Bibliography: Tom Tullius

  1. S. S. Jain & T. D. Tullius
    Footprinting protein-DNA complexes using the hydroxyl radical
    Nature Protocols     3, 1092-1100 (2008).
  2. Q. Wang, T. D. Tullius and J. R. Levin
    Effects of discontinuities in the DNA template on abortive initiation and promoter escape by Escherichia coli RNA polymerase
    J. Biol. Chem.     282, 26917-26927 (2007) .
  3. The ENCODE Consortium (authors include T. D. Tullius, J. A. Greenbaum and S. C. J. Parker)
    Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Nature     447, 799-816 (2007) .
  4. J. A. Greenbaum, B. Pang and T. D. Tullius
    Construction of a genome-scale structural map at single-nucleotide resolution
    Genome Research     17, 947-953.
  5. J. A. Greenbaum, S. C. J. Parker and T. D. Tullius
    Detection of DNA structural motifs in functional genomic elements
    Genome Research     17, 940-946 (2007) .
  6. A. J. Danford, D. Wang, Q. Wang, T. D. Tullius and S. J. Lippard
    Platinum Anticancer Drug Damage Enforces a Particular Rotational Setting of DNA in Nucleosomes
    Proc. Natl. Acad. Sci (USA) 102, 12311-12316 (2005)
  7. T. D. Tullius and J. A. Greenbaum
    Mapping Nucleic Acid Structure by Hydroxyl Radical Cleavage
    Curr. Opinion Chem. Biol. 9, 127–134 (2005)
  8. H. Guo and T. D. Tullius
    Gapped DNA is Anisotropically Bent
    Proc. Natl. Acad. Sci (USA) 100, 3743-3747 (2003)
  9. R. W. Frazee, J. A. Taylor and T. D. Tullius
    Interchange of DNA Binding Modes in the Deformed and Ultrabithorax Homeodomains: A Structural Role for the N-Terminal Arm
     J. Mol. Biol. 323, 665-683 (2002)
  10. B. Chen, E. R. Jamieson and T. D. Tullius
    A General Synthesis of Specifically Deuterated Nucleotides for Studies of DNA and RNA
    Bioorg. Med. Chem. Lett. 12, 3093-3096 (2002)
  11. T. D. Tullius
    Probing DNA Structure with Hydroxyl Radicals
    in Current Protocols in Nucleic Acid Chemistry. S. L. Beaucage, D. E. Bergstrom, G. D. Glick, and R. A. Jones, eds. (Wiley, 2001), pp. 6.7.1-6.7.8
  12. M. Wu, D. Stoermer, C. A. Townsend and T. D. Tullius
    Calicheamicin-Homeodomain Conjugate as an Efficient, Sequence-Specific DNA Cleavage and Mapping Tool
    J. Amer. Chem. Soc. 122, 12884-12885 (2000)
  13. L. M. Ottinger and T. D. Tullius
    High Resolution in vivo Footprinting of a Protein-DNA Complex Using Gamma Radiation
    J. Amer. Chem. Soc. 122, 5901-5902 (2000)
  14. J. R. Levin, J. J. Blake, R. A. Ganunis and T. D. Tullius
    The Roles of Specific Template Nucleotides in the Formation of Stable Transcription Complexes by Escherichia coli RNA Polymerase
    J. Biol. Chem. 275, 6885-6893 (2000)
  15. T. D. Tullius
    Structural Chemistry of DNA Cleavage by the Hydroxyl Radical
    Radiation Research, Volume 2 (Conference Proceedings), pp. 333-335 (2000)
  16. H. R. Widlund, P. N. Kuduvalli, M. Bengtsson, H. Cao, T. D. Tullius and M. Kubista
    Nucleosome structural features and intrinsic properties of the (TATAAACGCC)-repeat sequence
    J. Biol. Chem. 274, 31847-31852 (1999)
  17. C. P. J. McDaniels, L. T. Jensen, C. Srinivasan, D. R. Winge and T. D. Tullius
    The Yeast Transcription Factor Mac1 Binds to DNA in a Modular Fashion
    J. Biol. Chem. 274, 26962-26967 (1999)
  18. B. Balasubramanian, W. K. Pogozelski and T. D. Tullius
    DNA Strand Breaking by the Hydroxyl Radical is Governed by the Accessible Surface Areas of the Hydrogen Atoms of the DNA Backbone
    Proc. Natl. Acad. Sci. (USA) 95, 9738–9743 (1998)
  19. W. K. Pogozelski and T. D. Tullius
    Oxidative Strand Scission of Nucleic Acids: Routes Initiated by Hydrogen Abstraction from the Sugar Moiety
    Chem. Rev. 98, 1089-1107 (1998)
  20. A. Draganescu and T. D. Tullius
    The DNA Binding Specificity of Engrailed Homeodomain
    J. Mol. Biol. 276, 529-536 (1998)
  21. A. P. A. M. Eijkelenboom, F. M. I. van den Ent, A. Vos, J. F. Doreleijers, K. Hard, T. D. Tullius, R. H. A. Plasterk, R. Kaptein and R. Boelens
    The Solution Structure of the Amino-Terminal HHCC Domain of HIV-2 Integrase: A Three-Helix Bundle Stabilized by Zinc
    Curr. Biol. 7, 739-746 (1997)
  22. S. E. Shadle, D. F. Allen, H. Guo, W. K. Pogozelski, J. S. Bashkin and T. D. Tullius
    Quantitative Analysis of Electrophoresis Data: Novel Curve Fitting Methodology and its Application to the Determination of a Protein-DNA Binding Constant
    Nucleic Acids Res. 25, 850–861 (1997)
  23. R. M. Ganunis, H. Guo and T. D. Tullius
    Effect of the Crystallizing Agent 2-Methyl-2,4-pentanediol on the Structure of Adenine Tract DNA in Solution
    Biochemistry (Accelerated Publication) 35, 13729–13732 (1996)
  24. W. J. Dixon, C. Inouye, M. Karin and T. D. Tullius
    CUP2 Binds in a Bipartite Manner to Upstream Activation Sequence c in the Promoter of the Yeast Copper Metallothionein Gene
    J. Biol. Inorg. Chem. 1, 451–459 (1996)
  25. T. D. Tullius
    Footprinting of Nucleic Acids by Iron-Based Reagents
    in Comprehensive Supramolecular Chemistry. Volume 5 (Bioinorganic Systems). Series editor in chief, J-M. Lehn, volume editor, K. S. Suslick (Pergamon Press, 1996), pp. 317-343
  26. T. D. Tullius
    Chemical Mapping of Nucleic Acid Conformation
    in Bioorganic Chemistry: Nucleic Acids. S. M. Hecht, ed. (Oxford University Press, 1996), pp. 144-162
  27. J. A. Johnson, W. J. Dixon and T. D. Tullius
    Affinity of CUP2, a Copper-Dependent Transcription Factor, for DNA Sequences Upstream of the Yeast Metallothionein Gene
    Inorganica Chimica Acta 242, 233-238 (1996)
  28. A. Draganescu and T. D. Tullius
    Targeting of Nucleic Acids by Iron Complexes
    in Metal Ions and Biological Systems Volume 33. H. Sigel and A. Sigel, eds. (Marcel Dekker, New York, 1996), pp. 453-484
  29. T. D. Tullius
    Homeodomains: Together Again for the First Time
    Structure 3, 1143-1145 (1995)
  30. T. D. Tullius
    New Methods for Determining the Structure of DNA and DNA-Protein Complexes Based on the Chemistry of Iron(II) EDTA
    in Genetic Response to Metals. B. Sarkar, ed. (Marcel Dekker, 1995)
  31. A. S. Kimball, M. L. Kimball, M. Jayaram and T. D. Tullius
    Chemical Probe and Missing Nucleoside Analysis of Flp Recombinase Bound to the Recognition Target Sequence
    Nucleic Acids Res. 23, 3009–3017 (1995)
  32. M. Chatterjee, S. C. Mah, T. D. Tullius and C. A. Townsend
    The Role of the Aryl Iodide in the Sequence-Selective Cleavage of DNA by Calicheamicin. The Importance of Thermodynamic Binding vs. Kinetic Activation in the Cleavage Process
    J. Am. Chem. Soc. 117, 8074–8082 (1995)
  33. W. K. Pogozelski, T. J. McNeese and T. D. Tullius
    What Species is Responsible for Strand Scission in the Reaction of [Fe(EDTA)]2– and H2O2 with DNA?
    J. Am. Chem. Soc. 117, 6428–6433 (1995)
  34. A. Draganescu, J. R. Levin and T. D. Tullius
    Homeodomain Proteins: What Governs Their Ability to Recognize Specific DNA Sequences?
    J. Mol. Biol.     250, 595-608 (1995)
  35. P. N. Kuduvalli, C. A. Townsend and T. D. Tullius
    Cleavage by Calicheamicin g1I of DNA in a Nucleosome Formed on the 5S RNA Gene of Xenopus borealis
    Biochemistry (Accelerated Publication) 34, 3899-3906 (1995)
  36. S. C. Mah, M. A. Price, C. A. Townsend and T. D. Tullius
    Features of DNA Recognition for Oriented Binding and Cleavage by Calicheamicin
    Tetrahedron 50, 1361-1378 (1994)
  37. S. C. Mah, C. A. Townsend and T. D. Tullius
    Hydroxyl Radical Footprinting of Calicheamicin. Relationship of Binding to Cleavage
    Biochemistry 33, 614-621 (1994)
  38. J. S. Bashkin and T. D. Tullius
    Hydroxyl Radical Footprinting
    in Footprinting of Nucleic Acid-Protein Complexes. A. Revzin, ed. (Academic Press, San Diego, 1993) p. 75
  39. J. J. Hayes and T. D. Tullius
    Structure of the TFIIIA-DNA Complex
    in Nucleic Acids and Molecular Biology, Volume 7. F. Eckstein and D. M. J. Lilley, eds. (Springer-Verlag, Berlin Heidelberg, 1993), p. 106
  40. A. S. Kimball, J. Lee, M. Jayaram and T. D. Tullius
    Sequence-Specific Cleavage of DNA via Nucleophilic Attack of Hydrogen Peroxide, Assisted by Flp Recombinase
    Biochemistry (Accelerated Publication) 32, 4698-4701 (1993)
  41. J. Bashkin, J. J. Hayes, T. D. Tullius and A. P. Wolffe
    Structure of DNA in a Nucleosome Core Particle at High Salt Concentration and at High Temperature
    Biochemistry (Accelerated Publication) 32, 1895-1898 (1993)
  42. M. A. Price and T. D. Tullius
    How the Structure of an Adenine Tract Depends on Sequence Context. A New Model for the Structure of TnAn DNA Sequences
    Biochemistry 32, 127-136 (1993)
  43. J. J. Hayes and T. D. Tullius
    Structure of the TFIIIA-5S DNA Complex
    J. Mol. Biol. 227, 407-417 (1992)
  44. M. A. Price and T. D. Tullius
    Using the Hydroxyl Radical to Probe DNA Structure
    Meth. Enzymol., Vol. 212. D. M. J. Lilley and J. Dahlberg, eds., pp. 194-219 (1992)
  45. J. R. Levin, A. M. Burkhoff and T. D. Tullius
    Using the Chemistry of the Hydroxyl Radical to Determine Structural Details About DNA and Protein-DNA Complexes
    in A Laboratory Guide to In Vitro Studies of Protein/DNA Interactions. BioMethods Series, Volume 5, H. P. Saluz and J.-P. Jost, eds. (Birkhäuser Verlag, 1991), pp. 134-144
  46. W. J. Dixon, J. J. Hayes, J. R. Levin, M. F. Weidner, B. A. Dombroski and T. D. Tullius
    Hydroxyl Radical Footprinting
    Meth. Enzymol., Vol. 208 (Protein-DNA Interactions). R. T. Sauer, ed., p. 380 (1991)
  47. J. J. Hayes, J. Bashkin, T. D. Tullius and A. P. Wolffe
    The Histone Core Exerts a Dominant Constraint on the Structure of DNA in a Nucleosome
    Biochemistry 30, 8434-8440 (1991)
  48. T. D. Tullius
    DNA Footprinting With the Hydroxyl Radical
    Free Radical Res. Comm. 12–13, 521-529 (1991)
  49. T. D. Tullius
    The Use of Chemical Probes to Analyse DNA and RNA Structures
    Curr. Op. Struct. Biol. 1, 428-434 (1991)
  50. K. H. Nakagawa, C. Inouye, B. Hedman, M. Karin, T. D. Tullius and K. O. Hodgson
    Evidence From EXAFS for a Copper Cluster in the Metalloregulatory Protein CUP2 from Yeast
    J. Amer. Chem. Soc. 113, 3621-3623 (1991)
  51. T. D. Tullius
    Viewpoint: Bioinorganic Chemistry
    J. Cell. Biochem. 45, 5-6 (1991)
  52. Q. Guo, M. Lu, M. E. A. Churchill, T. D. Tullius and N. R. Kallenbach
    Asymmetric Structure of a Three-Arm DNA Junction
    Biochemistry 29, 10927-10934 (1990)
  53. J. J. Hayes, T. D. Tullius and A. P. Wolffe
    The Structure of DNA in a Nucleosome
    Proc. Natl. Acad. Sci. USA 87, 7405-7409 (1990)
  54. C. Buchman, P. Skroch, W. Dixon, T. D. Tullius and M. Karin
    A Single Amino Acid Change in CUP2 Alters Its Mode of DNA Binding
    Mol. Cell. Biol. 10, 4778-4787 (1990)
  55. J. J. Hayes, L. Kam and T. D. Tullius
    Footprinting Protein-DNA Complexes With Gamma Rays
    Meth. Enzymol., Vol. 186 (Oxygen Radicals In Biological Systems, Part B: Oxygen Radicals and Antioxidants). p. 545-549 (1990)
  56. M. E. A. Churchill, T. D. Tullius and A. Klug
    Mode of Interaction of the Zinc Finger Protein TFIIIA with a 5S RNA Gene of Xenopus
    Proc. Natl. Acad. Sci. USA 87, 5528-5532 (1990)
  57. N. C. Seeman, J. E. Mueller, J.-H. Chen, M. E. A. Churchill, A. Kimball, T. D. Tullius, B. Kemper, R. P. Cunningham and N. R. Kallenbach
    Immobile Junctions Suggest New Features of the Structural Chemistry of Recombination
    in Structure and Methods, Volume 1: Human Genome Initiative and DNA Recombination. R. H. Sarma and M. H. Sarma, eds. (Adenine, Guilderland, NY, 1990), p. 137-156.
  58. M. E. A. Churchill, J. J. Hayes and T. D. Tullius
    Detection of Drug Binding Sites by Hydroxyl Radical Footprinting. Relationship of Distamycin Binding to Nucleosome Positioning on the 5S RNA Gene of Xenopus
    Biochemistry 29, 6043-6050 (1990)
  59. A. Kimball, Q. Guo, M. Lu, R. P. Cunningham, N. R. Kallenbach, N. C. Seeman and T. D. Tullius
    Construction and Analysis of Parallel and Antiparallel Holliday Junctions
    J. Biol. Chem. 265, 6544-6547 (1990)
  60. J. J. Hayes and T. D. Tullius
    The Missing Nucleoside Experiment: A New Technique to Study Recognition of DNA by Protein
    Biochemistry 28, 9521-9527 (1989)
  61. T. D. Tullius
    Metals and Molecular Biology
    in Metal-DNA Chemistry. T. D. Tullius, ed. (ACS Symposium Series 402) (ACS Books, Washington, D. C., 1989), pp. 1-23
  62. T. D. Tullius
    Structural Studies of DNA Through Cleavage by the Hydroxyl Radical
    in Nucleic Acids and Molecular Biology, Volume 3. F. Eckstein and D. M. J. Lilley, eds. (Springer-Verlag, Berlin, 1989), pp. 1-12
  63. A. S. Kimball, G. Milman and T. D. Tullius
    High Resolution Footprints of the DNA Binding Domain of Epstein-Barr Virus Nuclear Antigen-1
    Mol. Cell. Biol. 9, 2738-2742 (1989)
  64. G. E. Shafer, M. A. Price and T. D. Tullius
    Use of the Hydroxyl Radical and Gel Electrophoresis to Study DNA Structure
    Electrophoresis 10, 397-404 (1989)
  65. Hayes, T. D. Tullius and A. P. Wolffe
    A Protein-Protein Interaction Is Essential for Stable Complex Formation on a 5S RNA Gene
    J. Biol. Chem. 264, 6009-6012 (1989)
  66. T. D. Tullius
    Physical Studies of Protein-DNA Complexes by Footprinting
    Ann. Rev. Biophys. Biophys. Chem. 18, 213–237 (1989)
  67. J-H. Chen, M. E. A. Churchill, T. D. Tullius, N. R. Kallenbach and N. C. Seeman
    Construction and Analysis of Mono-Mobile DNA Junctions
    Biochemistry 27, 6032-6038 (1988)
  68. M. E. A. Churchill, T. D. Tullius, N. R. Kallenbach and N. C. Seeman
    A Holliday Recombination Intermediate is Twofold Symmetric
    Proc. Natl. Acad. Sci. USA 85, 4653-4656 (1988)
  69. T. D. Tullius
    DNA Footprinting With Hydroxyl Radical
    Nature 332, 663-664 (1988)
  70. K. Vrana, M. E. A. Churchill, T. D. Tullius and D. D. Brown
    Mapping Functional Regions of the Transcription Factor TFIIIA
    Mol. Cell. Biol. 8, 1684-1696 (1988)
  71. T. D. Tullius and A. M. Burkhoff
    Using the Chemistry of the Hydroxyl Radical to Determine Structural Details of Bent DNA
    in Structure and Expression, Volume 3: DNA Bending and Curvature. W. K. Olson, M. H. Sarma, R. H. Sarma, and M. Sundaralingam, eds., pp. 77-85 (Adenine Press, Guilderland, NY, 1988)
  72. A. M. Burkhoff and T. D. Tullius
    Structural Details of an Adenine Tract That Does Not Cause DNA to Bend
    Nature 331, 455-457 (1988)
  73. T. D. Tullius, B. A. Dombroski, M. E. A. Churchill and L. Kam
    Hydroxyl Radical Footprinting: A High-Resolution Method for Mapping Protein-DNA Contacts
    Meth. Enzymol. 155, 537-558 (1987)
  74. T. D. Tullius
    Chemical ‘Snapshots’ of DNA: Using the Hydroxyl Radical to Study the Structure of DNA and DNA-Protein Complexes
    Trends Biochem. Sci. 12, 297-300 (1987)
  75. A. M. Burkhoff and T. D. Tullius
    The Unusual Conformation Adopted by the Adenine Tracts in Kinetoplast DNA
    Cell 48, 935-943 (1987)
  76. T. D. Tullius and B. A. Dombroski
    Hydroxyl Radical ‘Footprinting’: High-Resolution Information About DNA-Protein Contacts and Application to l Repressor and Cro Protein
    Proc. Natl. Acad. Sci. USA 83, 5469-5473 (1986)
  77. T. D. Tullius and B. A. Dombroski
    Iron(II) EDTA Used to Measure the Helical Twist Along Any DNA Molecule
    Science 230, 679-681 (1985)
  78. P. Frank, A. Licht, T. D. Tullius, K. O. Hodgson and I. Pecht
    A Selenomethionine-Containing Azurin from Pseudomonas Aeruginosa
    J. Biol. Chem. 260, 5518-5525 (1985)
  79. T. D. Tullius, H. M. Ushay, C. M. Merkel, J. P. Caradonna and S. J. Lippard
    Structural Chemistry of Platinum-DNA Adducts
    in Platinum, Gold and Other Metal Chemotherapeutic Agents. S. J. Lippard, ed. (ACS Symposium Series 209) (ACS Books, Washington, D. C., 1983), p. 51-74
  80. T. D. Tullius and S. J. Lippard
    Ethidium Bromide Changes the Nuclease-Sensitive Binding Sites of the Antitumor Drug cis-Diamminedichloroplatinum(II)
    Proc. Natl. Acad. Sci. USA 79, 3489-3492 (1982)
  81. T. D. Tullius and S. J. Lippard
    cis-Diamminedichloroplatinum(II) Binds in a Unique Manner to Oligo(dG)•Oligo(dC) Sequences in DNA – A New Assay Using Exonuclease III
    J. Am. Chem. Soc. 103, 4620-4622 (1981)
  82. H. M. Ushay, T. D. Tullius and S. J. Lippard
    Inhibition of the BamHI Cleavage and Unwinding of pBR322 Deoxyribonucleic Acid by the Antitumor Drug cis-Dichlorodiammineplatinum(II)
    Biochemistry 20, 3744-3748 (1981)
  83. T. D. Tullius, W. O. Gillum, R. M. K. Carlson and K. O. Hodgson
    Structural Study of the Vanadium Complex in Living Ascidian Blood Cells by X-Ray Absorption Spectroscopy
    J. Am. Chem. Soc. 102, 5670-5676 (1980)
  84. T. D. Tullius, S. D. Conradson, J. M. Berg and K. O. Hodgson
    Structural Chemistry of Molybdenum in Metalloenzymes as Elucidated by EXAFS
    in Molybdenum Chemistry of Biological Significance. W.E. Newton and S. Otsuka, eds., p. 139-155 (Plenum, New York, 1980)
  85. T. D. Tullius, D. M. Kurtz, S. D. Conradson and K. O. Hodgson
    The Molybdenum Site of Xanthine Oxidase. Structural Evidence from X-ray Absorption Spectroscopy
    J. Am. Chem. Soc. 101, 2776-2779 (1979)
  86. T. D. Tullius, P. Frank and K. O. Hodgson
    Characterization of the Blue Copper Site in Oxidized Azurin by Extended X-Ray Absorption Fine Structure: Determination of a Short Cu–S Distance
    Proc. Natl. Acad. Sci. USA 75, 4069-4073 (1978)
  87. J. P. Collman, R. K. Rothrock, J. P. Sen, T. D. Tullius and K. O. Hodgson
    Molecular Structure of trans-Bis(benzeneselenido)[difluoro-3,3'-trimethyldinitrilo)bis(2-pentanoneoximato)borate]rhodium(III)
    Inorg. Chem. 15, 2947-2498 (1976)
  88. W. D. Stanley, T. Davies, T. D. Tullius and C. S. Garner
    Kinetics of Spontaneous Thermal Reduction of cis-Tetraaquodiamminecobalt(III), cis-Diaquobis(trimethyl-enediamine)cobalt(III) and 1,2,3-Triaquo-N-(2-aminoethyl)-1,3-diaminopropane-cobalt(III) Cations in Hot Aqueous Perchloric Acid
    J. Inorg. Nucl. Chem. 35, 3857-3684 (1973)