University of Utah chemists have discovered a new way to detect chemical damage to DNA that sometimes leads to genetic mutations responsible for many diseases, including various cancers and neurological disorders.

Cynthia Burrows, University of Utah.

Cynthia Burrows, PhD, University of Utah.

“We are one step closer to understanding the underlying chemistry that leads to genetic diseases,” says Cynthia Burrows, PhD, distinguished professor and chair of chemistry at the university and senior author of a study published online in Nature Communications.1 “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.”

Jan Riedl, PhD, University of Utah.

Jan Riedl, PhD, University of Utah.

Jan Riedl, PhD, a University of Utah postdoctoral fellow and the study’s first author, says 99% of DNA lesions—damage to the chemical bases known as A, C, G, and T that help form the DNA double helix—are repaired naturally. The rest can lead to genetic mutations, which are errors in the sequence of bases and can cause disease. The new method can “identify and detect the position of lesions that lead to diseases,” he says.

“We are trying to look for the chemical changes in the base that can lead the cell to make a mistake, a mutation,” says Burrows. “One of the powerful things about our method is we can read more than a single damaged site [and up to dozens] on the same strand of DNA.”

Graphic DNAdamage Utah Nature study

A new method for identifying DNA lesions that can lead to disease-causing mutations. Graphic courtesy Aaron Fleming, University of Utah.

According to the researchers, the new method will enable researchers to study chemical details of DNA lesions or damage. Such lesions, if not repaired naturally, accumulate over time and can lead to mutations responsible for many age-related diseases, including clogged arteries; breast, colon, liver, lung, and melanoma skin cancers; and neurological ailments, such as Huntington’s disease and Lou Gehrig’s disease.

“A method capable of identifying the chemical identity and location in which lesions appear is crucial for determining the molecular etiology [cause] of these diseases,” the authors write.

The chemists tested their method on the KRAS gene, which can cause lung or breast cancer when it is mutated.

Burrows says most DNA sequencing methods reveal mutations because the methods read the bases A, C, G, and T. When sequencing reveals one of those bases out of place, that is a mutation. “However, what you don’t know is what chemistry—what modification—caused that mutation,” she says.

Scientists need to make millions to billions of copies of the DNA so they can sequence it and locate the gap where the damage was, Burrows continues. But the damage itself is “a train wreck” that either prevents making copies of the DNA or makes copies with errors, she says.

To overcome this obstacle, once the damaged base has been excised to create a gap, the chemists insert a third or unnatural base pair at the damage site as a way to label it while at the same time allowing millions of copies of the labeled DNA to be made.

Burrows says the key innovation in the new method is using base excision repair and unnatural base pairs “to copy the DNA and retain the information about damage that was in the original molecule.”

The chemists next use polymerase chain reaction amplification to make millions of copies of the DNA by heating it until strands in the double helix separate. The strands are put in a solution with lots of A, C, G, and T nucleotides—the bases attached to pieces of DNA backbone. A polymerase enzyme is attached to the end of each strand of DNA, and then moves along the strand grabbing T, G, C, and A nucleotides to make a second strand. Each DNA strand quickly becomes two. The number of strands reaches the millions in hours.

Once the chemists have millions of DNA strands with the damage labeled by an unnatural base pair, they then use nanopore sequencing to locate the damage. The DNA’s damage sites, which are labeled with unnatural bases, are labeled again with 18-crown-6 ether. Changes in electric current allow chemists to detect the bases A, C, G, and T and the labeled unnatural bases.

Finding the labeled unnatural bases identifies the DNA damage site to within 10 base pairs. Burrows says the nanopore sequencing method needs improvement or replacement by next-generation sequencing to actually pinpoint the damage sites.

The research was funded by the National Institutes of Health. Burrows and Riedl conducted the study with University of Utah chemists Aaron Fleming, PhD, a research assistant professor, and Yun Ding, PhD, a postdoctoral researcher.


  1. Riedl, J, Ding, Y, & Fleming, AM. Identification of DNA lesions using a third base pair for amplification and nanopore sequencing. Nat Commun. 2015;6. doi: 10.1038/ncomms9807.