enhanced
single molecule sensing. Nanoscale, 2021; 13 (11): 5780 DOI:
10.1039/d0nr07759c ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2021/04/210406092649.htm

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