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

Collaborators

  • Elliott H Margulies
  • Richard W Frazee
  • Stephen C J Parker
  • Jason A Greenbaum
  • Swapan S Jain
  • Andrew J Danford
  • Hong Guo
  • Bingzi Chen
  • Loren Hansen
  • Hatice Ozel Abaan
  • Bo Pang
  • Stephen J Lippard
  • Qun Wang
  • Dong Wang
  • Elizabeth R Jamieson

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...