DNA as you have never seen before, thanks to a new method of nanotechnology imaging

For biologists around the world, April 25 augurs well. This is DNA Day and commemorates the date in 1953 when scientists Francis Crick, Rosalind Franklin, James Watson, and Maurice Wilkins published leading scientific articles describing the helical structure of the molecule's ## 147 ## 39; DNA. In 2003, April 25 was used to announce the completion of the human genome project. Today's annual festivities celebrate the molecule of life with new discoveries. What better time to provide a new picture of the DNA.

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

For example, I would like to know where the process of replicating DNA on each chromosome begins. The duplication of DNA without error is essential to the production of healthy cells. When this process is incomplete or disrupted, the result can cause cancer and other diseases.

In our image, this well-known double-spiral staircase is not visible because this prospect is enlarged – as if you were looking at a country map versus a city. In addition, each of these molecules equates to 50,000 turns of the helical staircase – a substantial segment of a human chromosome.

Make a map of the DNA

This image, taken with a device called Bionano Genomics Saphyr Imager, features individual DNA molecules – stained in blue, green, and red. These strands of DNA were aligned by threading them into narrow tubes, called nanochannels, which contain only a single piece of DNA. When the DNA slips into the tube, the strands straighten up.

The entire DNA molecule is stained blue and the green graduations are benchmarks – or specific DNA sequences occurring on average every 4,500 base pairs. The landmarks pattern provides a unique fingerprint that tells us where we are on the length of a chromosome. The red fluorescent blips mark the locations where the DNA has begun to replicate. These sites are called "origins of replication" and are the place where DNA takes place so that the duplication process can begin.

Researchers at Bionano Genomics in San Diego have developed this nanochannel technology to map regions of chromosomes that were otherwise impossible to map due to complex genetic sequences that make it difficult to determine the order of the four bases. This device solved the problem by "looking at" the sequence arrangement on one molecule at a time and is able to read 30 billion base pairs in one hour, the equivalent of 10 human genomes.

My team and that of Nick Rhind from the University of Massachusetts have recognized that this nanochannel technology would allow us to achieve an experiment never attempted before: map all the locations where DNA replication starts simultaneously on millions of fibers. Unique DNA.

Before a cell can divide into two independent cells, the DNA must copy itself so that each receives a complete set of chromosomes. To understand how genetic material is duplicated, it is essential to know where the process begins along the chromosome. It is the biggest challenge to study how our own chromosomes replicate, and therefore what is wrong with so many diseases, such as cancer, in which replication goes awry.

Replication of DNA and cancer

The origins of replication have not been elucidated, as they occur on many sites of different molecules. It is therefore necessary to look for unique DNA molecules to detect them. Although scientists have been able to see unique DNA molecules since the early 1960s, we could not tell where the chromosome molecules came from, so we could not map anything out. is.

Kyle Klein, a Ph.D. A student in my lab labeled live human stem cells with red fluorescent molecules indicating the locations of DNA replication, mapped using the Bionano device. These images were then superimposed on the blue and green DNA maps of the same DNA molecules.

We hope this method will completely transform our understanding of human chromosome replication. In addition, as most chemotherapy drugs for the treatment of cancer and most carcinogens – or carcinogenic chemicals – act in our environment by attacking DNA when it replicates, we expect this method provides a quick and comprehensive test of how these products disrupt DNA replication. We also hope that it will show you how we can mitigate these negative consequences and develop better and less toxic chemotherapy treatments.