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Supercomputers Surprisingly Link Dna Crosses to Cancer

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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