Faculty Research

Breslauer, Kenneth J.

breslauer02t2Linus C. Pauling Distinguished University Professor

Research Synopsis: Enabled by an outstanding group of colleagues, Breslauer’s Lab pursues several interrelated biophysical research programs. Collectively, these programs focus on characterizing the intra- and intermolecular forces that modulate the regulation and dysregulation of biological processes crucial to human health. Deciphering this language used in molecular communications is essential for the rational deign of diagnostic and therapeutic protocols.

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Research 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.

Publications

2021 | Kenneth J. Breslauer The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication. J. Biol. Chem. 296 2021 100522

2020 | Klump HH, Völker J, Breslauer KJ. Energy mapping of the genetic code and genomic domains: implications for code evolution and molecular Darwinism. Quarterly Reviews of Biophysics. 53: e11. PMID 33143792 DOI: 10.1017/S0033583520000098

2020 | Völker J, Plum GE, Breslauer KJ. Heat Capacity Changes (ΔCp) for Interconversions Between Differentially-Ordered DNA States within Physiological Temperature Domains: Implications for Biological Regulatory Switches. The Journal of Physical Chemistry. B. PMID 32531155 DOI: 10.1021/acs.jpcb.0c04065

2019 | Völker J, Plum GE, Gindikin V, Breslauer KJ. Dynamic DNA Energy Landscapes and Substrate Complexity in Triplet Repeat Expansion and DNA Repair. Biomolecules. 9. PMID 31698848 DOI: 10.3390/biom9110709

2018 | Minetti CA, Sun JY, Jacobs DP, Kang I, Remeta DP, Breslauer KJ. Impact of bistrand abasic sites and proximate orientation on DNA global structure and duplex energetics. Biopolymers. PMID 29322505 DOI: 10.1002/bip.23098

2015 | Minetti CA, Remeta DP, Iden CR, Johnson F, Grollman AP, Breslauer KJ. Impact of thymine glycol damage on DNA duplex energetics: Correlations with lesion-induced biochemical and structural consequences. Biopolymers. 103: 491-508. PMID 25991500 DOI: 10.1002/bip.22680

2015 | Charnavets T, Nunvar J, Ne?asová I, Völker J, Breslauer KJ, Schneider B. Conformational diversity of single-stranded DNA from bacterial repetitive extragenic palindromes: Implications for the DNA recognition elements of transposases. Biopolymers. PMID 25951997 DOI: 10.1002/bip.22666

2014 | Li M, Völker J, Breslauer KJ, Wilson DM. APE1 incision activity at abasic sites in tandem repeat sequences. Journal of Molecular Biology. 426: 2183-98. PMID 24703901 DOI: 10.1016/j.jmb.2014.03.014

2014 | Völker J, Plum GE, Gindikin V, Klump HH, Breslauer KJ. Impact of bulge loop size on DNA triplet repeat domains: Implications for DNA repair and expansion. Biopolymers. 101: 1-12. PMID 23494673 DOI: 10.1002/bip.22236

2013 | Breslauer KJ, Case DA, Walter NG, Woodson SA. Biopolymers celebrates 50 years of nucleic acids research. Biopolymers. 99: 909. PMID 23893377 DOI: 10.1002/bip.22358

2013 | Braunlin W, Völker J, Plum GE, Breslauer KJ. DNA meter: Energy tunable, quantitative hybridization assay. Biopolymers. 99: 408-17. PMID 23529692 DOI: 10.1002/bip.22213

2012 | Völker J, Gindikin V, Klump HH, Plum GE, Breslauer KJ. Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states. Journal of the American Chemical Society. 134: 6033-44. PMID 22397401 DOI: 10.1021/ja3010896

2011 | Lukin M, Minetti CA, Remeta DP, Attaluri S, Johnson F, Breslauer KJ, de Los Santos C. Novel post-synthetic generation, isomeric resolution, and characterization of Fapy-dG within oligodeoxynucleotides: differential anomeric impacts on DNA duplex properties. Nucleic Acids Research. 39: 5776-89. PMID 21415012 DOI: 10.1093/nar/gkr082

2010 | Völker J, Plum GE, Klump HH, Breslauer KJ. Energy crosstalk between DNA lesions: implications for allosteric coupling of DNA repair and triplet repeat expansion pathways. Journal of the American Chemical Society. 132: 4095-7. PMID 20218680 DOI: 10.1021/ja1002857

2010 | Minetti CA, Remeta DP, Dickstein R, Breslauer KJ. Energetic signatures of single base bulges: thermodynamic consequences and biological implications. Nucleic Acids Research. 38: 97-116. PMID 19946018 DOI: 10.1093/nar/gkp1036

2010 | Minetti CA, Remeta DP, Johnson F, Iden CR, Breslauer KJ. Impact of alpha-hydroxy-propanodeoxyguanine adducts on DNA duplex energetics: opposite base modulation and implications for mutagenicity and genotoxicity. Biopolymers. 93: 370-82. PMID 19937758 DOI: 10.1002/bip.21355

2010 | Völker J, Plum GE, Klump HH, Breslauer KJ. Energetic coupling between clustered lesions modulated by intervening triplet repeat bulge loops: allosteric implications for DNA repair and triplet repeat expansion. Biopolymers. 93: 355-69. PMID 19890964 DOI: 10.1002/bip.21343

2009 | Völker J, Plum GE, Klump HH, Breslauer KJ. DNA repair and DNA triplet repeat expansion: the impact of abasic lesions on triplet repeat DNA energetics. Journal of the American Chemical Society. 131: 9354-60. PMID 19566100 DOI: 10.1021/ja902161e

2009 | Johnson MD, Völker J, Moeller HV, Laws E, Breslauer KJ, Falkowski PG. Universal constant for heat production in protists. Proceedings of the National Academy of Sciences of the United States of America. 106: 6696-9. PMID 19346469 DOI: 10.1073/pnas.0902005106

2008 | Völker J, Klump HH, Breslauer KJ. DNA energy landscapes via calorimetric detection of microstate ensembles of metastable macrostates and triplet repeat diseases. Proceedings of the National Academy of Sciences of the United States of America. 105: 18326-30. PMID 19015511 DOI: 10.1073/pnas.0810376105

2008 | Minetti CA, Remeta DP, Breslauer KJ. A continuous hyperchromicity assay to characterize the kinetics and thermodynamics of DNA lesion recognition and base excision. Proceedings of the National Academy of Sciences of the United States of America. 105: 70-5. PMID 18172202 DOI: 10.1073/pnas.0710363105

2007 | Lee BJ, Barch M, Castner EW, Völker J, Breslauer KJ. Structure and dynamics in DNA looped domains: CAG triplet repeat sequence dynamics probed by 2-aminopurine fluorescence. Biochemistry. 46: 10756-66. PMID 17718541 DOI: 10.1021/bi7005674

2007 | Völker J, Klump HH, Breslauer KJ. DNA metastability and biological regulation: conformational dynamics of metastable omega-DNA bulge loops. Journal of the American Chemical Society. 129: 5272-80. PMID 17397164 DOI: 10.1021/ja070258q

2007 | Plum GE, Breslauer DN, Breslauer KJ. High resolution protein-DNA binding energy landscapes via a novel high throughput method. Biopolymers. 85: vii-viii. PMID 17366530 DOI: 10.1002/bip.20723

2007 | Völker J, Klump HH, Breslauer KJ. The energetics of i-DNA tetraplex structures formed intermolecularly by d(TC5) and intramolecularly by d[(C5T3)3C5]. Biopolymers. 86: 136-47. PMID 17330895 DOI: 10.1002/bip.20712

2007 | Breslauer KJ. Julian Sturtevant: scientific giant, warm humanist, social activist, nature lover, gentle teacher, kind friend. Biophysical Chemistry. 126: 9-10. PMID 17330332 DOI: 10.1016/j.bpc.2006.03.016

2007 | Privalov PL, Dragan AI, Crane-Robinson C, Breslauer KJ, Remeta DP, Minetti CA. What drives proteins into the major or minor grooves of DNA? Journal of Molecular Biology. 365: 1-9. PMID 17055530 DOI: 10.1016/j.jmb.2006.09.059

2005 | Völker J, Breslauer KJ. Communication between noncontacting macromolecules. Annual Review of Biophysics and Biomolecular Structure. 34: 21-42. PMID 15869382 DOI: 10.1146/annurev.biophys.33.110502.133332

2004 | Braunlin WH, Giri I, Beadling L, Breslauer KJ. Conformational screening of oligonucleotides by variable-temperature high performance liquid chromatography: dissecting the duplex-hairpin-coil equilibria of d(CGCGAATTCGCG). Biopolymers. 74: 221-31. PMID 15150797 DOI: 10.1002/bip.20079

2003 | Minetti CA, Remeta DP, Miller H, Gelfand CA, Plum GE, Grollman AP, Breslauer KJ. The thermodynamics of template-directed DNA synthesis: base insertion and extension enthalpies. Proceedings of the National Academy of Sciences of the United States of America. 100: 14719-24. PMID 14623953 DOI: 10.1073/pnas.2336142100

2003 | Minetti CA, Remeta DP, Zharkov DO, Plum GE, Johnson F, Grollman AP, Breslauer KJ. Energetics of lesion recognition by a DNA repair protein: thermodynamic characterization of formamidopyrimidine-glycosylase (Fpg) interactions with damaged DNA duplexes. Journal of Molecular Biology. 328: 1047-60. PMID 12729740 DOI: 10.1016/S0022-2836(03)00365-6

2002 | Völker J, Makube N, Plum GE, Klump HH, Breslauer KJ. Conformational energetics of stable and metastable states formed by DNA triplet repeat oligonucleotides: implications for triplet expansion diseases. Proceedings of the National Academy of Sciences of the United States of America. 99: 14700-5. PMID 12417759 DOI: 10.1073/pnas.222519799

2001 | Plum GE, Breslauer KJ. Fluorescence energy transfer monitored competitive equilibria of nucleic acids: applications in thermodynamics and screening. Biopolymers. 61: 214-23. PMID 11987182 DOI: 10.1002/bip.10147

2001 | Völker J, Klump HH, Manning GS, Breslauer KJ. Counterion association with native and denatured nucleic acids: an experimental approach. Journal of Molecular Biology. 310: 1011-25. PMID 11501992 DOI: 10.1006/jmbi.2001.4841

2001 | Völker J, Klump HH, Breslauer KJ. Communication between noncontacting macromolecules. Proceedings of the National Academy of Sciences of the United States of America. 98: 7694-9. PMID 11438725 DOI: 10.1073/pnas.141221298

2000 | Pilch DS, Dunham SU, Jamieson ER, Lippard SJ, Breslauer KJ. 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. Journal of Molecular Biology. 296: 803-12. PMID 10677282 DOI: 10.1006/jmbi.2000.3496

1999 | Plum GE, Gelfand CA, Breslauer KJ. Effects of 3,N4-ethenodeoxycytidine on duplex stability and energetics. Iarc Scientific Publications. 169-77. PMID 10626218

1999 | Chalikian TV, Völker J, Srinivasan AR, Olson WK, Breslauer KJ. The hydration of nucleic acid duplexes as assessed by a combination of volumetric and structural techniques. Biopolymers. 50: 459-71. PMID 10479730 DOI: 10.1002/(SICI)1097-0282(19991015)50:5<459::AID-BIP1>3.0.CO;2-B

1999 | Völker J, Blake RD, Delcourt SG, Breslauer KJ. High-resolution calorimetric and optical melting profiles of DNA plasmids: resolving contributions from intrinsic melting domains and specifically designed inserts. Biopolymers. 50: 303-18. PMID 10397791 DOI: 10.1002/(SICI)1097-0282(199909)50:3<303::AID-BIP6>3.0.CO;2-U

1999 | Chalikian TV, Völker J, Plum GE, Breslauer KJ. A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric techniques. Proceedings of the National Academy of Sciences of the United States of America. 96: 7853-8. PMID 10393911 DOI: 10.1073/pnas.96.14.7853

1999 | Gelfand CA, Plum GE, Mielewczyk S, Remeta DP, Breslauer KJ. A quantitative method for evaluating the stabilities of nucleic acids. Proceedings of the National Academy of Sciences of the United States of America. 96: 6113-8. PMID 10339550 DOI: 10.1073/pnas.96.11.6113

1999 | Yu C, Mielewczyk SS, Breslauer KJ, Kohn J. Tyrosine-PEG-derived poly(ether carbonate)s as new biomaterials. Part II: study of inverse temperature transitions. Biomaterials. 20: 265-72. PMID 10030603 DOI: 10.1016/S0142-9612(98)00170-7

1999 | Pilch DS, Poklar N, Baird EE, Dervan PB, Breslauer KJ. The thermodynamics of polyamide-DNA recognition: hairpin polyamide binding in the minor groove of duplex DNA. Biochemistry. 38: 2143-51. PMID 10026298 DOI: 10.1021/bi982628g

1998 | Chalikian TV, Gindikin VS, Breslauer KJ. Hydration of diglycyl tripeptides with non-polar side chains: a volumetric study. Biophysical Chemistry. 75: 57-71. PMID 17027457 DOI: 10.1016/S0301-4622(98)00192-6

1998 I Chalikian TV, Breslauer KJ. Volumetric properties of nucleic acids. Biopolymers. 48: 264-80. PMID 10699844 DOI: 10.1002/(SICI)1097-0282(1998)48:4<264::AID-BIP6>3.0.CO;2-8

1998 | Chalikian TV, Breslauer KJ. Thermodynamic analysis of biomolecules: a volumetric approach. Current Opinion in Structural Biology. 8: 657-64. PMID 9818272 DOI: 10.1016/S0959-440X(98)80159-0

1998 | Gelfand CA, Plum GE, Grollman AP, Johnson F, Breslauer KJ. The impact of an exocyclic cytosine adduct on DNA duplex properties: significant thermodynamic consequences despite modest lesion-induced structural alterations. Biochemistry. 37: 12507-12. PMID 9730823 DOI: 10.1021/bi981090b

1998 | Gelfand CA, Plum GE, Grollman AP, Johnson F, Breslauer KJ. Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence. Biochemistry. 37: 7321-7. PMID 9585546 DOI: 10.1021/bi9803372

1998 I Xu Z, Li TK, Kim JS, LaVoie EJ, Breslauer KJ, Liu LF, Pilch DS. DNA minor groove binding-directed poisoning of human DNA topoisomerase I by terbenzimidazoles. Biochemistry. 37: 3558-66. PMID 9521677 DOI: 10.1021/bi9727747

1997 | Chalikian TV, Völker J, Anafi D, Breslauer KJ. The native and the heat-induced denatured states of alpha-chymotrypsinogen A: thermodynamic and spectroscopic studies. Journal of Molecular Biology. 274: 237-52. PMID 9398530 DOI: 10.1006/jmbi.1997.1394

1997 | Pilch DS, Xu Z, Sun Q, LaVoie EJ, Liu LF, Breslauer KJ. A terbenzimidazole that preferentially binds and conformationally alters structurally distinct DNA duplex domains: a potential mechanism for topoisomerase I poisoning. Proceedings of the National Academy of Sciences of the United States of America. 94: 13565-70. PMID 9391066 DOI: 10.1073/pnas.94.25.13565

1997 | Pilch DS, Yu C, Makhey D, LaVoie EJ, Srinivasan AR, Olson WK, Sauers RR, Breslauer KJ, Geacintov NE, Liu LF. Minor groove-directed and intercalative ligand-DNA interactions in the poisoning of human DNA topoisomerase I by protoberberine analogs. Biochemistry. 36: 12542-53. PMID 9376359 DOI: 10.1021/bi971272q

1997 | Xu Z, Pilch DS, Srinivasan AR, Olson WK, Geacintov NE, Breslauer KJ. Modulation of nucleic acid structure by ligand binding: induction of a DNA.RNA.DNA hybrid triplex by DAPI intercalation. Bioorganic & Medicinal Chemistry. 5: 1137-47. PMID 9222508 DOI: 10.1016/S0968-0896(97)00050-3

1997 | Liu Y, Breslauer K, Anderson S. 'Designing out' disulfide bonds: Thermodynamic properties of 30-51 cystine substitution mutants of bovine pancreatic trypsin inhibitor. Biochemistry. 36: 5323-5335. PMID 9154914 DOI: 10.1021/bi962423c

1997 | Völker J, Osborne SE, Glick GD, Breslauer KJ. Thermodynamic properties of a conformationally constrained intramolecular DNA triple helix. Biochemistry. 36: 756-67. PMID 9020773 DOI: 10.1021/bi962271l

1996 | Tung CH, Breslauer KJ, Stein S. Stabilization of DNA triple-helix formation by appended cationic peptides. Bioconjugate Chemistry. 7: 529-31. PMID 8889011 DOI: 10.1021/bc960040l

1996 | Chalikian TV, Breslauer KJ. On volume changes accompanying conformational transitions of biopolymers. Biopolymers. 39: 619-626. PMID 8875817 DOI: 10.1002/(SICI)1097-0282(199611)39:5<619::AID-BIP1>3.0.CO;2-Z

1996 | Pilch DS, Xu Z, Sun Q, Lavoie EJ, Liu LF, Geacintov NE, Breslauer KJ. Characterizing the DNA binding modes of a topoisomerase I-poisoning terbenzimidazole: evidence for both intercalative and minor groove binding properties. Drug Design and Discovery. 13: 115-33. PMID 8874049

1996 | Gelfand CA, Plum GE, Grollman AP, Johnson F, Breslauer KJ. The impact of a bistrand abasic lesion on DNA duplex properties. Biopolymers. 38: 439-45. PMID 8867207 DOI: 10.1002/(SICI)1097-0282(199604)38:4<439::AID-BIP1>3.0.CO;2-U

1996 | Law SM, Eritja R, Goodman MF, Breslauer KJ. Spectroscopic and calorimetric characterizations of DNA duplexes containing 2-aminopurine. Biochemistry. 35: 12329-37. PMID 8823167 DOI: 10.1021/bi9614545

1996 | Mielewczyk SS, Breslauer KJ, Anachi RB, Brodsky B. Binding studies of a triple-helical peptide model of macrophage scavenger receptor to tetraplex nucleic acids. Biochemistry. 35: 11396-402. PMID 8784195 DOI: 10.1021/bi960706z

1996 | Chalikian TV, Totrov M, Abagyan R, Breslauer KJ. The hydration of globular proteins as derived from volume and compressibility measurements: cross correlating thermodynamic and structural data. Journal of Molecular Biology. 260: 588-603. PMID 8759322 DOI: 10.1006/jmbi.1996.0423

1996 | Poklar N, Pilch DS, Lippard SJ, Redding EA, Dunham SU, Breslauer KJ. Influence of cisplatin intrastrand crosslinking on the conformation, thermal stability, and energetics of a 20-mer DNA duplex. Proceedings of the National Academy of Sciences of the United States of America. 93: 7606-11. PMID 8755522 DOI: 10.1073/pnas.93.15.7606

1996 | Pilch DS, Poklar N, Gelfand CA, Law SM, Breslauer KJ, Baird EE, Dervan PB. Binding of a hairpin polyamide in the minor groove of DNA: sequence-specific enthalpic discrimination. Proceedings of the National Academy of Sciences of the United States of America. 93: 8306-11. PMID 8710866 DOI: 10.1073/pnas.93.16.8306

1996 | Wei Z, Tung CH, Zhu T, Dickerhof WA, Breslauer KJ, Georgopoulos DE, Leibowitz MJ, Stein S. Hybridization properties of oligodeoxynucleotide pairs bridged by polyarginine peptides. Nucleic Acids Research. 24: 655-61. PMID 8604306 DOI: 10.1093/nar/24.4.655

1996 | Chalikian TV, Breslauer KJ. Compressibility as a means to detect and characterize globular protein states. Proceedings of the National Academy of Sciences of the United States of America. 93: 1012-4. PMID 8577705 DOI: 10.1073/pnas.93.3.1012

1996 | Chalikian TV, Gindikin VS, Breslauer KJ. Spectroscopic and volumetric investigation of cytochrome c unfolding at alkaline pH: characterization of the base-induced unfolded state at 25 degrees C. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 10: 164-70. PMID 8566538

1996 | Osborne SE, Völker J, Stevens SY, Breslauer KJ, Glick GD. Design, synthesis, and analysis of disulfide cross-linked DNA duplexes. Journal of the American Chemical Society. 118: 11993-12003. DOI: 10.1021/ja962386c

1996 | Kaletunç G, Breslauer KJ. Construction of a wheat-flour state diagram: Application to extrusion processing. Journal of Thermal Analysis. 47: 1267-1288.

1995 | Plum GE, Breslauer KJ. Calorimetry of proteins and nucleic acids. Current Opinion in Structural Biology. 5: 682-90. PMID 8574705 DOI: 10.1016/0959-440X(95)80062-X

1995 | Breslauer KJ. Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions. Methods in Enzymology. 259: 221-42. PMID 8538456 DOI: 10.1016/0076-6879(95)59046-3

1995 | Plum GE, Grollman AP, Johnson F, Breslauer KJ. Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex. Biochemistry. 34: 16148-60. PMID 8519772

1995 | Pilch DS, Kirolos MA, Breslauer KJ. Berenil binding to higher ordered nucleic acid structures: complexation with a DNA and RNA triple helix. Biochemistry. 34: 16107-24. PMID 8519768

1995 | Plum GE, Breslauer KJ. Thermodynamics of an intramolecular DNA triple helix: a calorimetric and spectroscopic study of the pH and salt dependence of thermally induced structural transitions. Journal of Molecular Biology. 248: 679-95. PMID 7752233 DOI: 10.1006/jmbi.1995.0251

1995 | Plum GE, Pilch DS, Singleton SF, Breslauer KJ. Nucleic acid hybridization: triplex stability and energetics. Annual Review of Biophysics and Biomolecular Structure. 24: 319-50. PMID 7663120 DOI: 10.1146/annurev.bb.24.060195.001535

1995 | Pilch DS, Kirolos MA, Liu X, Plum GE, Breslauer KJ. Berenil [1,3-bis(4'-amidinophenyl)triazene] binding to DNA duplexes and to a RNA duplex: evidence for both intercalative and minor groove binding properties. Biochemistry. 34: 9962-76. PMID 7632695

1995 | Chalikian TV, Gindikin VS, Breslauer KJ. Volumetric characterizations of the native, molten globule and unfolded states of cytochrome c at acidic pH. Journal of Molecular Biology. 250: 291-306. PMID 7608975 DOI: 10.1006/jmbi.1995.0377

1995 | Pilch DS, Plum GE, Breslauer KJ. The thermodynamics of DNA structures that contain lesions or guanine tetrads. Current Opinion in Structural Biology. 5: 334-42. PMID 7583632 DOI: 10.1016/0959-440X(95)80095-6

1995 | Barrett A, Kaletunç G, Rosenburg S, Breslauer KJ. Effect of sucrose on the structure, mechanical strength and thermal properties of corn extrudates. Carbohydrate Polymers. 26: 261-269. DOI: 10.1016/0144-8617(95)00024-2

1994 | Chalikian TV, Sarvazyan AP, Plum GE, Breslauer KJ. Influence of base composition, base sequence, and duplex structure on DNA hydration: apparent molar volumes and apparent molar adiabatic compressibilities of synthetic and natural DNA duplexes at 25 degrees C. Biochemistry. 33: 2394-401. PMID 8117699

1994 | Plum GE, Breslauer KJ. DNA lesions. A thermodynamic perspective. Annals of the New York Academy of Sciences. 726: 45-55; discussion 55. PMID 8092707

1994 | Chalikian TV, Plum GE, Sarvazyan AP, Breslauer KJ. Influence of drug binding on DNA hydration: acoustic and densimetric characterizations of netropsin binding to the poly(dAdT).poly(dAdT) and poly(dA).poly(dT) duplexes and the poly(dT).poly(dA).poly(dT) triplex at 25 degrees C. Biochemistry. 33: 8629-40. PMID 8038152 DOI: 10.1021/bi00195a003

1994 | Chalikian TV, Sarvazyan AP, Breslauer KJ. Hydration and partial compressibility of biological compounds. Biophysical Chemistry. 51: 89-107; discussion 1. PMID 7919045 DOI: 10.1016/0301-4622(94)85007-0

1994 | Pilch DS, Breslauer KJ. Ligand-induced formation of nucleic acid triple helices. Proceedings of the National Academy of Sciences of the United States of America. 91: 9332-6. PMID 7524074

1994 | Breslauer KJ. Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions. Methods in Molecular Biology (Clifton, N.J.). 26: 347-72. PMID 7508801

1994 | Chalikian TV, Sarvazyan AP, Funck T, Cain CA, Breslauer KJ. Partial molar characteristics of glycine and alanine in aqueous solutions at high pressures calculated from ultrasonic velocity data. Journal of Physical Chemistry. 98: 321-328.

1994 | Chalikian TV, Sarvazyan AP, Funck T, Breslauer KJ. Partial molar volumes, expansibilities, and compressibilities of oligoglycines in aqueous solutions at 18-55°C. Biopolymers. 34: 541-553.

1993 | Remeta DP, Mudd CP, Berger RL, Breslauer KJ. Thermodynamic characterization of daunomycin-DNA interactions: comparison of complete binding profiles for a series of DNA host duplexes. Biochemistry. 32: 5064-73. PMID 8494883

1993 | Erie DA, Breslauer KJ, Olson WK. A Monte Carlo method for generating structures of short single-stranded DNA sequences. Biopolymers. 33: 75-105. PMID 8427940 DOI: 10.1002/bip.360330109

1993 | Erie DA, Suri AK, Breslauer KJ, Jones RA, Olson WK. Theoretical predictions of DNA hairpin loop conformations: correlations with thermodynamic and spectroscopic data. Biochemistry. 32: 436-54. PMID 8422353

1993 | Zhu T, Wei Z, Tung CH, Dickerhof WA, Breslauer KJ, Georgopoulos DE, Leibowitz MJ, Stein S. Oligonucleotide-poly-L-ornithine conjugates: binding to complementary DNA and RNA. Antisense Research and Development. 3: 265-75. PMID 8286927

1993 | Tung CH, Breslauer KJ, Stein S. Polyamine-linked oligonucleotides for DNA triple helix formation. Nucleic Acids Research. 21: 5489-94. PMID 8265366

1993 | Jin R, Chapman WH, Srinivasan AR, Olson WK, Breslow R, Breslauer KJ. Comparative spectroscopic, calorimetric, and computational studies of nucleic acid complexes with 2',5"-versus 3',5"-phosphodiester linkages. Proceedings of the National Academy of Sciences of the United States of America. 90: 10568-72. PMID 8248146 DOI: 10.1073/pnas.90.22.10568

1993 | Zhu T, Tung CH, Breslauer KJ, Dickerhof WA, Stein S. Preparation and physical properties of conjugates of oligodeoxynucleotides with poly(delta)ornithine peptides. Antisense Research and Development. 3: 349-56. PMID 8155976

1993 | Chalikian TV, Sarvazyan AP, Breslauer KJ. Partial molar volumes, expansibilities, and compressibilities of α,ω-aminocarboxylic acids in aqueous solutions between 18 and 55°C. Journal of Physical Chemistry. 97: 13017-13026.

1992 | Jin R, Gaffney BL, Wang C, Jones RA, Breslauer KJ. Thermodynamics and structure of a DNA tetraplex: a spectroscopic and calorimetric study of the tetramolecular complexes of d(TG3T) and d(TG3T2G3T). Proceedings of the National Academy of Sciences of the United States of America. 89: 8832-6. PMID 1528900

1992 | Plum GE, Grollman AP, Johnson F, Breslauer KJ. Influence of an exocyclic guanine adduct on the thermal stability, conformation, and melting thermodynamics of a DNA duplex. Biochemistry. 31: 12096-102. PMID 1457406

1992 | Breslauer KJ, Freire E, Straume M. Calorimetry: a tool for DNA and ligand-DNA studies. Methods in Enzymology. 211: 533-67. PMID 1406326 DOI: 10.1016/0076-6879(92)11030-M

1992 | Park YW, Breslauer KJ. Drug binding to higher ordered DNA structures: netropsin complexation with a nucleic acid triple helix. Proceedings of the National Academy of Sciences of the United States of America. 89: 6653-7. PMID 1321445 DOI: 10.1073/pnas.89.14.6653

1991 | Vesnaver G, Breslauer KJ. The contribution of DNA single-stranded order to the thermodynamics of duplex formation. Proceedings of the National Academy of Sciences of the United States of America. 88: 3569-73. PMID 2023903

1991 | Park YW, Breslauer KJ. A spectroscopic and calorimetric study of the melting behaviors of a "bent" and a "normal" DNA duplex: [d(GA4T4C)]2 versus [d(GT4A4C)]2. Proceedings of the National Academy of Sciences of the United States of America. 88: 1551-5. PMID 1996356

1991 | Remeta DP, Mudd CP, Berger RL, Breslauer KJ. Thermodynamic characterization of daunomycin-DNA interactions: microcalorimetric measurements of daunomycin-DNA binding enthalpies. Biochemistry. 30: 9799-809. PMID 1911765

1991 | Wang Y, Jin R, Gaffney B, Jones RA, Breslauer KJ. Characterization by 1H NMR of glycosidic conformations in the tetramolecular complex formed by d(GGTTTTTGG). Nucleic Acids Research. 19: 4619-22. PMID 1891352

1991 | Breslauer KJ. A thermodynamic perspective of DNA bending. Current Opinion in Structural Biology. 1: 416-422. DOI: 10.1016/0959-440X(91)90041-Q

1990 | Plum GE, Park YW, Singleton SF, Dervan PB, Breslauer KJ. Thermodynamic characterization of the stability and the melting behavior of a DNA triplex: a spectroscopic and calorimetric study. Proceedings of the National Academy of Sciences of the United States of America. 87: 9436-40. PMID 2251285 DOI: 10.1073/pnas.87.23.9436

1990 | Jin RZ, Breslauer KJ, Jones RA, Gaffney BL. Tetraplex formation of a guanine-containing nonameric DNA fragment. Science (New York, N.Y.). 250: 543-6. PMID 2237404

1990 | Chan SS, Breslauer KJ, Hogan ME, Kessler DJ, Austin RH, Ojemann J, Passner JM, Wiles NC. Physical studies of DNA premelting equilibria in duplexes with and without homo dA.dT tracts: correlations with DNA bending. Biochemistry. 29: 6161-71. PMID 2207065

1989 | Snyder JG, Hartman NG, D'Estantoit BL, Kennard O, Remeta DP, Breslauer KJ. Binding of actinomycin D to DNA: evidence for a nonclassical high-affinity binding mode that does not require GpC sites. Proceedings of the National Academy of Sciences of the United States of America. 86: 3968-72. PMID 2726760

1989 | Vesnaver G, Chang CN, Eisenberg M, Grollman AP, Breslauer KJ. Influence of abasic and anucleosidic sites on the stability, conformation, and melting behavior of a DNA duplex: correlations of thermodynamic and structural data. Proceedings of the National Academy of Sciences of the United States of America. 86: 3614-8. PMID 2726738

1989 | Erie DA, Jones RA, Olson WK, Sinha NK, Breslauer KJ. Melting behavior of a covalently closed, single-stranded, circular DNA. Biochemistry. 28: 268-73. PMID 2706250

1989 | Lee M, Shea RG, Hartley JA, Lown JW, Kissinger K, Dabrowiak JC, Vesnaver G, Breslauer KJ, Pon RT. Molecular recognition between oligopeptides and nucleic acids. Sequence specific binding of (4S)-(+)- and (4R)-(-)-dihydrokikumycin B to DNA deduced from 1H NMR, footprinting studies and thermodynamic data. Journal of Molecular Recognition : Jmr. 2: 6-17. PMID 2636895 DOI: 10.1002/jmr.300020103

1989 | Lee M, Shea RG, Hartley JA, Kissinger K, Pon RT, Vesnaver G, Breslauer KJ, Dabrowiak JC, Lown JW. Molecular recognition between oligopeptides and nucleic acids: Sequence-specific binding of the naturally occurring antibiotic (4S)-(+)-anthelvencin A and its (4R)-(-) enantiomer to deoxyribonucleic acids deduced from 1H NMR, footprinting, and thermodynamic data. Journal of the American Chemical Society. 111: 345-354.

1988 | Senior MM, Jones RA, Breslauer KJ. Influence of loop residues on the relative stabilities of DNA hairpin structures. Proceedings of the National Academy of Sciences of the United States of America. 85: 6242-6. PMID 3413094

1988 | Senior M, Jones RA, Breslauer KJ. Influence of dangling thymidine residues on the stability and structure of two DNA duplexes. Biochemistry. 27: 3879-85. PMID 3408733

1988 | Roe JA, Butler A, Scholler DM, Valentine JS, Marky L, Breslauer KJ. Differential scanning calorimetry of Cu,Zn-superoxide dismutase, the apoprotein, and its zinc-substituted derivatives. Biochemistry. 27: 950-8. PMID 2835081

1988 | Jin R, Breslauer KJ. Characterization of the minor groove environment in a drug-DNA complex: bisbenzimide bound to the poly[d(AT)].poly[d(AT)]duplex. Proceedings of the National Academy of Sciences of the United States of America. 85: 8939-42. PMID 2461559

1988 | Marky LA, Blumenfeld KS, Breslauer KJ. Differential effect of tetramethylammonium chloride and sodium chloride on duplex melting temperatures of deoxyoligonucleotides: Resolution of a salt effect into specific and non-specific components Canadian Journal of Chemistry. 66: 836-839.

1987 | Marky LA, Kallenbach NR, McDonough KA, Seeman NC, Breslauer KJ. The melting behavior of a DNA junction structure: a calorimetric and spectroscopic study. Biopolymers. 26: 1621-34. PMID 3663876 DOI: 10.1002/bip.360260912

1987 | Marky LA, Breslauer KJ. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers - Peptide Science Section. 26: 1601-1620. PMID 3663875

1987 | Erie D, Sinha N, Olson W, Jones R, Breslauer K. A dumbbell-shaped, double-hairpin structure of DNA: A thermodynamic investigation. Biochemistry. 26: 7150-7159. PMID 3427065

1987 | Chou WY, Marky LA, Zaunczkowski D, Breslauer KJ. The thermodynamics of drug-dna interactions: Ethidium bromide and propidium iodide. Journal of Biomolecular Structure and Dynamics. 5: 345-362. PMID 3271479 DOI: 10.1080/07391102.1987.10506399

1987 | Marky LA, Breslauer KJ. Origins of netropsin binding affinity and specificity: correlations of thermodynamic and structural data. Proceedings of the National Academy of Sciences of the United States of America. 84: 4359-4363. PMID 3037518

1987 | Breslauer KJ, Remeta DP, Chou WY, Ferrante R, Curry J, Zaunczkowski D, Snyder JG, Marky LA. Enthalpy-entropy compensations in drug-DNA binding studies. Proceedings of the National Academy of Sciences of the United States of America. 84: 8922-6. PMID 2827160

1986 | Sutherland JC, Lin BH, Mugavero J, Trunk J, Tomasz M, Santella R, Marky L, Breslauer KJ. Vacuum ultraviolet circular dichroism of double stranded nucleic acids. Photochemistry and Photobiology. 44: 295-301. PMID 3786449

1986 | Breslauer KJ, Frank R, Blocker H, Marky LA. Predicting DNA duplex stability from the base sequence. Proceedings of the National Academy of Sciences of the United States of America. 83: 3746-3750. PMID 3459152

1986 | Wishart JF, Taube H, Breslauer KJ, Isied SS. Enthalpy of formation of nitrosylpentaammineruthenium(II) from NO+(aq) and aquopentaammineruthenium (II). Inorganic Chemistry. 25: 1479-1481.

1985 | Marky LA, Curry J, Breslauer KJ. Netropsin binding to polyd(AT) X polyd(AT) and to polydA X polydT: a comparative thermodynamic study. Progress in Clinical and Biological Research. 172: 155-173. PMID 2986168

1984 | Wishart JF, Taube H, Breslauer KJ, Isied SS. Enthalpies of reaction of pentaammineruthenium(II) complexes. Inorganic Chemistry. 23: 2997-3001. DOI: 10.1021/ic00187a020

1984 | Moss RA, Hendrickson TF, Swarup S, Hui Y, Marky L, Breslauer KJ. Trans-membrane transport of 1-anilino-8-naphthalenesulfonate in simple cationic surfactant vesicles. Tetrahedron Letters. 25: 4063-4066. DOI: 10.1016/S0040-4039(01)90182-0

1983 | Marky LA, Snyder JG, Breslauer KJ. Calorimetric and spectroscopic investigation of drug-DNA interactions: II. Dipyrandlam binding to poly d(AT). Nucleic Acids Research. 11: 5701-5715. PMID 6889134 DOI: 10.1093/nar/11.16.5701

1983 | Marky LA, Blumenfeld KS, Kozlowski S, Breslauer KJ. Salt-dependent conformational transitions in the self-complementary deoxydodecanucleotide d(CGCAATTCGCG): Evidence for hairpin formation. Biopolymers. 22: 1247-1257. PMID 6850063 DOI: 10.1002/bip.360220416

1983 | Marky LA, Snyder JG, Remeta DP, Breslauer KJ. Thermodynamics of drug-dna interactions. Journal of Biomolecular Structure and Dynamics. 1: 487-507. PMID 6400886 DOI: 10.1080/07391102.1983.10507457

1983 | Marky LA, Blumenfeld KS, Breslauer KJ. Calorimetric and spectroscoptc investigation of drug - DNA interactions. I. The binding of netropsin to poly d(AT). Nucleic Acids Research. 11: 2857-2870. PMID 6304658 DOI: 10.1093/nar/11.9.2857

1982 | Marky LA, Breslauer KJ. Calorimetric determination of base-stacking enthalpies in double-helical DNA molecules. Biopolymers - Peptide Science Section. 21: 2185-2194. PMID 7171732 DOI: 10.1002/bip.360211107

1982 | Patel DJ, Kozlowski SA, Marky LA, Rice JA, Broka C, Itakura K, Breslauer KJ. Structure and energetics of a hexanucleotide duplex with stacked trinucleotide ends formed by the sequence d(GAATTCGCG). Biochemistry. 21: 451-5. PMID 7066297 DOI: 10.1021/bi00532a005

1982 | Patel DJ, Kozlowski SA, Marky LA, Rice JA, Broka C, Itakura K, Breslauer KJ. Extra adenosine stacks into the self-complementary d(CGCAGAATTCGCG) duplex in solution. Biochemistry. 21: 445-51. PMID 7066296 DOI: 10.1021/bi00532a004

1982 | Patel DJ, Kozlowski SA, Marky LA, Rice JA, Broka C, Dallas J, Itakura K, Breslauer KJ. Structure, dynamics, and energetics of deoxyguanosine . thymidine wobble base pair formation in the self-complementary d(CGTGAATTCGCG) duplex in solution. Biochemistry. 21: 437-44. PMID 7066295 DOI: 10.1021/bi00532a003

1982 | Patel DJ, Kozlowski SA, Marky LA, Broka C, Rice JA, Itakura K, Breslauer KJ. Premelting and melting transitions in the d(CGCGAATTCGCG) self-complementary duplex in solution. Biochemistry. 21: 428-36. PMID 7066294 DOI: 10.1021/bi00532a002

1981 | Marky LA, Canuel L, Jones RA, Breslauer KJ. Calorimetric and spectroscopic investigation of the helix-to-coil transition of the self-complementary deoxyribonucleotide ATGCAT. Biophysical Chemistry. 13: 141-149. PMID 7260332 DOI: 10.1016/0301-4622(81)80013-0

1981 | Marky LA, Patel D, Breslauer KJ. Effect of tetramethylammonium ion on the helix-to-coil transition of poly(deoxyadenylylthymidine): A nuclear magnetic resonance and calorimetric investigation. Biochemistry. 20: 1427-1431. PMID 7225341

1981 | Freier SM, Hill KO, Dewey TG, Marky LA, Breslauer KJ, Turner DH. Solvent effects on the kinetics and thermodynamics of stacking in poly(cytidylic acid). Biochemistry. 20: 1419-1426. PMID 7225340 DOI: 10.1021/bi00509a003

1981 | Albergo DD, Marky LA, Breslauer KJ, Turner DH. Thermodynamics of (dG-dC)3 double-helix formation in water and deuterium oxide. Biochemistry. 20: 1409-1413. PMID 6261793 DOI: 10.1021/bi00509a001

1979 | Breslauer KJ. A calorimetric determination of enthalpies and heat capacities of protonation. The Journal of Chemical Thermodynamics. 11: 527-530. DOI: 10.1016/0021-9614(79)90090-9

1979 | Breslauer KJ, Witkowski L, Bulas K. THERMODYNAMICS OF TRANSFER OF PHENOL AND ANILINE BETWEEN NONPOLAR AND AQUEOUS ENVIRONMENTS. Information Circular - United States, Bureau of Mines. 124-133.

1978 | Breslauer KJ, Bodnar CM, Mccarthy JE. The role of solvent in the stabilization of helical structure: The low pH RIBO A8 and A10 double helices in mixed solvents. Biophysical Chemistry. 9: 71-78. PMID 37935 DOI: 10.1016/0301-4622(78)87017-3

1978 | Breslauer KJ, Charko G, Hrabar D, Oken C. Base stacking in the dinucleoside phosphate rApA. Biophysical Chemistry. 8: 393-397. PMID 31949 DOI: 10.1016/0301-4622(78)80021-0

1978 | Breslauer KJ, Witkowski L, Bulas K. The thermodynamics of transfer of phenol and aniline between nonpolar and aqueous environments. Journal of Physical Chemistry. 82: 675-678.

1977 | Breslauer KJ, Bina-Stein M. Relaxation kinetics of the helix-coil transition of a self-complementary ribo-oligonucleotide: A7U7. Biophysical Chemistry. 7: 211-216. PMID 911989 DOI: 10.1016/0301-4622(77)87024-5

1977 | Breslauer KJ, Sturtevant JM. A calorimetric investigation of single stranded base stacking in the ribo-oligonucleotide A7. Biophysical Chemistry. 7: 205-9. PMID 911988 DOI: 10.1016/0301-4622(77)87023-3

1975 | Breslauer KJ, Sturtevant JM, Tinoco I. Calorimetric and spectroscopic investigation of the helix-to-coil transition of a ribo-oligonucleotide: rA7U7. Journal of Molecular Biology. 99: 549-65. PMID 1214299 DOI: 10.1016/S0022-2836(75)80171-9

1974 | Breslauer KJ, Terrin B, Sturtevant JM. Thermodynamics of transfer of molecules and groups from nonpolar to aqueous environments. I. Method. n-butyric acid at 25°. Journal of Physical Chemistry. 78: 2363-2366. DOI: 10.1021/j150671a012

1974 | Breslauer KJ, Kabakoff DS. Enthalpy of the Diels-Alder reaction of cyclopentadiene and maleic anhydride. Journal of Organic Chemistry. 39: 721-722.

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