Monday , July 26 2021

DNA you have never seen before thanks to the new nanotechnology imaging method

Double-stranded DNA map, stained in blue, green landmarks, and starting points for copying the molecule to red. David Gilbert / Kyle Klein, CC BY-ND

For biologists everywhere, April 25 is favorable. This is a DNA Day and marks the date in 1953 when scientists Francis Crick, Rosalind Franklin, James Watson and Morris Wilkins published scientific papers describing the spiral structure of the DNA molecule. In 2003, April 25 was used to announce the completion of the human genome project. Today's annual holidays celebrate this day with the new discoveries of the molecule of life. What better time to provide a new picture of DNA.

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I am DNA DAVE (or at least my 1984 registration plate), and one of the things my lab likes to do is "see" DNA. We take images of DNA so that we can directly measure things that are difficult to quantify by using indirect methods that usually involve sequencing the four chemical units of DNA called bases.

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For example, I would like to know where each chromosome starts the process of replicating DNA. Duplication of DNA without errors is essential for the production of healthy cells. When this process is incomplete or disturbed, the result may cause cancer and other illnesses.

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In our opinion, the familiar double-spiral ladder is not visible because this perspective is reduced – as a look at the map of a country against a city. Also, each of these molecules is equivalent to 50,000 turns of the spiral staircase – a substantial segment of the human chromosome.

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Create a DNA map

Single strands of DNA are stained in blue. Green marks the location of specific landmarks. Red highlights the places where DNA replication begins.
David Gilbert / Kyle Klein, CC BY-ND

This image, taken with a device called Bionano Genomics Saphyr, contains separate DNA molecules – colored in blue, green and red. These DNA strands are aligned by piercing them through narrow tubes called nanoculars that fit into only one piece of DNA. As the DNA slides into the tube, the strands stand out.

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The entire DNA molecule is stained in blue, and green – in specific DNA sequences that occur on average every 4,500 base pairs. The landmark model provides a unique fingerprint that tells us where we are along the chromosome. Red fluorescent feet mark the sites where DNA has begun to replicate. These sites are called "origin of replication" and where the DNA first develops, so the duplication process can begin.

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Researchers from Bionano Genomics in San Diego have developed this nanocapillary technology to map regions of chromosomes that are otherwise immeasurable due to difficult genetic sequences that make it difficult to determine the order of the four bases. This device solves the problem by looking at the sequencing of one molecule at a time and is able to read 30 billion base pairs per hour – the equivalent of 10 human genomes.

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My team and that of Nick Reed, of the University of Massachusetts, admitted that this nanoconchant technology would allow us to carry out an experiment that was never done before: to map all the places where DNA replication starts at the same time millions of single DNA fibers.

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Before the cell can be divided into two independent cells, the DNA has to make a copy of itself so that everyone can get a full set of chromosomes. To understand how genetic material duplicates, it's important to know where the process begins on the chromosome. This is the greatest challenge for studying how replication of our own chromosomes occurs and therefore what happens in so many diseases as cancer in which replication fails.

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DNA replication and cancer

Each time the cell divides the DNA double strand, it must duplicate to provide a copy of the genetic instructions for the two cells.
Soleil Nordic /

The origin of replication is elusive because they occur in many places on different molecules, so we have to look at separate DNA molecules to find them. Although scientists have been able to see separate DNA molecules since the early 1960s, we can not tell where each molecule originates from the chromosomes, so we can not map anything.

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Kyle Klein, Ph.D., a student of my lab, who called living human stem cells with red fluorescent molecules that marked the DNA replication sites that were mapped to the Bionano device. These images were then superimposed on the blue and green DNA maps of the same DNA molecules.

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We expect this method to fully transform our understanding of the replication of human chromosomes. Furthermore, since most chemotherapeutic drugs for treating cancer and most carcinogens or cancer chemicals in our environment work by attacking DNA when reproduced, we expect this method to provide a quick and exhaustive test of how these chemicals break down the replication of DNA. We also hope to reveal how we can mitigate these negative consequences and how we can develop better and less toxic chemotherapeutic procedures.The conversation

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David M. Gilbert, Professor of Molecular Biology, State University of Florida

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This article is reissued from the Creative Commons license conversation. Read the original article.

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