Probing Non-Canonical DNA Structures With Anticancer Drugs

123 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2000.T:G mismatched base pair is associated with many genetic mutations. Understanding its biological consequences can be aided by studying the structural perturbation of DNA caused by T:G base pair and by specific probing of the mismatch using small molecular ligands. We have shown that AR-1-144, a tri-imidazole minor groove binder, recognizes the CCGG sequence. The NMR structural analysis of the symmetric 2:1 complex of AR-1-144 and GAACCGGTTC revealed that each AR-1-144 binds to four base pairs with the guanine N2 amino group forming a bifurcated hydrogen bond to a side-by-side Im/Im pair. We then predicted that the free G-N2 amino group in a T:G wobble base pair can form two individual hydrogen bonds to a side-by-side Im/Im pair. Thus an Im/Im pair may be a good recognition motif for a T:G base pair in DNA. The cooperative and tight binding of an AR-1-144 homo-dimer to GAA CTGGTTC permits a detailed structural analysis by 2D-NOE NMR refinement and the refined structure confirms our prediction. Surprisingly, AR-1-144 does not bind to GAATCGGTTC. We further show that both the Im-Im-Im/Im-Py-Im hetero-dimer and the Im-Im-Im/Im-Im-Im homo-dimer bind strongly to the CACGG&barbelow;GTC+GACT&barbelow;CGTG duplex. These results suggest that an Im/Im pair can specifically recognize a single T:G mismatch. Together with other sequence-specific recognition rules, our results may be useful in future design of drugs that can recognize and act on a certain gene sequence specifically.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD