THOMAS TULLIUS

Summary

Affiliation: Boston University
Country: USA

Publications

  1. doi request reprint Probing DNA structure with hydroxyl radicals
    Thomas D Tullius
    Boston University, Boston, Massachussetts, USA
    Curr Protoc Nucleic Acid Chem . 2002
  2. ncbi request reprint Mapping nucleic acid structure by hydroxyl radical cleavage
    Thomas D Tullius
    Department of Chemistry, Boston University, Boston MA 02215, USA
    Curr Opin Chem Biol 9:127-34. 2005
  3. ncbi request reprint The relationship between fine scale DNA structure, GC content, and functional elements in 1% of the human genome
    Stephen C J Parker
    Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
    Genome Inform 20:199-211. 2008
  4. pmc Local DNA topography correlates with functional noncoding regions of the human genome
    Stephen C J Parker
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Science 324:389-92. 2009
  5. ncbi request reprint A general synthesis of specifically deuterated nucleotides for studies of DNA and RNA
    Bingzi Chen
    Department of Chemistry, Boston University, Boston, MA 02215, USA
    Bioorg Med Chem Lett 12:3093-6. 2002
  6. ncbi request reprint Interchange of DNA-binding modes in the deformed and ultrabithorax homeodomains: a structural role for the N-terminal arm
    Richard W Frazee
    Department of Chemistry, University of Michigan Flint, Flint, MI 48502, USA
    J Mol Biol 323:665-83. 2002
  7. pmc Platinum anticancer drug damage enforces a particular rotational setting of DNA in nucleosomes
    Andrew J Danford
    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Proc Natl Acad Sci U S A 102:12311-6. 2005
  8. ncbi request reprint Footprinting protein-DNA complexes using the hydroxyl radical
    Swapan S Jain
    Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
    Nat Protoc 3:1092-1100. 2008
  9. pmc Construction of a genome-scale structural map at single-nucleotide resolution
    Jason A Greenbaum
    Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA
    Genome Res 17:947-53. 2007
  10. pmc Detection of DNA structural motifs in functional genomic elements
    Jason A Greenbaum
    Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA
    Genome Res 17:940-6. 2007

Research Grants

Collaborators

Detail Information

Publications11

  1. doi request reprint Probing DNA structure with hydroxyl radicals
    Thomas D Tullius
    Boston University, Boston, Massachussetts, USA
    Curr Protoc Nucleic Acid Chem . 2002
    ....
  2. ncbi request reprint Mapping nucleic acid structure by hydroxyl radical cleavage
    Thomas D Tullius
    Department of Chemistry, Boston University, Boston MA 02215, USA
    Curr Opin Chem Biol 9:127-34. 2005
    ..Advances have been made in methods for analysis of hydroxyl radical data, so that the large datasets that result from kinetic folding experiments can be analyzed in a semi-automated and quantitative manner...
  3. ncbi request reprint The relationship between fine scale DNA structure, GC content, and functional elements in 1% of the human genome
    Stephen C J Parker
    Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
    Genome Inform 20:199-211. 2008
    ....
  4. pmc Local DNA topography correlates with functional noncoding regions of the human genome
    Stephen C J Parker
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Science 324:389-92. 2009
    ..These results support the idea that the molecular shape of DNA is under selection and can identify evolutionary history...
  5. ncbi request reprint A general synthesis of specifically deuterated nucleotides for studies of DNA and RNA
    Bingzi Chen
    Department of Chemistry, Boston University, Boston, MA 02215, USA
    Bioorg Med Chem Lett 12:3093-6. 2002
    ..Milligram quantities of the desired products were obtained with an average deuterium content of 96+/-1%...
  6. ncbi request reprint Interchange of DNA-binding modes in the deformed and ultrabithorax homeodomains: a structural role for the N-terminal arm
    Richard W Frazee
    Department of Chemistry, University of Michigan Flint, Flint, MI 48502, USA
    J Mol Biol 323:665-83. 2002
    ..Thus, N-terminal arm position dictates the binding mode and the interaction of the recognition helix with nucleosides in the major groove...
  7. pmc Platinum anticancer drug damage enforces a particular rotational setting of DNA in nucleosomes
    Andrew J Danford
    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Proc Natl Acad Sci U S A 102:12311-6. 2005
    ..We suggest that these phasing phenomena may be central to the recognition and processing of platinum-DNA adducts in cancer cells treated with these drugs and possibly may be common to other DNA damaging events...
  8. ncbi request reprint Footprinting protein-DNA complexes using the hydroxyl radical
    Swapan S Jain
    Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
    Nat Protoc 3:1092-1100. 2008
    ..This protocol can be completed in 2 d...
  9. pmc Construction of a genome-scale structural map at single-nucleotide resolution
    Jason A Greenbaum
    Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA
    Genome Res 17:947-53. 2007
    ..We have used the prediction algorithm to produce a structural map of the 30 Mb of the ENCODE regions of the human genome...
  10. pmc Detection of DNA structural motifs in functional genomic elements
    Jason A Greenbaum
    Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA
    Genome Res 17:940-6. 2007
    ....
  11. pmc Gapped DNA is anisotropically bent
    Hong Guo
    Protometrix, Inc, 66 High Street, Guilford, CT 06437, USA
    Proc Natl Acad Sci U S A 100:3743-7. 2003
    ..Our results demonstrate that a single-nucleoside gap in a DNA duplex leads to an anisotropic, directional bend in the DNA helix axis. The implications of our findings for recognition of this lesion by DNA repair proteins are discussed...

Research Grants14

  1. Structure of genomic DNA at single-nucleotide resolution
    THOMAS TULLIUS; Fiscal Year: 2006
    ..Computational tools, including hidden Markov models, will be trained on the database of hydroxyl radical cleavage patterns in order to recognize structural patterns in genomic DNA sequences. ..
  2. FOOTPRINTING WITH IRON (II)-GENERATED HYDROXYL RADICAL
    THOMAS TULLIUS; Fiscal Year: 2003
    ..abstract_text> ..
  3. USING THE CHEMISTRY OF IRON(II) TO STUDY DNA STRUCTURE
    THOMAS TULLIUS; Fiscal Year: 2002
    ..The high resolution and structural sensitivity of the hydroxyl radical will be used to determine structural details of these DNA molecules in solution. ..
  4. Structure of genomic DNA at single-nucleotide resolution
    Thomas D Tullius; Fiscal Year: 2010
    ..Experimental data production and informatics pipelines, data verification and validation protocols, and plans for data deposition are detailed in the application. ..