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Summary

The research conducted in my laboratory combines both biophysical and bioorganic chemistry to investigate the following four interrelated programs of research.

DNA Stability and Flexibilty: A Thermodynamic Study (NIH GM)

Thermodynamic characterization of the molecular forces that dictate and control the sequence-dependent structure and conformational transitions of nucleic acid molecules. Characterization of the influence of structural modifications (e.g. Wobble base pairs, bulge loops, mismatches etc.), salt, and drug binding on the helix-to-coil and helix-to-helix transitions of DNA molecules. Use of these data to construct comprehensive phase diagrams for DNA polymorphism so that under a given set of solution conditions and ligand binding DNA secondary structures can be predicted from primary sequence data. Thermodynamic characterization of higher-order DNA structures such as triplexes and tetraplexes. Evaluating the relative binding affinity and specificity of third strand oligomers to target DNA duplex domains, as a function of base sequence and solution conditions. Use of such information to rationally design sequences and to tune solution conditions to modulate biochemical events and to develop diagnostic protocols.

Drug-DNA Interactions: The Thermodynamics of Molecular Recognition (NIH GM)

Elucidation of the molecular recognition patterns and characterization of the driving forces that give rise to the binding affinities and sequence/conformational preferences exhibited by DNA binding ligands. Defining the relative contributions of van der Waals contacts, hydrogen bonding, electrostatics, etc. to the binding affinities and specificities of DNA-directed ligands. Correlating specific drug structural features with their DNA binding affinities and specificities. Synergism in DNA drug binding studies. Using the information gained from these studies, drug analogues can be designed rationally which should exhibit altered binding properties and perhaps desired biological functions.

The Chemistry and Biology of Mutagenic DNA Lesions and Repair Intermediates: The Relationship of DNA Structure and Binding Properties to Biological Function (NIH CA)

Characterizations of the impacts of mutagenic lesions and repair intermediates on the structure, stability, and conformation of DNA duplexes. The goal of these studies is to evaluate if the lesion-induced alterations in duplex properties are consistent with or can be used to define biological mechanisms of repair and/or of mutagenesis. A logical extension of these studies, which we currently are pursuing, involves the design and testing of drugs that selectively target DNA sites which contain mutagenic lesions.

Development of Topoisomerase I-Directed Anticancer Drugs (Cancer Institute of New Jersey)

The ultimate goal of this program is to develop a series of bis- (BBD) and trisbenzimidazole (TBD) derivatives that can serve as effective anticancer, chemotherapeutic agents via their action as topoisomerase I poisons. To this end, we are characterizing the properties of these drugs when free in solution and upon binding to duplex DNA, and attempting to discern empirical correlations between specific physiochemical observables [e.g. binding mode(s), binding energetics, binding site size, etc.] and the expression of cell transport, cytotoxicity, and anti-topoisomerase activities. Such empirical correlations will serve to direct the design and synthesis of new compounds with predictably altered properties.

J. Völker, S.E. Osborne, G.D. Glick, and K.J. Breslauer. Thermodynamic properties of a conformationally constrained intramolecular DNA triple helix, Biochemistry 36, 756-767 (1997).

Y. Liu, K.J. Breslauer, and S. Anderson. Designing out disulfide bonds: thermodynamic properties of 30-51 cystine substitution mutants of bovine pancreatic trypsin inhibitor, Biochemistry 36, 5323-5335 (1997).

Z. Xu, D.S. Pilch, A.R. Srinivasan, W.K. Olson, N. Geacintov, and K.J. Breslauer. Modulation of nucleic acid structure by ligand binding: Induction of a DNA-RNA-DNA hybrid triplex by DAPI intercalation, Bioorganic & Medicinal Chemistry 5, 1137-1147 (1997).

D.S. Pilch, C. Yu, D. Makhey, E.J. LaVoie, A.R. Srinivasan, W.K. Olson, R.R. Sauers, K.J. Breslauer, N.E. Geacintov, and L.F. Liu. Minor groove-directed and intercalative ligand-DNA interactions in the poisoning of human DNA topoisomerase I by protoberberine analogs, Biochemistry 36, 12542-12553 (1997).

T.V. Chalikian, J. Völker, D. Anafi, and K.J. Breslauer. The native and the heat-induced denatured states of α-chymotrypsinogen A: A thermodynamic and spectroscopic study, J. Molec. Biol. 274, 237-252 (1997).

D.S. Pilch, Z. Xu, Q. Sun, E.J. LaVoie, L.F. Liu, and K.J. Breslauer. A terbenzmidazole that perferentially binds and conformationally alters structurally distinct DNA duplex domains: A potential mechanism for topoiosmerase I poisoning, Proc. Natl. Acad. Sci. USA 94, 13565-13570 (1997).

Z. Xu, T-K Li, J.S. Kim, E.J. LaVoie, K.J. Breslauer, L.F. Liu, and D.S. Pilch. DNA minor groove binding-directed poisoning of human DNA topoisomerase I by terbenzimidazoles, Biochemistry 37, 3558-3566 (1998).

C.A. Gelfand, G.E. Plum, A.P. Grollman, F. Johnson, and K.J. Breslauer. Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence, Biochemistry 37, 7321-7327 (1998).

C.A. Gelfand, G.E. Plum, A.P. Grollman, F. Johnson, and K.J. Breslauer. The impact of an exocyclic cytosine adduct on DNA duplex properties: Significant thermodynamic consequences despite modest lesion-induced structural alterations, Biochemistry 37, 12507-12512 (1998).

T.V. Chalikian and K.J. Breslauer. Thermodynamic analysis of biomolecules: a volumetric approach, Curr. Opin. Struct. Biol. 8, 657-664 (1998).

T.V. Chalikian, V.S. Gindikin, and K.J. Breslauer. Hydration of diglycyl tripeptides with nonpolar side chains: a volumetric study, Biophys. Chem. 75, 57-71 (1998).

G.E. Plum, K.J. Breslauer, and R.W. Roberts. Thermodynamics and kinetics of nucleic acid association/dissociation and folding processes, in Comprehensive Natural Products Chemistry. Elsevier Science Ltd., Oxford, UK. Vol. 7, ch. 2, pp 15-33 (1999).

C. Yu, S. Mielewczyk, K.J. Breslauer, and J. Kohn. Tyrosine-PEG-Derived Poly(ether carbonate)s as new biomaterials. Part II. Study of inverse temperature transitions, Biomaterials 20, 265-272 (1999).

D.S. Pilch, N. Poklar, E.E. Baird, P.B. Dervan, and K.J. Breslauer. The thermodynamics of polyamide-DNA recognition: hairpin polyamide binding in the minor groove of duplex DNA, Biochemistry 38, 2143-2151 (1999).

G.E. Plum and K.J. Breslauer. Thermodynamic state diagrams of oligonucleotide triple helices, in Triple Helix Forming Oligonucleotides. Kluwer Academic Pubs., MA. pp. 33-47 (1999).

J. Völker, R.D. Blake, S.G. Delcourt, and K.J. Breslauer. High resolution calorimetric and optical melting profiles of DNA plasmids: resolving contributions from intrinsic melting domains and specifically designed inserts, Biopolymers 50, 303-318 (1999).

C.A. Gelfand, G.E. Plum, S. Mielewczyk, D.P. Remeta, K.J. Breslauer. A quantitative method for evaluating the stabilities of nucleic acid complexes, Proc. Natl. Acad. Sci. 96 6113-6118 (1999).

T.V. Chalikian, J. Völker, G.E. Plum, and K.J. Breslauer. A unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric techniques, Proc. Natl. Acad. Sci. 96, 7853-7858 (1999).

G.E. Plum and K.J. Breslauer. Hybridization, Nucleic Acids, in Encyclopedia of Molecular Biology. John Wiley & Sons, NY, NY. Vol. 1-4 (1999).

T.V. Chalikian, J. Volker, A.R. Srinivasan, W.K. Olson, and K.J. Breslauer. The hydration of nucleic acid duplexes as assessed by a combination of volumetric and structural techniques, Biopolymers 50, 459-471 (1999).

G.E. Plum, C.A. Gelfand, and K.J. Breslauer. Effects of 3,N⁴-ethenodeoxycytidine on duplex stability and energetics, in DNA Cyclic Adducts. (B. Singer & H. Bartsch, eds.) IARC Scientific Pubs #150. Chapter IV, pp. 169-177 (1999).

D.S. Pilch, S.U. Dunham, E.R. Jamieson, S.J. Lippard, and K.J. Breslauer. DNA sequence context modulates the impact of a cisplatin 1,2-d(GpG) intrastrand cross-link on the conformational and thermodynamic properties of duplex DNA, J. Mol. Biol. 296, 803-812 (2000).

T.V. Chalikian and K.J. Breslauer. Volumetric properties of nucleic acids, Biopolymers: Nucl. Acid Sciences 48, 264-280 (2000).

J. Völker, H. Klump, and K.J. Breslauer. Communication between non-contacting macromolecules, Proc. Natl. Acad. Sci. USA 98, 7694-7699 (2001).

J. Völker, H. Klump, G.S Manning and K.J. Breslauer. Counterion association with native and denatured DNA: an experimental approach, J. Mol. Biol. 310, 1011-1025 (2001).

G. Kaletunç and K.J. Breslauer. Calorimetry of pre- and postextruded cereal flours, in Characterization of Cereals and Flours: Properties, Analysis, and Applications. G. Kaletunç and K.J. Breslauer, Eds. Marcel Dekker, Inc., NY, NY pp. 1-35 (2003).

G.E. Plum and K.J. Breslauer. Fluorescence energy transfer monitored competitive equilibria of nucleic acids: Applications in thermodynamics and screening, Biopolymers: Nucleic Acid Sciences 61, 214-223 (2002).

J. Völker, N. Makube, G.E. Plum, H.H. Klump, and K.J. Breslauer. Conformational Energetics of Stable and Metastable States Formed by DNA Triplet Repeat Oligonucleotides: Implications for Triplet Expansion Diseases, Proc. Natl. Acad. Sci. USA 99, 14700-14705 (2002).

C.A.S.A Minetti, D.P. Remeta, D. Zharkov, G.E. Plum, F. Johnson, A.P. Grollman, and K.J. Breslauer. Energetics of lesion recognition by a DNA repair protein: thermodynamic characterization of formamidopyrimidine-glycosylase (Fpg) interactions with damaged DNA duplexes, J. Molec. Biol. 328, 1047-1060 (2003).

C.A.S.A. Minetti, D.P. Remeta, H. Miller, C. Gelfand, G.E. Plum, A.P. Grollman, and K.J. Breslauer. The thermodynamics of template-directed DNA synthesis: base insertion and extension enthalpies, Proc. Natl. Acad. Sci. USA 100, 14719-14724 (2003).

W.H. Braunlin, I. Giri, L. Beadling, and K.J. Breslauer. Conformational screening of oligonucleotides by variable-temperature HPLC: Dissecting the duplex-hairpin-coil equilibria of d(CGCGAATTCGCG), Biopolymers 74, 221-231 (2004).

J. Völker and K.J. Breslauer. Communication between noncontacting macromolecules, Annu. Rev. Biophys. Biomol. Struct. 34, 21-42 (2005).

G.E. Plum, J. Völker and K.J. Breslauer. Thermodynamic properties of DNA. In.Encyclopedia Reference of Genomics & Proteomics in Molecular Medicine. D. Ganten & K. Ruckpaul, (Eds.) Springer-Verlag, Berlin, Germany, Vol. 1, pp. 1851-1855 (2006).

P.L. Privalov, A.I. Dragan, C. Crane-Robinson, K.J. Breslauer, D.P. Remeta, and C.A.S.A. Minetti, What drives proteins into the major or minor grooves of DNA? J. Mol. Biol.. 365, 1-9 (2007).

J. Völker, H.H. Klump, and K.J. Breslauer. The Energetics of i-DNA Tetraplex Structures formed Intermolecularly by d(TC5) and Intramolecularly by d[(C5T3)3C5], .Biopolymers 86, 136-147 (2007).

K.J. Breslauer. Julian Sturtevant: Scientific giant, warm humanist, social activist, nature lover, gentle teacher, kind friend” Biophys. Chem. 126, 9-10 (2007).

J. Völker, H.H. Klump, and K.J. Breslauer. DNA Metastability and Biological Regulation: Conformational Dynamics of Meta-stable Omega-DNA Bulge Loops, J. Am. Chem. Soc. 129, 5272-5280 (2007).

B. Lee, M. Barch, E. Castner, J. Völker, K. Breslauer. Structure and Dynamics in DNA looped Domains: CAG Triplet Repeat Sequence Dynamics Probed by 2-Aminopurine Fluorescence, .Biochemistry, in press. (2007).