Battle of the DNA bulge may help thwart cancer

UH Research Aims to Understand How Mistakes In DNA Replication Lead To Disease

Studies at the University of Houston are shedding light on the mechanisms our bodies use to recognize and repair mistakes in our genetic code, mistakes that, left unchecked, could lead to cancer.

DNA is the body’s blueprint found in every cell, and it carries all our genetic information. Every time a living cell divides to make new cells, it must first make a copy of its DNA, or transcribe it, similar to the way monks used to transcribe old scrolls. If a DNA transcription error is made, the body’s “spellcheckers” may find it and fix it. But if they fail to detect and repair the mistake, the cell’s instructions are altered.

“When a mistake gets through, you have a problem that could lead to a dangerous mutation,” says B. Montgomery Pettitt, the Hugh Roy and Lille Cranz Cullen Distinguished Professor of Chemistry at UH. “If that mistake has turned a good instruction into a bad instruction that says ‘please make nonsense,’ then that could lead to cancer.”

Pettitt and his research group are studying a particular type of DNA transcription error called a bulge, as well as the protein “spellcheckers” responsible for finding and repairing bulges.

“Some of the worst places to get these errors are in the genes that determine cell growth and death,” Pettitt says. “One of the characteristics of cancer cells is that they are essentially immortal, and they’re like Peter Pan – they never grow up. So this inhibiting of normal cell death is one of the real problems.”

Ultimately, the UH studies may lead to more targeted cancer treatments, says Pettitt, who also is director of the Institute for Molecular Design at UH.

Pettitt will present his research on DNA bulges and recognition proteins Sept. 7 at the 226th annual American Chemical Society national meeting in New York, N.Y.

Pettit’s work describing DNA bulges comes fifty years after scientists first described what the normal structure of DNA looks like – a ladder twisted into a helix, or coil. The sides of that ladder are made of sugar and phosphate groups, and the “rungs” are chemical building blocks called bases. There are four different bases, abbreviated A, G, T and C. A pair of bases, joined together, makes up each rung.

As DNA is being copied, a protein untwists and unzips the double helix that joins the base pairs. Another protein then comes along and begins synthesizing the appropriate bases to latch on to each side of the now separated strands, resulting in two new DNA strands.

Pettitt and his group are particularly interested in the protein that proofs and checks the DNA strands for errors during this process.

“Understanding what these proteins look for as they ‘proofread’ the DNA, where they look, and how they recognize a DNA bulge will help us better understand what goes wrong when the protein can’t recognize the errors,” Pettitt says.

A DNA bulge occurs where an extra base winds up on one side of the DNA strand.

“A bulge is like having a ladder with one extra rung that only goes halfway across,” Pettitt explains.

The bulge can be either a missing base, or an extra one that has been inserted during the DNA copying process. Most bulges happen during replication.

In the research to be presented at the ACS meeting, Pettitt’s team looked at all the various ways a bulge can orient itself along the DNA strand. The researchers built sophisticated computer models of the bulges, based on experimental data. Their computer simulations help them determine how probable each of the various bulge orientation models is.

“No one has looked at these things in the way we have. What we found was that the bulge could sit there on the inside of the helix with nobody across from it, or it could flip outward and point into the solution,” Pettitt says. These were the most likely orientations, but an errant base also could try to bully its way in to the strand and make weird distortions in the whole DNA ladder.

“There’s a range of things that it can wind up doing,” Pettitt says. “We want to focus on the orientations that happen a lot, those that are very probable.”

As for how prevalent bulges are in general, Pettitt says, “this is something we’re definitely working on.”

The UH research is funded by the National Cancer Institute, which is part of the National Institutes of Health.

SOURCE: Pettitt, 713-743-3263; pettitt@uh.edu