Researchers Discover New Way to Find DNA Damage

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DNA DamageDNA damage is thought to threaten the gene pool and can sometimes cause various diseases, such as neurological disorders and certain cancers.

In a new study published in the online journal Nature Communications, University of Utah chemists have created a new way to find chemical damage. As a result, they are one step closer to understanding the chemistry behind DNA damage or lesions that lead to genetic conditions.

“We have a way of marking and copying DNA damage sites so that we can preserve the information of where and what the damage was,” explained the study’s senior author Cynthia Burrows, a distinguished professor and chair of chemistry at the University of Utah.

The DNA chemical bases are called A, C, T, and G, and they form the DNA double helix. It is known that 99% of the DNA will be repaired naturally; however, the other one percent will lead to genetic mutations. They are errors in DNA sequencing that can produce mutations responsible for diseases like neurological disorders like Lou Gehrig’s disease and Huntington’s disease; clogged arteries; and cancers such as skin (melanoma), colon, liver, lung, and breast cancers. The new method discovered by the researchers will identify and find the position of the DNA lesions that cause those diseases.

For the study, the researchers found the damage to the DNA and cut it out using a method called “base excision repair.” It is the same method that won English scientist Tomas Lindahl a Nobel Prize in Chemistry earlier this year. Next, an “unnatural base pair” is placed at the snipped-out DNA damage site. The Utah chemists used an unnatural base pair invented by chemists from the Scripps Research Institute in California, instead of using natural base pairs A-T and C-G.

Next, the DNA with the damage site labeled with an unnatural third base pair is copied millions of times using the PCR (polymerase chain reaction) method. The key innovation here has the researchers use base excision repair to cut out the damage, and insert the unnatural base pair at the damaged DNA site. This allows for the production of millions of DNA copies. Finally, another chemical called 18-crown-6 ether is placed into the unnatural base pair on each DNA strand. They are then sequenced using a type of molecule-sized pore, or nanopore, sequencing developed by Burrows and Henry White, a chemist from Utah. This form of sequencing allows the location and order of bases of a DNA strand to be determined by passing the strand through a nanopore.

Burrows believes that the new method seeks, “molecular details that define how our genome responds to what we eat and the air we breathe, and ends up being healthy or not.”

In the study, the chemists applied their method on a gene named KRAS. When KRAS is mutated it can cause breast or lung cancer. In most DNA sequencing methods, scientists have a problem finding the strand that caused the DNA damage in time. They often will make up to billions of DNA copies before they can assess the damage.

The University of Utah researchers then insert the unnatural base pair at the damaged DNA site to label it. This process also helps in the labeling of millions of DNA copies at the same time. Next, the chemists used the PCR method to create millions of DNA copies by separating the strands in the double helix from heating them. The strands are put into a solution with DNA bases, and a polymerase enzyme is attached to the end of each DNA strand, while grabbing A, C, G, and T nucleotides in order to make a second strand. In the process, each DNA strand will double, and strands will become millions in just hours.

When the chemists have millions of DNA strands with the damage labeled by the unnatural base pair, the nanopore sequencing can then conveniently assess the damage. However, Burrows believes it is necessary to improve or replace the nanopore sequencing method with next generation sequencing to help pinpoint the damaged DNA sites.

Sources for Today’s Article:
Riedl, J., et al., “Identification of DNA lesions using a third base pair for amplification and nanopore sequencing,” Nature Communications 2015; 6(8807), doi: 10.1038/ncomms9807.
“New Way to Find DNA Damage,” The University of Utah web site, November 6, 2015;