Design and Characterization of DNA Interactive Agents

Summary

Principal Investigator: Jennifer Brodbelt
Affiliation: University of Texas
Country: USA
Abstract: The proposed project joins the synthetic and pharmacological expertise of the Kerwin group (Division of Medicinal Chemistry, College of Pharmacy) with the analytical expertise of the Brodbelt group (Department of Chemistry and Biochemistry) and the molecular biology expertise of the Ellington group (Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology) to provide a strategy for the design and characterization of DNA-interactive agents. The overall goal of the project is to develop the capabilities of electrospray ionization mass spectrometry (ESI-MS) for characterization of metal-mediated drug/DNA and drug/quadruplex interactions along with rapid in vitro selection methods to provide insights into the processes by which drug-metal and drug-drug association affect drug/DNA binding, selectivity and enzyme inhibition. Specific objectives include: 1) the design and synthesis of metal-mediated DNA interactive compounds and G-quadruplex DNA binding compounds with a focus on addressing specific structural aspects of metal-mediated drug/DNA binding and drug/G-quadruplex DNA binding and for use as directed libraries for specific ESI-MS based screening applications. Individual compounds and libraries of analogs of the Mg 2+ ion-mediated DNA binding antitumor agents UK-1 and A62176, perylene diimides, and benzannulated UK-1and A-62176 analogs will be prepared by solution and solid-phase methods. 2) the development and application of ESI-MS and in vitro selection methods for investigation of metal-mediated drug/DNA complexes and drug/quadruplex complexes. ESI-MS and spectrophotometric/isothermal calorimetric measurements of binding affinities and selectivities will be undertaken. Energy-variable collision activated dissociation methods will be used to investigate the fragmentation of drug/DNA complexes, and an array of novel gas-phase footprinting methods will be developed to map the binding sites. Rapid selection methods based on affinity capture and release involving immobilized DNA or drugs will be developed. 3) the characterization of the consequences of metal-mediated DNA binding of drug/DNA and drug/G-quadruplex complexes to establish functional correlates of DNA binding in biologically relevant systems. One aspect involves determining the ability of the metal-mediated DNA binding agents and G-quadruplex DNA ligands to inhibit specific DNA processing enzymes. Separate SV40 large T antigen double-stranded DNA and Gquadruplex DNA helicase inhibition studies will be carried out on select DNA ligands. Human topoiomerase II inhibition studies will be carried out on the UK-1 and A-62176 analogs in order to establish the relationship between metal ion-mediated DNA binding and enzyme inhibition. Human telomerase inhibition assays will be performed with the perylene diimide analogs using DNA primers. The anticancer and antibacterial effects of UK-1 and A-62176 analogs will be examined in a range of human cancer cell lines and Gram negative and Gram positive bacteria.
Funding Period: 2003-05-01 - 2007-10-31
more information: NIH RePORT

Top Publications

  1. pmc Differentiation and Distributions of DNA/Cisplatin Crosslinks by Liquid Chromatography-Electrospray Ionization-Infrared Multiphoton Dissociation Mass Spectrometry
    Zhe Xu
    Department of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, TX, 78712, USA
    J Am Soc Mass Spectrom 25:71-9. 2014
  2. pmc Comparison of MS/MS methods for characterization of DNA/cisplatin adducts
    Zhe Xu
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    J Am Soc Mass Spectrom 24:265-73. 2013
  3. pmc Tandem mass spectrometry for characterization of covalent adducts of DNA with anticancer therapeutics
    Catherine Silvestri
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    Mass Spectrom Rev 32:247-66. 2013
  4. pmc Infrared multiphoton dissociation of small-interfering RNA anions and cations
    Myles W Gardner
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712 0165, USA
    J Am Soc Mass Spectrom 21:580-91. 2010
  5. pmc Asymmetric charge partitioning upon dissociation of DNA duplexes
    James A Madsen
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712 0165, USA
    J Am Soc Mass Spectrom 21:1144-50. 2010
  6. pmc Characterization of aziridinylbenzoquinone DNA cross-links by liquid chromatography-infrared multiphoton dissociation-mass spectrometry
    Sarah E Pierce
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
    Chem Res Toxicol 23:1097-104. 2010
  7. pmc Rapid characterization of cross-links, mono-adducts, and non-covalent binding of psoralens to deoxyoligonucleotides by LC-UV/ESI-MS and IRMPD mass spectrometry
    Suncerae I Smith
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    Analyst 135:943-52. 2010
  8. pmc Increased sequence coverage of thymine-rich oligodeoxynucleotides by infrared multiphoton dissociation compared to collision-induced dissociation
    Carol Parr
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    J Mass Spectrom 45:1098-103. 2010
  9. pmc Characterization of oligodeoxynucleotides and modifications by 193 nm photodissociation and electron photodetachment dissociation
    Suncerae I Smith
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    Anal Chem 82:7218-26. 2010
  10. pmc Hybrid activation methods for elucidating nucleic acid modifications
    Suncerae I Smith
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
    Anal Chem 83:303-10. 2011

Detail Information

Publications32

  1. pmc Differentiation and Distributions of DNA/Cisplatin Crosslinks by Liquid Chromatography-Electrospray Ionization-Infrared Multiphoton Dissociation Mass Spectrometry
    Zhe Xu
    Department of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, TX, 78712, USA
    J Am Soc Mass Spectrom 25:71-9. 2014
    ..Comparison of the IRMPD fragmentation patterns of the unmodified ODNs and the intramolecular platinated crosslinks indicated that backbone cleavage was significantly suppressed near the crosslink. ..
  2. pmc Comparison of MS/MS methods for characterization of DNA/cisplatin adducts
    Zhe Xu
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    J Am Soc Mass Spectrom 24:265-73. 2013
    ..We conclude that IRMPD and UVPD methods generally offer the best characteristics for pinpointing the cisplatin adduction sites in the fragment-rich spectra...
  3. pmc Tandem mass spectrometry for characterization of covalent adducts of DNA with anticancer therapeutics
    Catherine Silvestri
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    Mass Spectrom Rev 32:247-66. 2013
    ..This review focuses on the array of tandem mass spectrometric strategies developed and applied for characterization of covalent adducts formed between DNA and anticancer ligands...
  4. pmc Infrared multiphoton dissociation of small-interfering RNA anions and cations
    Myles W Gardner
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712 0165, USA
    J Am Soc Mass Spectrom 21:580-91. 2010
    ..With longer irradiation times, however, the individual single-strands underwent secondary dissociation to yield informative sequence ions not obtained by CID...
  5. pmc Asymmetric charge partitioning upon dissociation of DNA duplexes
    James A Madsen
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712 0165, USA
    J Am Soc Mass Spectrom 21:1144-50. 2010
    ..Comparisons were made with the dissociation behavior previously studied for protein noncovalent complexes and past studies of the gas-phase conformations and dissociation of DNA complexes...
  6. pmc Characterization of aziridinylbenzoquinone DNA cross-links by liquid chromatography-infrared multiphoton dissociation-mass spectrometry
    Sarah E Pierce
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
    Chem Res Toxicol 23:1097-104. 2010
    ....
  7. pmc Rapid characterization of cross-links, mono-adducts, and non-covalent binding of psoralens to deoxyoligonucleotides by LC-UV/ESI-MS and IRMPD mass spectrometry
    Suncerae I Smith
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    Analyst 135:943-52. 2010
    ..IRMPD of DNA/AMP complexes after UV irradiation also produced high abundances of the intact single strands with the AMP ligand attached, products indicative of a significant population of mono-adducts...
  8. pmc Increased sequence coverage of thymine-rich oligodeoxynucleotides by infrared multiphoton dissociation compared to collision-induced dissociation
    Carol Parr
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    J Mass Spectrom 45:1098-103. 2010
    ....
  9. pmc Characterization of oligodeoxynucleotides and modifications by 193 nm photodissociation and electron photodetachment dissociation
    Suncerae I Smith
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    Anal Chem 82:7218-26. 2010
    ....
  10. pmc Hybrid activation methods for elucidating nucleic acid modifications
    Suncerae I Smith
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
    Anal Chem 83:303-10. 2011
    ..The numerous products generated by the hybrid MS/MS techniques resulted in specific and extensive backbone cleavages which allowed the modification sites of multiply modified oligonucleotides to be elucidated...
  11. pmc Interactions of sulfur-containing acridine ligands with DNA by ESI-MS
    Suncerae I Smith
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    Analyst 134:2058-66. 2009
    ..At higher irradiation times, a variety of sequence ions were observed, some retaining the AS4/AN1 ligand, which was indicative of covalent binding...
  12. pmc Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats
    Sarah E Pierce
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, USA
    Chemistry 15:11244-55. 2009
    ....
  13. pmc Evaluation of binding selectivities and affinities of platinum-based quadruplex interactive complexes by electrospray ionization mass spectrometry
    Sarah E Pierce
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, USA
    Biopolymers 91:233-43. 2009
    ..The chemical probe reactions using glyoxal indicated increased reactivity when the platinum phenanthroimidazole complexes were bound to the quadruplexes, thus suggesting a conformational change that alters guanine accessibility...
  14. pmc ESI-MS characterization of a novel pyrrole-inosine nucleoside that interacts with guanine bases
    Sarah E Pierce
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712 1167, United States
    Anal Chim Acta 627:129-35. 2008
    ..The specific binding of 1 to guanine-rich DNA emphasizes the necessity of careful ligand design for specific sequence recognition...
  15. ncbi Duplex and quadruplex DNA binding and photocleavage by trioxatriangulenium ion
    Arti Pothukuchy
    Division of Medicinal Chemistry and Institute for Cellular and Molecular Biology, The University of Texas, Austin, Texas 78712, USA
    Biochemistry 44:2163-72. 2005
    ..Analysis by denaturing polyacrylamide gel electrophoresis reveals significantly less TOTA photocleavage of these quadruplex telomeric repeats when compared to the duplex repeats...
  16. ncbi Electrospray ionization of nucleic acid aptamer/small molecule complexes for screening aptamer selectivity
    Karin M Keller
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin TX 78712, USA
    J Mass Spectrom 40:1327-37. 2005
    ..These results indicate that in at least some cases, mass spectrometric data on aptamer/ligand binding affinities should be used in conjunction with complementary techniques to fully assess aptamer molecular recognition properties...
  17. ncbi Influence of initial charge state on fragmentation patterns for noncovalent drug/DNA duplex complexes
    Karin M Keller
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin TX 78712, USA
    J Mass Spectrom 40:1362-71. 2005
    ..The dissociation pathways for the lower charge state complexes are probably more reflective of specific drug-DNA interactions because Coulombic and/or conformational effects are less marked for these precursors...
  18. ncbi Evaluation of binding of perylene diimide and benzannulated perylene diimide ligands to DNA by electrospray ionization mass spectrometry
    Carolyn L Mazzitelli
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 58712 0165, USA
    J Am Soc Mass Spectrom 17:593-604. 2006
    ..Our results indicate that Tel01, Tel12, and Tel34 are the most selective for G-quadruplex DNA...
  19. ncbi Identification of the adduct between a 4-Aza-3-ene-1,6-diyne and DNA using electrospray ionization mass spectrometry
    Courtney L Sherman
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    J Am Soc Mass Spectrom 17:1342-52. 2006
    ....
  20. pmc Screening of threading bis-intercalators binding to duplex DNA by electrospray ionization tandem mass spectrometry
    Carolyn L Mazzitelli
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712 0165, USA
    J Am Soc Mass Spectrom 18:311-21. 2007
    ....
  21. pmc Infrared multiphoton dissociation of duplex DNA/drug complexes in a quadrupole ion trap
    Jeffrey J Wilson
    Department of Chemistry and Biochemistry, 1 University Station A5300, University of Texas at Austin, Austin, Texas 78712, USA
    Anal Chem 79:2067-77. 2007
    ....
  22. ncbi Gas-phase hydrogen/deuterium exchange of 5'- and 3'-mononucleotides in a quadrupole ion trap: exploring the role of conformation and system energy
    Joseph E Chipuk
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    J Am Soc Mass Spectrom 18:724-36. 2007
    ..These observations also highlight the importance of the distance between the various participating groups in addition to their gas-phase acidity and basicity...
  23. ncbi Evaluation of relative DNA binding affinities of anthrapyrazoles by electrospray ionization mass spectrometry
    Suncerae I Smith
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
    J Mass Spectrom 42:681-8. 2007
    ..However, for complexes containing AP2 or mitoxantrone, strand separation with the ligand remaining on one of the single strands was observed, indicative of a different binding mode or stronger binding...
  24. pmc Probing ligand binding to duplex DNA using KMnO4 reactions and electrospray ionization tandem mass spectrometry
    Carolyn L Mazzitelli
    Department of Chemistry and Biochemistry, 1 University Station A5300, University of Texas at Austin, Austin, Texas 78712, USA
    Anal Chem 79:4636-47. 2007
    ..Collisional activated dissociation (CAD) and infrared multiphoton dissociation (IRMPD) experiments were used to determine the site of oxidation based on oligonucleotide fragmentation patterns...
  25. pmc Evaluation of metal-mediated DNA binding of benzoxazole ligands by electrospray ionization mass spectrometry
    Carolyn L Mazzitelli
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
    J Am Soc Mass Spectrom 19:209-18. 2008
    ..Metal ions also enhanced the DNA binding of the ligands with the long side chains, especially for 9, which also exhibited the highest level of cytotoxicity of the long side-chain compounds...
  26. pmc Gas-phase stability of G-quadruplex DNA determined by electrospray ionization tandem mass spectrometry and molecular dynamics simulations
    Carolyn L Mazzitelli
    Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    J Am Soc Mass Spectrom 18:1760-73. 2007
    ..This discrepancy is attributed to differences in the fragmentation pathway of the quadruplex...
  27. pmc Synthesis, metal ion binding, and biological evaluation of new anticancer 2-(2'-hydroxyphenyl)benzoxazole analogs of UK-1
    Mireya L McKee
    Department of Chemistry and Biochemistry, Division of Medicinal Chemistry, Institute of Cellular and Molecular Biology, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
    Bioorg Med Chem 16:1775-83. 2008
    ..The potential role of Cu2+ ions in the cytotoxic action of UK-1 is further supported by the observation that UK-1 in the presence of Cu2+ displays enhanced cytotoxicity to MCF-7 and A549 cells when compared to UK-1 alone...
  28. doi Simian virus 40 large T-antigen G-quadruplex DNA helicase inhibition by G-quadruplex DNA-interactive agents
    Bodin Tuesuwan
    Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, USA
    Biochemistry 47:1896-909. 2008
    ..The identification of potent and selective inhibitors of the G-quadruplex helicase activity of T-ag provides tools for probing the specific role of this activity in SV40 replication...
  29. ncbi Charge state-dependent fragmentation of oligonucleotide/metal complexes
    Karin M Keller
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
    J Am Soc Mass Spectrom 16:28-37. 2005
    ..ODN/metal adducts in high charge states possess only a few acidic protons, and the juxtaposition of these neutral phosphate groups near thymine residues and the bound Ba(+2) ion may direct formation of the metallated a(n)(-m) species...