Chemotherapy is an important tool in the clinical management of cancer. The long-term objective of the research proposed here is to elucidate the structure and dynamics of anticancer drug-DNA complexes in order to enhance our understanding of their mechanism of action and our ability to design new, more effective drugs. In order to achieve this objective, we propose to apply a variety of spectroscopic techniques to the analysis of drug-DNA interactions. The principal tool proposed for structural investigation is high resolution proton NMR in one and two dimensions. We plan to study the oligonucleotide complexes of several different antitumor antibiotics, including chromomycin and its analogs mithramycin and olivomycin, along with actinomycin and nogalomycin. We will be investigating the structure and sequence specificity of these drug-DNA complexes using one dimensional experiments and two dimensional COSY, HOHAHA and NOESY experiments. Results will be analyzed by a combination of computer graphics, complete relaxation matrix analysis, energy minimization, and distance geometry. In addition to standard DNA duplexes, we will examine the effects of DNA modification, such as methylation, on the structure of these complexes. Finally, the proposed structural studies based on NMR methods will be complemented by equilibrium and kinetic binding studies to provide a thermodynamic framework for their interpretation.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM051650-15
Application #
2190325
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Project Start
1980-07-01
Project End
1996-12-31
Budget Start
1995-01-01
Budget End
1995-12-31
Support Year
15
Fiscal Year
1995
Total Cost
Indirect Cost
Name
University of California San Francisco
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
073133571
City
San Francisco
State
CA
Country
United States
Zip Code
94143
Keniry, M A; Owen, E A; Shafer, R H (2000) The three-dimensional structure of the 4:1 mithramycin:d(ACCCGGGT)(2) complex: evidence for an interaction between the E saccharides. Biopolymers 54:104-14
Keniry, M A (2000) Quadruplex structures in nucleic acids. Biopolymers 56:123-46
Strahan, G D; Keniry, M A; Shafer, R H (1998) NMR structure refinement and dynamics of the K+-[d(G3T4G3)]2 quadruplex via particle mesh Ewald molecular dynamics simulations. Biophys J 75:968-81
Shafer, R H (1998) Stability and structure of model DNA triplexes and quadruplexes and their interactions with small ligands. Prog Nucleic Acid Res Mol Biol 59:55-94
He, Y; Scaria, P V; Shafer, R H (1997) Studies on formation and stability of the d[G(AG)5]* d[G(AG)5]. d[C(TC)5] and d[G(TG)5]* d[G(AG)5]. d[C(TC)5] triple helices. Biopolymers 41:431-41
Keniry, M A; Owen, E A; Shafer, R H (1997) The contribution of thymine-thymine interactions to the stability of folded dimeric quadruplexes. Nucleic Acids Res 25:4389-92
Chen, Q; Shafer, R H; Kuntz, I D (1997) Structure-based discovery of ligands targeted to the RNA double helix. Biochemistry 36:11402-7
Chen, Q; Kuntz, I D; Shafer, R H (1996) Spectroscopic recognition of guanine dimeric hairpin quadruplexes by a carbocyanine dye. Proc Natl Acad Sci U S A 93:2635-9
Nikolaev, V A; Grokhovsky, S L; Surovaya, A N et al. (1996) Design of sequence-specific DNA binding ligands that use a two-stranded peptide motif for DNA sequence recognition. J Biomol Struct Dyn 14:31-47
Keniry, M A; Strahan, G D; Owen, E A et al. (1995) Solution structure of the Na+ form of the dimeric guanine quadruplex [d(G3T4G3)]2. Eur J Biochem 233:631-43

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