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Supercomputers Surprisingly Link Dna Crosses to Cancer


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Short inverted repeat sequences of DNA nucleotides are enriched at human cancer breakpoints.

Researchers at the University of Texas at Austin used supercomputers to uncover a link between cross-shaped pieces of DNA and human cancer.

Credit: Karen Vasquez

University of Texas at Austin (UT Austin) researchers used supercomputers to discover a surprising link between cross-shaped pieces of DNA, or cruciforms, and human cancer. The researchers found DNA cruciforms are mutagenic, altering DNA in a way that can increase the risk of cancer in humans.

UT Austin's Stampede and Lonestar supercomputers helped the researchers find short inverted repeats of 30 base pairs in a reference database of mutations in human cancer that are somatic, meaning not inherited.

The researchers discovered two different mechanistic pathways. One involves DNA replication where the structures cause a roadblock to DNA replication, and the other involves DNA repairing proteins and recognizing these alternative DNA structures as damage, which can then cause DNA double-strand breaks and lead to serious problems including neoplastic transformation.

The researchers arrived at their conclusions using an algorithm that takes a string of letters corresponding to the DNA bases A-T-C-G and checks if nearby strings of letters match the reverse complement of the first string. "We certainly cannot do this kind of work on our laptop or anything like a normal system in our laboratories; we need a very powerful computing system to accomplish our gene sequence searches," says UT Austin's Albino Bacolla.

From Texas Advanced Computing Center
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