The biological information that makes us unique is encoded in our DNA. DNA damage is a natural biological occurrence that happens every time cells divide and multiply. External factors such as overexposure to sunlight can also damage DNA.
Michael Feig, professor of biochemistry and molecular biology at Michigan State University, studies the proteins MutS and MSH2-MSH6, which recognize defective DNA and initiate DNA repair. Natural DNA repair occurs when proteins like MutS (the primary protein responsible for recognizing a variety of DNA mismatches) scan the DNA, identify a defect, and recruit other enzymes to carry out the actual repair.
“The key here is to understand how these defects are recognized,” Feig explained. “DNA damage occurs frequently and if you couldn’t repair your DNA, then you won’t live for very long.” This is because damaged DNA, if left unrepaired, can compromise cells and lead to diseases such as cancer.
DNA bending is believed to facilitate the initial recognition of the mismatched base for repair. The repair efficiencies are dependent on both the mismatch type and neighboring nucleotide sequence. We have studied bending of several DNA duplexes containing canonical matches: A:T and G:C; various mismatches: A:A, A:C, G:A, G:G, G:T, C:C, C:T, and T:T; and a bis-abasic site: X:X. Free-energy profiles were generated for DNA bending using umbrella sampling. The highest energetic cost associated with DNA bending is observed for canonical matches while bending free energies are lower in the presence of mismatches, with the lowest value for the abasic site. In all of the sequences, DNA duplexes bend toward the major groove with widening of the minor groove.
For homoduplexes, DNA bending is observed to occur via smooth deformations, whereas for heteroduplexes, kinks are observed at the mismatch site during strong bending. In general, pyrimidine:pyrimidine mismatches are the most destabilizing, while purine:purine mismatches lead to intermediate destabilization, and purine:pyrimidine mismatches are the least destabilizing. The ease of bending is partially correlated with the binding affinity of MutS to the mismatch pairs and subsequent repair efficiencies, indicating that intrinsic DNA bending propensities are a key factor of mismatch recognition.
The biological repair machinery seems to take advantage of this propensity by ‘testing’ DNA to determine whether it can be bent easily. If that is the case, the protein has found a mismatch and repair is initiated.
“When the MutS protein is deficient in certain people, they have a high propensity to develop certain types of cancer,” Feig said. “We’re interested in understanding, first of all, how exactly this protein works. The long-term idea is to develop strategies for compensating for this protein, basically substituting some other mechanism for recognizing defective DNA and enabling repair.”
The strongest link between diseases and defects from the MutS protein has been made for a specific type of genetically inherited colon cancer.
“If an essential protein like MutS is missing or less than adequate, then the cells will not behave in a normal way,” he explained. “They will turn cancerous. The cells will refuse to die and proliferate in an uncontrollable state.”
In these cases, cancer is not a result of damaged DNA, but occurs because of a problem in the DNA repair mechanism itself.
“It probably has effects on many other cancers as well, because all the cancers are ultimately linked to defective DNA,” he said. “If DNA damage is not recognized and repaired in time then it can lead to any type of cancer. It is a fairly generic mechanism.”
According to Matt Cowperthwaite, TACC’s medical informatics programs coordinator, Feig’s research is enormously important for advancing our understanding of how cells repair the mistakes that inevitably occur during DNA replication. “For the first time, we have a mechanistic insight of how MutS finds mutations. This is extremely important research because the process of mutation underlies some of the deadliest diseases to affect humans, such as cancer.”
Research in this area, being very fundamental in nature, throws up many challenges, but its potential in future impact, Feig believes, is tremendous.