Thomas D. Tullius, Ph.D. - Publications

Affiliations: 
1982-1997 Chemistry Johns Hopkins University, Baltimore, MD 
 1997- Chemistry Boston University, Boston, MA, United States 
Area:
General Biophysics, Molecular Biology, Biostatistics Biology
Website:
http://dna.bu.edu/tullius

83 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Chiu TP, Yang L, Zhou T, Main BJ, Parker SC, Nuzhdin SV, Tullius TD, Rohs R. GBshape: a genome browser database for DNA shape annotations. Nucleic Acids Research. 43: D103-9. PMID 25326329 DOI: 10.1093/nar/gku977  1
2011 Bishop EP, Rohs R, Parker SC, West SM, Liu P, Mann RS, Honig B, Tullius TD. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. Acs Chemical Biology. 6: 1314-20. PMID 21967305 DOI: 10.1021/cb200155t  1
2011 Parker SC, Harlap A, Tullius TD. A computational method to search for DNA structural motifs in functional genomic elements. Methods in Molecular Biology (Clifton, N.J.). 759: 367-79. PMID 21863498 DOI: 10.1007/978-1-61779-173-4_21  1
2011 Parker SC, Tullius TD. DNA shape, genetic codes, and evolution. Current Opinion in Structural Biology. 21: 342-7. PMID 21439813 DOI: 10.1016/j.sbi.2011.03.002  1
2009 Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH. Local DNA topography correlates with functional noncoding regions of the human genome. Science (New York, N.Y.). 324: 389-92. PMID 19286520 DOI: 10.1126/science.1169050  1
2008 Parker SC, Margulies EH, Tullius TD. The relationship between fine scale DNA structure, GC content, and functional elements in 1% of the human genome. Genome Informatics. International Conference On Genome Informatics. 20: 199-211. PMID 19425134  1
2008 Jain SS, Tullius TD. Footprinting protein-DNA complexes using the hydroxyl radical. Nature Protocols. 3: 1092-1100. PMID 18546600 DOI: 10.1038/nprot.2008.72  1
2007 Wang Q, Tullius TD, Levin JR. Effects of discontinuities in the DNA template on abortive initiation and promoter escape by Escherichia coli RNA polymerase. The Journal of Biological Chemistry. 282: 26917-27. PMID 17650506 DOI: 10.1074/jbc.M702473200  1
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Tullius TD, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/nature05874  1
2007 Greenbaum JA, Pang B, Tullius TD. Construction of a genome-scale structural map at single-nucleotide resolution. Genome Research. 17: 947-53. PMID 17568010 DOI: 10.1101/gr.6073107  1
2007 Greenbaum JA, Parker SC, Tullius TD. Detection of DNA structural motifs in functional genomic elements. Genome Research. 17: 940-6. PMID 17568009 DOI: 10.1101/gr.5602807  1
2005 Danford AJ, Wang D, Wang Q, Tullius TD, Lippard SJ. Platinum anticancer drug damage enforces a particular rotational setting of DNA in nucleosomes. Proceedings of the National Academy of Sciences of the United States of America. 102: 12311-6. PMID 16116097 DOI: 10.1073/pnas.0506025102  1
2005 Tullius TD, Greenbaum JA. Mapping nucleic acid structure by hydroxyl radical cleavage. Current Opinion in Chemical Biology. 9: 127-34. PMID 15811796 DOI: 10.1016/j.cbpa.2005.02.009  1
2004 Kellman R, Deardorff D, Dorhout P, Haegel N, Iverson BL, Morrison M, Pladziewicz J, Selen M, Tullius TD, Zwier TS. Research corporation and John Schaefer [2] (multiple letters) Science. 306: 1133.  1
2003 Guo H, Tullius TD. Gapped DNA is anisotropically bent. Proceedings of the National Academy of Sciences of the United States of America. 100: 3743-7. PMID 12644712 DOI: 10.1073/pnas.0737062100  1
2002 Tullius TD. Probing DNA structure with hydroxyl radicals. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 6.7. PMID 18428898 DOI: 10.1002/0471142700.nc0607s07  1
2002 Frazee RW, Taylor JA, Tullius TD. Interchange of DNA-binding modes in the deformed and ultrabithorax homeodomains: a structural role for the N-terminal arm. Journal of Molecular Biology. 323: 665-83. PMID 12419257 DOI: 10.1016/S0022-2836(02)00996-8  1
2002 Chen B, Jamieson ER, Tullius TD. A general synthesis of specifically deuterated nucleotides for studies of DNA and RNA. Bioorganic & Medicinal Chemistry Letters. 12: 3093-6. PMID 12372509 DOI: 10.1016/S0960-894X(02)00650-9  1
2000 Levin JR, Blake JJ, Ganunis RA, Tullius TD. The roles of specific template nucleosides in the formation of stable transcription complexes by Escherichia coli RNA polymerase Journal of Biological Chemistry. 275: 6885-6893. PMID 10702248 DOI: 10.1074/jbc.275.10.6885  1
2000 Wu M, Stoermer D, Tullius TD, Townsend CA. Calicheamicin - Homeodomain conjugate as an efficient, sequence-specific DNA cleavage and mapping tool [11] Journal of the American Chemical Society. 122: 12884-12885. DOI: 10.1021/ja002280o  1
2000 Ottinger LM, Tullius TD. High-resolution in vivo footprinting of a protein - DNA complex using γ-radiation [13] Journal of the American Chemical Society. 122: 5901-5902. DOI: 10.1021/ja000285f  1
1999 Widlund HR, Kuduvalli PN, Bengtsson M, Cao H, Tullius TD, Kubista M. Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence Journal of Biological Chemistry. 274: 31847-31852. PMID 10542209 DOI: 10.1074/jbc.274.45.31847  1
1999 Jamison McDaniels CP, Jensen LT, Srinivasan C, Winge DR, Tullius TD. The yeast transcription factor Mac1 binds to DNA in a modular fashion. The Journal of Biological Chemistry. 274: 26962-7. PMID 10480908 DOI: 10.1074/jbc.274.38.26962  1
1998 Pogozelski WK, Tullius TD. Oxidative Strand Scission of Nucleic Acids: Routes Initiated by Hydrogen Abstraction from the Sugar Moiety. Chemical Reviews. 98: 1089-1108. PMID 11848926  1
1998 Balasubramanian B, Pogozelski WK, Tullius TD. DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone Proceedings of the National Academy of Sciences of the United States of America. 95: 9738-9743. PMID 9707545 DOI: 10.1073/pnas.95.17.9738  1
1998 Draganescu A, Tullius TD. The DNA binding specificity of engrailed homeodomain. Journal of Molecular Biology. 276: 529-36. PMID 9551094 DOI: 10.1006/jmbi.1997.1567  1
1998 Tullius TD. Chemical snapshots of DNA Faseb Journal. 12.  1
1997 Eijkelenboom AP, van den Ent FM, Vos A, Doreleijers JF, Hård K, Tullius TD, Plasterk RH, Kaptein R, Boelens R. The solution structure of the amino-terminal HHCC domain of HIV-2 integrase: a three-helix bundle stabilized by zinc. Current Biology : Cb. 7: 739-46. PMID 9368756  1
1997 Shadle SE, Allen DF, Guo H, Pogozelski WK, Bashkin JS, Tullius TD. Quantitative analysis of electrophoresis data: Novel curve fitting methodology and its application to the determination of a protein-DNA binding constant Nucleic Acids Research. 25: 850-860. PMID 9016637 DOI: 10.1093/nar/25.4.850  1
1996 Ganunis RM, Guo H, Tullius TD. Effect of the crystallizing agent 2-methyl-2,4-pentanediol on the structure of adenine tract DNA in solution Biochemistry. 35: 13729-13732. PMID 8901514 DOI: 10.1021/bi961880q  1
1996 Draganescu A, Tullius TD. Targeting of nucleic acids by iron complexes. Metal Ions in Biological Systems. 33: 453-84. PMID 8742852  1
1996 Johnson JA, Dixon WJ, Tullius TD. Affinity of CUP2, a copper-dependent transcription factor, for DNA sequences upstream of the yeast metallothionein gene Inorganica Chimica Acta. 242: 233-238.  1
1996 Dixon WJ, Inouye C, Karin M, Tullius TD. CUP2 binds in a bipartite manner to upstream activation sequence c in the promoter of the yeast copper metallothionein gene Journal of Biological Inorganic Chemistry. 1: 451-459.  1
1995 Kuduvalli PN, Townsend CA, Tullius TD. Cleavage by calicheamicin gamma 1I of DNA in a nucleosome formed on the 5S RNA gene of Xenopus borealis. Biochemistry. 34: 3899-906. PMID 7696253  1
1995 Kimball AS, Kimball ML, Jayaram M, Tullius TD. Chemical probe and missing nucleoside analysis of flp recombinase bound to the recombination target sequence Nucleic Acids Research. 23: 3009-3017. PMID 7659525 DOI: 10.1093/nar/23.15.3009  1
1995 Draganescu A, Levin JR, Tullius TD. Homeodomain proteins: what governs their ability to recognize specific DNA sequences? Journal of Molecular Biology. 250: 595-608. PMID 7623378 DOI: 10.1006/jmbi.1995.0401  1
1995 Chatterjee M, Mah SC, Tullius TD, Townsend CA. Role of the aryl iodide in the sequence-selective cleavage of DNA by calicheamicin. Importance of thermodynamic binding vs kinetic activation in the cleavage process Journal of the American Chemical Society. 117: 8074-8082. DOI: 10.1021/ja00136a004  1
1995 Pogozelski WK, McNeese TJ, Tullius TD. What species is responsible for strand scission in the reaction of [FeIIEDTA]2- and H2O2 with DNA? Journal of the American Chemical Society. 117: 6428-6433.  1
1994 Mah SC, Townsend CA, Tullius TD. Hydroxyl radical footprinting of calicheamicin. Relationship of DNA binding to cleavage. Biochemistry. 33: 614-21. PMID 8286393  1
1994 Mah SC, Price MA, Townsend CA, Tullius TD. Features of DNA recognition for oriented binding and cleavage by calicheamicin Tetrahedron. 50: 1361-1378. DOI: 10.1016/S0040-4020(01)80624-4  1
1993 Kimball AS, Lee J, Jayaram M, Tullius TD. Sequence-specific cleavage of DNA via nucleophilic attack of hydrogen peroxide, assisted by Flp recombinase Biochemistry. 32: 4698-4701. PMID 8490015  1
1993 Bashkin J, Hayes JJ, Tullius TD, Wolffe AP. Structure of DNA in a nucleosome core at high salt concentration and at high temperature Biochemistry. 32: 1895-1898. PMID 8383529  1
1992 Hayes JJ, Tullius TD. Structure of the TFIIIA-5 S DNA complex Journal of Molecular Biology. 227: 407-417. PMID 1404361 DOI: 10.1016/0022-2836(92)90897-S  1
1992 Price MA, Tullius TD. Using hydroxyl radical to probe DNA structure Methods in Enzymology. 212: 194-219. PMID 1325598 DOI: 10.1016/0076-6879(92)12013-G  1
1991 Tullius TD. Bioinorganic chemistry Journal of Cellular Biochemistry. 45: 5-6. PMID 1706345  1
1991 Tullius TD. DNA footprinting with the hydroxyl radical Free Radical Research. 13: 521-529. DOI: 10.3109/10715769109145826  1
1991 Tullius TD. The use of chemical probes to analyse DNA and RNA structures Current Opinion in Structural Biology. 1: 428-434. DOI: 10.1016/0959-440X(91)90043-S  1
1991 Nakagawa KH, Inouye C, Hedman B, Karin M, Tullius TD, Hodgson KO. Evidence from EXAFS for a copper cluster in the metalloregulatory protein CUP2 from yeast Journal of the American Chemical Society. 113: 3621-3623.  1
1990 Kimball A, Guo Q, Lu M, Cunningham RP, Kallenbach NR, Seeman NC, Tullius TD. Construction and analysis of parallel and antiparallel Holliday junctions. The Journal of Biological Chemistry. 265: 15348. PMID 2394725  1
1990 Guo Q, Lu M, Churchill ME, Tullius TD, Kallenbach NR. Asymmetric structure of a three-arm DNA junction. Biochemistry. 29: 10927-34. PMID 2176888  1
1990 Hayes JJ, Kam L, Tullius TD. Footprinting protein-DNA complexes with γ-rays Methods in Enzymology. 186: 545-549. PMID 2172714 DOI: 10.1016/0076-6879(90)86148-O  1
1990 Hayes JJ, Tullius TD, Wolffe AP. The structure of DNA in a nucleosome Proceedings of the National Academy of Sciences of the United States of America. 87: 7405-7409. PMID 2170977  1
1990 Buchman C, Skroch P, Dixon W, Tullius TD, Karin M. A single amino acid change in CUP2 alters its mode of DNA binding Molecular and Cellular Biology. 10: 4778-4787. PMID 2167439  1
1990 Churchill ME, Tullius TD, Klug A. Mode of interaction of the zinc finger protein TFIIIA with a 5S RNA gene of Xenopus. Proceedings of the National Academy of Sciences of the United States of America. 87: 5528-32. PMID 2164687  1
1990 Kimball A, Guo Q, Lu M, Cunningham RP, Kallenbach NR, Seeman NC, Tullius TD. Construction and analysis of parallel and antiparallel Holliday junctions. The Journal of Biological Chemistry. 265: 6544-7. PMID 2157702  1
1990 Churchill MEA, Hayes JJ, Tullius TD. Detection of drug binding to DNA by hydroxyl radical footprinting. Relationship of distamycin binding sites to DNA structure and positioned nucleosomes on 5S RNA genes of Xenopus Biochemistry. 29: 6043-6050. PMID 1696501  1
1989 Hayes J, Tullius TD, Wolffe AP. A protein-protein interaction is essential for stable complex formation on a 5 S RNA gene Journal of Biological Chemistry. 264: 6009-6012. PMID 2703476  1
1989 Tullius TD. Physical studies of protein-DNA complexes by footprinting Annual Review of Biophysics and Biophysical Chemistry. 18: 213-237. PMID 2660824  1
1989 Hayes JJ, Tullius TD. The missing nucleoside experiment: A new technique to study recognition of DNA by protein Biochemistry. 28: 9521-9527. PMID 2611245 DOI: 10.1021/bi00450a041  1
1989 Kimball AS, Milman G, Tullius TD. High-resolution footprints of the DNA-binding domain of Epstein-Barr virus nuclear antigen 1 Molecular and Cellular Biology. 9: 2738-2742. PMID 2548088  1
1989 Shafer GE, Price MA, Tullius TD. Use of the hydroxyl radical and gel electrophoresis to study DNA structure Electrophoresis. 10: 397-404. PMID 2504579  1
1988 Churchill ME, Tullius TD, Kallenbach NR, Seeman NC. A Holliday recombination intermediate is twofold symmetric. Proceedings of the National Academy of Sciences of the United States of America. 85: 4653-6. PMID 3387432  1
1988 Burkhoff AM, Tullius TD. Structural details of an adenine tract that does not cause DNA to bend Nature. 331: 455-457. PMID 3340190  1
1988 Chen JH, Churchill ME, Tullius TD, Kallenbach NR, Seeman NC. Construction and analysis of monomobile DNA junctions. Biochemistry. 27: 6032-8. PMID 3191106  1
1988 Vrana KE, Churchill ME, Tullius TD, Brown DD. Mapping functional regions of transcription factor TFIIIA. Molecular and Cellular Biology. 8: 1684-96. PMID 2837652  1
1988 Tullius TD. DNA footprinting with hydroxyl radical Nature. 332: 663-664. PMID 2833707  1
1987 Burkhoff AM, Tullius TD. The unusual conformation adopted by the adenine tracts in kinetoplast DNA Cell. 48: 935-943. PMID 3030560 DOI: 10.1016/0092-8674(87)90702-1  1
1987 Tullius TD, Dombroski BA, Churchill MEA, Kam L. Hydroxyl radical footprinting: A high-resolution method for mapping protein-DNA contacts Methods in Enzymology. 155: 537-558. PMID 2828876  1
1987 Tullius TD. Chemical 'snapshots' of DNA: using the hydroxyl radical to study the structure of DNA and DNA-protein complexes Trends in Biochemical Sciences. 12: 297-300. DOI: 10.1016/0968-0004(87)90145-9  1
1986 Tullius TD, Dombroski BA. Hydroxyl radical 'footprinting': High-resolution information about DNA-protein contacts and application to λ repressor and Cro protein Proceedings of the National Academy of Sciences of the United States of America. 83: 5469-5473. PMID 3090544  1
1985 Tullius TD, Dombroski BA. Iron(II) EDTA used to measure the helical twist along any DNA molecule Science. 230: 679-681. PMID 2996145  1
1985 Frank P, Licht A, Tullius TD, Hodgson KO, Pecht I. A selenomethionine-containing azurin from an auxotroph of Pseudomonas aeruginosa. The Journal of Biological Chemistry. 260: 5518-25. PMID 2985597  1
1982 Tullius TD, Lippard SJ. Ethidium bromide changes the nuclease-sensitive DNA binding sites of the antitumor drug cis-diamminedichloroplatinum(II). Proceedings of the National Academy of Sciences of the United States of America. 79: 3489-92. PMID 6954494 DOI: 10.1073/pnas.79.11.3489  1
1981 Ushay HM, Tullius TD, Lippard SJ. Inhibition of the BamHI cleavage and unwinding of pBR322 deoxyribonucleic acid by the antitumor drug cis-dichlorodiammineplatinum(II). Biochemistry. 20: 3744-8. PMID 6268142 DOI: 10.1021/bi00516a012  1
1981 Tullius TD, Lippard SJ. cis-Diamminedichloroplatinum(II) binds in a unique manner to oligo(dG).oligo(dC) sequences in DNA - a new assay using exonuclease III Journal of the American Chemical Society. 103: 4620-4622. DOI: 10.1021/ja00405a073  1
1981 Tullius TD, Lippard SJ. cis-Diamminedichloroplatinum(II) binds in a unique manner to oligo(dG)·oligo(dC) sequences in DNA - A new assay using exonuclease III Journal of the American Chemical Society. 103: 4620-4622.  1
1980 Tullius TD, Gillum WO, Carlson RMK, Hodgson KO. Structural study of the vanadium complex in living ascidian blood cells by X-ray absorption spectroscopy Journal of the American Chemical Society. 102: 5670-5676.  1
1979 Tullius TD, Kurtz DM, Conradson SD, Hodgson KO. The molybdenum site of xanthine oxidase. Structural evidence from X-ray absorption spectroscopy [30] Journal of the American Chemical Society. 101: 2776-2779.  1
1978 Tullius TD, Frank P, Hodgson KO. Characterization of the blue copper site in oxidized azurin by extended x-ray absorption fine structure: Determination of a short Cu-S distance. Proceedings of the National Academy of Sciences of the United States of America. 75: 4069-73. PMID 16592557  0.64
1977 COLLMAN JP, ROTHROCK RK, SEN JP, TULLIUS TD, HODGSON KO. ChemInform Abstract: MOLECULAR STRUCTURE OF TRANS-BIS(BENZENESELENIDO)(DIFLUORO-3,3′-(TRIMETHYLENEDINITRILO)BIS(2-PENTANONE OXIMATO)BORATE)RHODIUM(III) Chemischer Informationsdienst. 8: no-no. DOI: 10.1002/chin.197705062  0.64
1976 Collman JP, Rothrock RK, Sen JP, Tullius TD, Hodgson KO. Molecular structure of trans-bis(benzeneselenido)[difluoro-3,3'-(trimethylenedinitrilo)bis(2-pentanone oximato)borate]rhodium(III) Inorganic Chemistry. 15: 2947-2948. DOI: 10.1021/ic50165a085  0.64
1976 Collman JP, Rothrock RK, Sen JP, Tullius TD, Hodgson KO. Molecular structure of trans-bis(benzeneselenido)[difluoro-3,3′-(trimethylenedinitrilo)bis(2- pentanone oximato)borate]rhodium(III) Inorganic Chemistry. 15: 2947-2948.  1
1973 Stanley WD, Davies T, Tullius TD, Garner CS. Kinetics of spontaneous thermal reduction of cis-tetraaquodiamminecobalt(III), cis-diaquobis-(trimethylenediamine)cobalt(III) and 1,2,3-triaquo-N-(2-aminoethyl)-1,3-diaminopropanecobalt(III) cations in hot aqueous perchloric acid Journal of Inorganic and Nuclear Chemistry. 35: 3857-3864. DOI: 10.1016/0022-1902(73)80079-X  1
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