DOI: 10.1093/nar/gkt357. Control of DNA minor groove width and Fis protein binding by the purine 2-amino group

Control of DNA minor groove width and Fis protein binding by the purine 2-amino group

10.1093/nar/gkt357

Crossref journal-article

Oxford University Press (OUP)

Nucleic Acids Research (286)

Bibliography

Hancock, S. P., Ghane, T., Cascio, D., Rohs, R., Di Felice, R., & Johnson, R. C. (2013). Control of DNA minor groove width and Fis protein binding by the purine 2-amino group. Nucleic Acids Research, 41(13), 6750â6760.

Authors 6

Stephen P. Hancock (first)
Tahereh Ghane (additional)
Duilio Cascio (additional)
Remo Rohs (additional)
Rosa Di Felice (additional)
Reid C. Johnson (additional)

References 70 Referenced 76

10.1093/nar/29.13.2860 / Nucleic Acids Res. / Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level by Luscombe (2001)
10.1073/pnas.73.3.804 / Proc. Natl Acad. Sci. USA / Sequence-specific recognition of double helical nucleic acids by proteins by Seeman (1976)
10.1038/335321a0 / Nature / Crystal structure of Trp repressor/operator complex at atomic resolution by Otwinowski (1988)
10.1146/annurev-biochem-060408-091030 / Annu. Rev. Biochem. / Origins of specificity in protein-DNA recognition by Rohs (2010)
10.1039/9781847558268-00176 / Protein-Nucleic Acid Interactions by Johnson (2008)
10.1038/287755a0 / Nature / Crystal structure analysis of a complete turn of B-DNA by Wing (1980)
10.1016/j.cell.2007.09.024 / Cell / Functional specificity of a Hox protein mediated by the recognition of minor groove structure by Joshi (2007)
10.1038/nature08473 / Nature / The role of DNA shape in protein-DNA recognition by Rohs (2009)
10.1021/cb200155t / ACS Chem. Biol. / A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA by Bishop (2011)
10.1093/nar/gkr204 / Nucleic Acids Res. / A DNA minor groove electronegative potential genome map based on photo-chemical probing by Lindemose (2011)
10.1016/S0022-2836(03)00529-1 / J. Mol. Biol. / Integration host factor: putting a twist on protein-DNA recognition by Lynch (2003)
10.1073/pnas.1102544108 / Proc. Natl Acad. Sci. USA / Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins by Gordon (2011)
10.1039/9781849735056-00053 / Innovations in Biomolecular Modeling and Simulation by Harris (2012)
10.1126/science.7973627 / Science / Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices by Schumacher (1994)
10.1126/science.271.5253.1247 / Science / Crystal structure of the lactose operon repressor and its complexes with DNA and inducer by Lewis (1996)
10.1016/j.tibs.2012.09.003 / Trends Biochem. Sci. / The high mobility group box: the ultimate utility player of a cell by Malarkey (2012)
10.1126/science.3187531 / Science / Recognition of a DNA operator by the repressor of phage 434: a view at high resolution by Aggarwal (1988)
10.1146/annurev.biophys.31.100901.142129 / Annu. Rev. Biophys. Biomol. Struct. / The papillomavirus E2 proteins: structure, function, and biology by Hegde (2002)
10.1101/gad.1900610 / Genes Dev. / The shape of the DNA minor groove directs binding by the DNA-bending protein Fis by Stella (2010)
10.1016/j.jmb.2009.12.050 / J. Mol. Biol. / Sequence recognition of DNA by protein-induced conformational transitions by Watkins (2010)
10.1111/j.1365-2958.1992.tb02193.x / Mol. Microbiol. / The Fis protein: it's not just for DNA inversion anymore by Finkel (1992)
10.1128/9781555817640.ch5 / The Bacterial Chromosome by Johnson (2005)
10.1016/j.gde.2005.08.006 / Curr. Opin. Genet. Dev. / Bacterial chromatin by Travers (2005)
10.1016/S0065-2164(08)01002-2 / Adv. Appl. Microbiol. / Nucleoid-associated proteins and bacterial physiology by Dorman (2009)
10.1016/j.jmb.2006.09.043 / J. Mol. Biol. / Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein Fis by Skoko (2006)
10.1016/j.jmb.2007.11.101 / J. Mol. Biol. / Functional characterization of the Escherichia coli Fis-DNA binding sequence by Shao (2008)
10.1101/gr.070276.107 / Genome Res. / Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts by Cho (2008)
10.1093/nar/gkq934 / Nucleic Acids Res. / Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli by Kahramanoglou (2011)
10.1093/nar/25.24.4994 / Nucleic Acids Res. / Information analysis of Fis binding sites by Hengen (1997)
10.1038/349178a0 / Nature / Three-dimensional structure of the E. coli DNA-binding protein FIS by Kostrewa (1991)
10.1073/pnas.88.21.9558 / Proc. Natl Acad. Sci. USA / The molecular structure of wild-type and a mutant Fis protein: relationship between mutational changes and recombinational enhancer function or DNA binding by Yuan (1991)
10.1017/S0033583509004752 / Q. Rev. Biophys. / The unique structure of A-tracts and intrinsic DNA bending by Haran (2009)
10.1093/oso/9780198500384.003.0014 / Oxford Handbook of Nucleic Acid Structure by Crothers (1999)
{'key': 'key\n\t\t\t\t20170512092921_gkt357-B34', 'first-page': '1', 'volume-title': 'Oxford Handbook of Nucleic Acid Structure', 'author': 'Dickerson', 'year': '1999'} / Oxford Handbook of Nucleic Acid Structure by Dickerson (1999)
10.1006/jmbi.2001.4994 / J. Mol. Biol. / Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts by Mack (2001)
10.1021/ja045207x / J. Am. Chem. Soc. / High-resolution structure of an extended A-tract: [d(CGCAAATTTGCG)]2 by Woods (2004)
10.1002/bip.10364 / Biopolymers / A unified model for the origin of DNA sequence-directed curvature by Hud (2003)
10.1039/a705982e / Nat. Prod. Rep. / DNA minor-groove recognition by small molecules by Neidle (2001)
10.1093/nar/26.19.4309 / Nucleic Acids Res. / The use of diaminopurine to investigate structural properties of nucleic acids and molecular recognition between ligands and DNA by Bailly (1998)
10.1016/S0959-440X(99)80040-2 / Opin. Struct. Biol. / DNA structure: cations in charge? Curr by McFail-Isom (1999)
10.1146/annurev.biophys.27.1.105 / Annu. Rev. Biophys. Biomol. Struct. / Minor groove-binding architectural proteins: structure, function, and DNA recognition by Bewley (1998)
10.1016/S0959-440X(00)00205-0 / Curr. Opin. Struct. Biol. / DNA-cation interactions: The major and minor grooves are flexible ionophores by Hud (2001)
10.1093/nar/20.20.5457 / Nucleic Acids Res. / Crystal structure of a B-DNA dodecamer containing inosine, d(CGCIAATTCGCG), at 2.4 Å resolution and its comparison with other B-DNA dodecamers by Xuan (1992)
10.1021/bi00056a024 / Biochemistry / Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformational flexibility of B-DNA by Lipanov (1993)
10.1006/jmbi.1996.0669 / J. Mol. Biol. / Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts by Pan (1996)
10.1107/S0021889807021206 / J. Appl. Crystallogr. / Phaser crystallographic software by McCoy (2007)
10.1107/S0907444902016657 / Acta Crystallogr. D Biol. Crystallogr. / PHENIX: building new software for automated crystallographic structure determination by Adams (2002)
10.1107/S0907444996012255 / Acta Crystallogr. D Biol. Crystallogr. / Refinement of macromolecular structures by the maximum-likelihood method by Murshudov (1997)
10.1093/nar/gkg680 / Nucleic Acids Res. / 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures by Lu (2003)
10.1073/pnas.95.19.11163 / Proc. Natl Acad. Sci. USA / DNA sequence-dependent deformability deduced from protein-DNA crystal complexes by Olson (1998)
10.1002/jcc.20289 / J. Comput. Chem. / Scalable molecular dynamics with NAMD by Phillips (2005)
10.1529/biophysj.106.097782 / Biophys. J. / Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers by Perez (2007)
10.1016/S0006-3495(01)76028-6 / Biophys. J. / Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine by Stefl (2001)
10.1093/nar/29.12.2522 / Nucleic Acids Res. / The effect of amino groups on the stability of DNA duplexes and triplexes based on purines derived from inosine by Cubero (2001)
10.1063/1.445869 / J. Chem. Phys. / Comparison of simple potential functions for simulating liquid water by Jorgensen (1983)
10.1080/07391102.1989.10507728 / J. Biomol. Struct. Dynam. / Defining the structure of irregular nucleic acids: conventions and principles by Lavery (1989)
10.1021/jp304818s / J. Phys. Chem. B / Optical properties of triplex DNA from time-dependent density functional theory by Ghane (2012)
10.1016/0021-9991(77)90098-5 / J. Comput. Phys. / Numerical-integration of cartesian equations of motion of a system with constraints—molecular-dynamics of N-alkanes by Ryckaert (1977)
10.1063/1.448118 / J. Chem. Phys. / Molecular-dynamics with coupling to an external bath by Berendsen (1984)
10.1016/j.jmb.2008.04.075 / J. Mol. Biol. / Biochemical identification of base and phosphate contacts between Fis and a high-affinity DNA binding site by Shao (2008)
10.1021/bi701826f / Biochemistry / P22 c2 repressor-operator complex: mechanisms of direct and indirect readout by Watkins (2008)
10.1038/355089a0 / Nature / DNA twisting and the effects of non-contacted bases on affinity of 434 operator for 434 repressor by Koudelka (1992)
10.1074/jbc.M004541200 / J. Biol. Chem. / The structural basis of DNA target discrimination by papillomavirus E2 proteins by Kim (2000)
10.1074/jbc.M212667200 / J. Biol. Chem. / The role of the minor groove substituents in indirect readout of DNA sequence by 434 repressor by Mauro (2003)
10.1146/annurev.biophys.29.1.497 / Annu. Rev. Biophys. Biomol. Struct. / Electrostatic mechanisms of DNA deformation by Williams (2000)
10.1016/0022-2836(91)90619-H / J. Mol. Biol. / Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G by Prive (1991)
10.1073/pnas.97.2.629 / Proc. Natl Acad. Sci. USA / Sequence-specific binding of counterions to B-DNA by Denisov (2000)
10.1021/ja0753546 / J. Am. Chem Soc. / Dynamics of B-DNA on the microsecond time scale by Pérez (2007)
10.1093/nar/gkf472 / Nucleic Acids Res. / Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies by Hamelberg (2002)
10.1093/nar/gkn082 / Nucleic Acids Res. / Towards a molecular dynamics consensus view of B-DNA flexibility by Pérez (2008)

Dates

Type	When
Created	12 years, 3 months ago (May 9, 2013, 10:55 p.m.)
Deposited	1 year, 3 months ago (May 10, 2024, 8:18 a.m.)
Indexed	3 months ago (June 4, 2025, 5:31 a.m.)
Issued	12 years, 3 months ago (May 9, 2013)
Published	12 years, 3 months ago (May 9, 2013)
Published Online	12 years, 3 months ago (May 9, 2013)
Published Print	12 years, 2 months ago (July 1, 2013)

Funders 0

None

BibTeX

@article{Hancock_2013, title={Control of DNA minor groove width and Fis protein binding by the purine 2-amino group}, volume={41}, ISSN={0305-1048}, url={http://dx.doi.org/10.1093/nar/gkt357}, DOI={10.1093/nar/gkt357}, number={13}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Hancock, Stephen P. and Ghane, Tahereh and Cascio, Duilio and Rohs, Remo and Di Felice, Rosa and Johnson, Reid C.}, year={2013}, month=may, pages={6750–6760} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        6,
        4
      ]
    ],
    "date-time": "2025-06-04T09:31:33Z",
    "timestamp": 1749029493989
  },
  "reference-count": 70,
  "publisher": "Oxford University Press (OUP)",
  "issue": "13",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2016,
            10,
            4
          ]
        ],
        "date-time": "2016-10-04T00:00:00Z",
        "timestamp": 1475539200000
      },
      "content-version": "vor",
      "delay-in-days": 1244,
      "URL": "http://creativecommons.org/licenses/by/3.0/"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2013,
        7
      ]
    ]
  },
  "DOI": "10.1093/nar/gkt357",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2013,
        5,
        10
      ]
    ],
    "date-time": "2013-05-10T02:55:05Z",
    "timestamp": 1368154505000
  },
  "page": "6750-6760",
  "source": "Crossref",
  "is-referenced-by-count": 76,
  "title": "Control of DNA minor groove width and Fis protein binding by the purine 2-amino group",
  "prefix": "10.1093",
  "volume": "41",
  "author": [
    {
      "given": "Stephen P.",
      "family": "Hancock",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "Tahereh",
      "family": "Ghane",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Duilio",
      "family": "Cascio",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Remo",
      "family": "Rohs",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Rosa",
      "family": "Di Felice",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "Reid C.",
      "family": "Johnson",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "286",
  "published-online": {
    "date-parts": [
      [
        2013,
        5,
        9
      ]
    ]
  },
  "reference": [
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B1",
      "doi-asserted-by": "crossref",
      "first-page": "2860",
      "DOI": "10.1093/nar/29.13.2860",
      "article-title": "Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level",
      "volume": "29",
      "author": "Luscombe",
      "year": "2001",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B2",
      "doi-asserted-by": "crossref",
      "first-page": "804",
      "DOI": "10.1073/pnas.73.3.804",
      "article-title": "Sequence-specific recognition of double helical nucleic acids by proteins",
      "volume": "73",
      "author": "Seeman",
      "year": "1976",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B3",
      "doi-asserted-by": "crossref",
      "first-page": "321",
      "DOI": "10.1038/335321a0",
      "article-title": "Crystal structure of Trp repressor/operator complex at atomic resolution",
      "volume": "335",
      "author": "Otwinowski",
      "year": "1988",
      "journal-title": "Nature"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B4",
      "doi-asserted-by": "crossref",
      "first-page": "233",
      "DOI": "10.1146/annurev-biochem-060408-091030",
      "article-title": "Origins of specificity in protein-DNA recognition",
      "volume": "79",
      "author": "Rohs",
      "year": "2010",
      "journal-title": "Annu. Rev. Biochem."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B5",
      "doi-asserted-by": "crossref",
      "first-page": "176",
      "DOI": "10.1039/9781847558268-00176",
      "volume-title": "Protein-Nucleic Acid Interactions",
      "author": "Johnson",
      "year": "2008"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B6",
      "doi-asserted-by": "crossref",
      "first-page": "755",
      "DOI": "10.1038/287755a0",
      "article-title": "Crystal structure analysis of a complete turn of B-DNA",
      "volume": "287",
      "author": "Wing",
      "year": "1980",
      "journal-title": "Nature"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B7",
      "doi-asserted-by": "crossref",
      "first-page": "530",
      "DOI": "10.1016/j.cell.2007.09.024",
      "article-title": "Functional specificity of a Hox protein mediated by the recognition of minor groove structure",
      "volume": "131",
      "author": "Joshi",
      "year": "2007",
      "journal-title": "Cell"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B8",
      "doi-asserted-by": "crossref",
      "first-page": "1248",
      "DOI": "10.1038/nature08473",
      "article-title": "The role of DNA shape in protein-DNA recognition",
      "volume": "461",
      "author": "Rohs",
      "year": "2009",
      "journal-title": "Nature"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B9",
      "doi-asserted-by": "crossref",
      "first-page": "1314",
      "DOI": "10.1021/cb200155t",
      "article-title": "A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA",
      "volume": "6",
      "author": "Bishop",
      "year": "2011",
      "journal-title": "ACS Chem. Biol."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B10",
      "doi-asserted-by": "crossref",
      "first-page": "6269",
      "DOI": "10.1093/nar/gkr204",
      "article-title": "A DNA minor groove electronegative potential genome map based on photo-chemical probing",
      "volume": "39",
      "author": "Lindemose",
      "year": "2011",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B11",
      "doi-asserted-by": "crossref",
      "first-page": "493",
      "DOI": "10.1016/S0022-2836(03)00529-1",
      "article-title": "Integration host factor: putting a twist on protein-DNA recognition",
      "volume": "330",
      "author": "Lynch",
      "year": "2003",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B12",
      "doi-asserted-by": "crossref",
      "first-page": "10690",
      "DOI": "10.1073/pnas.1102544108",
      "article-title": "Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins",
      "volume": "108",
      "author": "Gordon",
      "year": "2011",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B13",
      "doi-asserted-by": "crossref",
      "first-page": "53",
      "DOI": "10.1039/9781849735056-00053",
      "volume-title": "Innovations in Biomolecular Modeling and Simulation",
      "author": "Harris",
      "year": "2012"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B14",
      "doi-asserted-by": "crossref",
      "first-page": "763",
      "DOI": "10.1126/science.7973627",
      "article-title": "Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices",
      "volume": "266",
      "author": "Schumacher",
      "year": "1994",
      "journal-title": "Science"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B15",
      "doi-asserted-by": "crossref",
      "first-page": "1247",
      "DOI": "10.1126/science.271.5253.1247",
      "article-title": "Crystal structure of the lactose operon repressor and its complexes with DNA and inducer",
      "volume": "271",
      "author": "Lewis",
      "year": "1996",
      "journal-title": "Science"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B16",
      "doi-asserted-by": "crossref",
      "first-page": "553",
      "DOI": "10.1016/j.tibs.2012.09.003",
      "article-title": "The high mobility group box: the ultimate utility player of a cell",
      "volume": "37",
      "author": "Malarkey",
      "year": "2012",
      "journal-title": "Trends Biochem. Sci."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B17",
      "doi-asserted-by": "crossref",
      "first-page": "899",
      "DOI": "10.1126/science.3187531",
      "article-title": "Recognition of a DNA operator by the repressor of phage 434: a view at high resolution",
      "volume": "242",
      "author": "Aggarwal",
      "year": "1988",
      "journal-title": "Science"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B18",
      "doi-asserted-by": "crossref",
      "first-page": "343",
      "DOI": "10.1146/annurev.biophys.31.100901.142129",
      "article-title": "The papillomavirus E2 proteins: structure, function, and biology",
      "volume": "31",
      "author": "Hegde",
      "year": "2002",
      "journal-title": "Annu. Rev. Biophys. Biomol. Struct."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B19",
      "doi-asserted-by": "crossref",
      "first-page": "814",
      "DOI": "10.1101/gad.1900610",
      "article-title": "The shape of the DNA minor groove directs binding by the DNA-bending protein Fis",
      "volume": "24",
      "author": "Stella",
      "year": "2010",
      "journal-title": "Genes Dev."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B20",
      "doi-asserted-by": "crossref",
      "first-page": "1145",
      "DOI": "10.1016/j.jmb.2009.12.050",
      "article-title": "Sequence recognition of DNA by protein-induced conformational transitions",
      "volume": "396",
      "author": "Watkins",
      "year": "2010",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B21",
      "doi-asserted-by": "crossref",
      "first-page": "3257",
      "DOI": "10.1111/j.1365-2958.1992.tb02193.x",
      "article-title": "The Fis protein: it's not just for DNA inversion anymore",
      "volume": "6",
      "author": "Finkel",
      "year": "1992",
      "journal-title": "Mol. Microbiol."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B22",
      "doi-asserted-by": "crossref",
      "first-page": "65",
      "DOI": "10.1128/9781555817640.ch5",
      "volume-title": "The Bacterial Chromosome",
      "author": "Johnson",
      "year": "2005"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B23",
      "doi-asserted-by": "crossref",
      "first-page": "507",
      "DOI": "10.1016/j.gde.2005.08.006",
      "article-title": "Bacterial chromatin",
      "volume": "15",
      "author": "Travers",
      "year": "2005",
      "journal-title": "Curr. Opin. Genet. Dev."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B24",
      "doi-asserted-by": "crossref",
      "first-page": "47",
      "DOI": "10.1016/S0065-2164(08)01002-2",
      "article-title": "Nucleoid-associated proteins and bacterial physiology",
      "volume": "67",
      "author": "Dorman",
      "year": "2009",
      "journal-title": "Adv. Appl. Microbiol."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B25",
      "doi-asserted-by": "crossref",
      "first-page": "777",
      "DOI": "10.1016/j.jmb.2006.09.043",
      "article-title": "Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein Fis",
      "volume": "364",
      "author": "Skoko",
      "year": "2006",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B26",
      "doi-asserted-by": "crossref",
      "first-page": "771",
      "DOI": "10.1016/j.jmb.2007.11.101",
      "article-title": "Functional characterization of the Escherichia coli Fis-DNA binding sequence",
      "volume": "376",
      "author": "Shao",
      "year": "2008",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B27",
      "doi-asserted-by": "crossref",
      "first-page": "900",
      "DOI": "10.1101/gr.070276.107",
      "article-title": "Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts",
      "volume": "18",
      "author": "Cho",
      "year": "2008",
      "journal-title": "Genome Res."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B28",
      "doi-asserted-by": "crossref",
      "first-page": "2073",
      "DOI": "10.1093/nar/gkq934",
      "article-title": "Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli",
      "volume": "39",
      "author": "Kahramanoglou",
      "year": "2011",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B29",
      "doi-asserted-by": "crossref",
      "first-page": "4994",
      "DOI": "10.1093/nar/25.24.4994",
      "article-title": "Information analysis of Fis binding sites",
      "volume": "25",
      "author": "Hengen",
      "year": "1997",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B30",
      "doi-asserted-by": "crossref",
      "first-page": "178",
      "DOI": "10.1038/349178a0",
      "article-title": "Three-dimensional structure of the E. coli DNA-binding protein FIS",
      "volume": "349",
      "author": "Kostrewa",
      "year": "1991",
      "journal-title": "Nature"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B31",
      "doi-asserted-by": "crossref",
      "first-page": "9558",
      "DOI": "10.1073/pnas.88.21.9558",
      "article-title": "The molecular structure of wild-type and a mutant Fis protein: relationship between mutational changes and recombinational enhancer function or DNA binding",
      "volume": "88",
      "author": "Yuan",
      "year": "1991",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B32",
      "doi-asserted-by": "crossref",
      "first-page": "41",
      "DOI": "10.1017/S0033583509004752",
      "article-title": "The unique structure of A-tracts and intrinsic DNA bending",
      "volume": "42",
      "author": "Haran",
      "year": "2009",
      "journal-title": "Q. Rev. Biophys."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B33",
      "doi-asserted-by": "crossref",
      "first-page": "455",
      "DOI": "10.1093/oso/9780198500384.003.0014",
      "volume-title": "Oxford Handbook of Nucleic Acid Structure",
      "author": "Crothers",
      "year": "1999"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B34",
      "first-page": "1",
      "volume-title": "Oxford Handbook of Nucleic Acid Structure",
      "author": "Dickerson",
      "year": "1999"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B35",
      "doi-asserted-by": "crossref",
      "first-page": "1037",
      "DOI": "10.1006/jmbi.2001.4994",
      "article-title": "Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts",
      "volume": "312",
      "author": "Mack",
      "year": "2001",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B36",
      "doi-asserted-by": "crossref",
      "first-page": "15330",
      "DOI": "10.1021/ja045207x",
      "article-title": "High-resolution structure of an extended A-tract: [d(CGCAAATTTGCG)]2",
      "volume": "126",
      "author": "Woods",
      "year": "2004",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B37",
      "doi-asserted-by": "crossref",
      "first-page": "144",
      "DOI": "10.1002/bip.10364",
      "article-title": "A unified model for the origin of DNA sequence-directed curvature",
      "volume": "69",
      "author": "Hud",
      "year": "2003",
      "journal-title": "Biopolymers"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B38",
      "doi-asserted-by": "crossref",
      "first-page": "291",
      "DOI": "10.1039/a705982e",
      "article-title": "DNA minor-groove recognition by small molecules",
      "volume": "18",
      "author": "Neidle",
      "year": "2001",
      "journal-title": "Nat. Prod. Rep."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B39",
      "doi-asserted-by": "crossref",
      "first-page": "4309",
      "DOI": "10.1093/nar/26.19.4309",
      "article-title": "The use of diaminopurine to investigate structural properties of nucleic acids and molecular recognition between ligands and DNA",
      "volume": "26",
      "author": "Bailly",
      "year": "1998",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B40",
      "doi-asserted-by": "crossref",
      "first-page": "298",
      "DOI": "10.1016/S0959-440X(99)80040-2",
      "article-title": "DNA structure: cations in charge? Curr",
      "volume": "9",
      "author": "McFail-Isom",
      "year": "1999",
      "journal-title": "Opin. Struct. Biol."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B41",
      "doi-asserted-by": "crossref",
      "first-page": "105",
      "DOI": "10.1146/annurev.biophys.27.1.105",
      "article-title": "Minor groove-binding architectural proteins: structure, function, and DNA recognition",
      "volume": "27",
      "author": "Bewley",
      "year": "1998",
      "journal-title": "Annu. Rev. Biophys. Biomol. Struct."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B42",
      "doi-asserted-by": "crossref",
      "first-page": "293",
      "DOI": "10.1016/S0959-440X(00)00205-0",
      "article-title": "DNA-cation interactions: The major and minor grooves are flexible ionophores",
      "volume": "11",
      "author": "Hud",
      "year": "2001",
      "journal-title": "Curr. Opin. Struct. Biol."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B43",
      "doi-asserted-by": "crossref",
      "first-page": "5457",
      "DOI": "10.1093/nar/20.20.5457",
      "article-title": "Crystal structure of a B-DNA dodecamer containing inosine, d(CGCIAATTCGCG), at 2.4 \u00c5 resolution and its comparison with other B-DNA dodecamers",
      "volume": "20",
      "author": "Xuan",
      "year": "1992",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B44",
      "doi-asserted-by": "crossref",
      "first-page": "1373",
      "DOI": "10.1021/bi00056a024",
      "article-title": "Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformational flexibility of B-DNA",
      "volume": "32",
      "author": "Lipanov",
      "year": "1993",
      "journal-title": "Biochemistry"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B45",
      "doi-asserted-by": "crossref",
      "first-page": "675",
      "DOI": "10.1006/jmbi.1996.0669",
      "article-title": "Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts",
      "volume": "264",
      "author": "Pan",
      "year": "1996",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B46",
      "doi-asserted-by": "crossref",
      "first-page": "658",
      "DOI": "10.1107/S0021889807021206",
      "article-title": "Phaser crystallographic software",
      "volume": "40",
      "author": "McCoy",
      "year": "2007",
      "journal-title": "J. Appl. Crystallogr."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B47",
      "doi-asserted-by": "crossref",
      "first-page": "1948",
      "DOI": "10.1107/S0907444902016657",
      "article-title": "PHENIX: building new software for automated crystallographic structure determination",
      "volume": "58",
      "author": "Adams",
      "year": "2002",
      "journal-title": "Acta Crystallogr. D Biol. Crystallogr."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B48",
      "doi-asserted-by": "crossref",
      "first-page": "240",
      "DOI": "10.1107/S0907444996012255",
      "article-title": "Refinement of macromolecular structures by the maximum-likelihood method",
      "volume": "53",
      "author": "Murshudov",
      "year": "1997",
      "journal-title": "Acta Crystallogr. D Biol. Crystallogr."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B49",
      "doi-asserted-by": "crossref",
      "first-page": "5108",
      "DOI": "10.1093/nar/gkg680",
      "article-title": "3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures",
      "volume": "31",
      "author": "Lu",
      "year": "2003",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B50",
      "doi-asserted-by": "crossref",
      "first-page": "11163",
      "DOI": "10.1073/pnas.95.19.11163",
      "article-title": "DNA sequence-dependent deformability deduced from protein-DNA crystal complexes",
      "volume": "95",
      "author": "Olson",
      "year": "1998",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B51",
      "doi-asserted-by": "crossref",
      "first-page": "1781",
      "DOI": "10.1002/jcc.20289",
      "article-title": "Scalable molecular dynamics with NAMD",
      "volume": "26",
      "author": "Phillips",
      "year": "2005",
      "journal-title": "J. Comput. Chem."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B52",
      "doi-asserted-by": "crossref",
      "first-page": "3817",
      "DOI": "10.1529/biophysj.106.097782",
      "article-title": "Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers",
      "volume": "92",
      "author": "Perez",
      "year": "2007",
      "journal-title": "Biophys. J."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B53",
      "doi-asserted-by": "crossref",
      "first-page": "455",
      "DOI": "10.1016/S0006-3495(01)76028-6",
      "article-title": "Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine",
      "volume": "80",
      "author": "Stefl",
      "year": "2001",
      "journal-title": "Biophys. J."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B54",
      "doi-asserted-by": "crossref",
      "first-page": "2522",
      "DOI": "10.1093/nar/29.12.2522",
      "article-title": "The effect of amino groups on the stability of DNA duplexes and triplexes based on purines derived from inosine",
      "volume": "29",
      "author": "Cubero",
      "year": "2001",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B55",
      "doi-asserted-by": "crossref",
      "first-page": "926",
      "DOI": "10.1063/1.445869",
      "article-title": "Comparison of simple potential functions for simulating liquid water",
      "volume": "79",
      "author": "Jorgensen",
      "year": "1983",
      "journal-title": "J. Chem. Phys."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B56",
      "doi-asserted-by": "crossref",
      "first-page": "655",
      "DOI": "10.1080/07391102.1989.10507728",
      "article-title": "Defining the structure of irregular nucleic acids: conventions and principles",
      "volume": "6",
      "author": "Lavery",
      "year": "1989",
      "journal-title": "J. Biomol. Struct. Dynam."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B57",
      "doi-asserted-by": "crossref",
      "first-page": "10693",
      "DOI": "10.1021/jp304818s",
      "article-title": "Optical properties of triplex DNA from time-dependent density functional theory",
      "volume": "116",
      "author": "Ghane",
      "year": "2012",
      "journal-title": "J. Phys. Chem. B"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B58",
      "doi-asserted-by": "crossref",
      "first-page": "327",
      "DOI": "10.1016/0021-9991(77)90098-5",
      "article-title": "Numerical-integration of cartesian equations of motion of a system with constraints\u2014molecular-dynamics of N-alkanes",
      "volume": "23",
      "author": "Ryckaert",
      "year": "1977",
      "journal-title": "J. Comput. Phys."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B59",
      "doi-asserted-by": "crossref",
      "first-page": "3684",
      "DOI": "10.1063/1.448118",
      "article-title": "Molecular-dynamics with coupling to an external bath",
      "volume": "81",
      "author": "Berendsen",
      "year": "1984",
      "journal-title": "J. Chem. Phys."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B60",
      "doi-asserted-by": "crossref",
      "first-page": "327",
      "DOI": "10.1016/j.jmb.2008.04.075",
      "article-title": "Biochemical identification of base and phosphate contacts between Fis and a high-affinity DNA binding site",
      "volume": "380",
      "author": "Shao",
      "year": "2008",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B61",
      "doi-asserted-by": "crossref",
      "first-page": "2325",
      "DOI": "10.1021/bi701826f",
      "article-title": "P22 c2 repressor-operator complex: mechanisms of direct and indirect readout",
      "volume": "47",
      "author": "Watkins",
      "year": "2008",
      "journal-title": "Biochemistry"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B62",
      "doi-asserted-by": "crossref",
      "first-page": "89",
      "DOI": "10.1038/355089a0",
      "article-title": "DNA twisting and the effects of non-contacted bases on affinity of 434 operator for 434 repressor",
      "volume": "355",
      "author": "Koudelka",
      "year": "1992",
      "journal-title": "Nature"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B63",
      "doi-asserted-by": "crossref",
      "first-page": "31245",
      "DOI": "10.1074/jbc.M004541200",
      "article-title": "The structural basis of DNA target discrimination by papillomavirus E2 proteins",
      "volume": "275",
      "author": "Kim",
      "year": "2000",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B64",
      "doi-asserted-by": "crossref",
      "first-page": "12955",
      "DOI": "10.1074/jbc.M212667200",
      "article-title": "The role of the minor groove substituents in indirect readout of DNA sequence by 434 repressor",
      "volume": "278",
      "author": "Mauro",
      "year": "2003",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B65",
      "doi-asserted-by": "crossref",
      "first-page": "497",
      "DOI": "10.1146/annurev.biophys.29.1.497",
      "article-title": "Electrostatic mechanisms of DNA deformation",
      "volume": "29",
      "author": "Williams",
      "year": "2000",
      "journal-title": "Annu. Rev. Biophys. Biomol. Struct."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B66",
      "doi-asserted-by": "crossref",
      "first-page": "177",
      "DOI": "10.1016/0022-2836(91)90619-H",
      "article-title": "Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G",
      "volume": "217",
      "author": "Prive",
      "year": "1991",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B67",
      "doi-asserted-by": "crossref",
      "first-page": "629",
      "DOI": "10.1073/pnas.97.2.629",
      "article-title": "Sequence-specific binding of counterions to B-DNA",
      "volume": "97",
      "author": "Denisov",
      "year": "2000",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B68",
      "doi-asserted-by": "crossref",
      "first-page": "14739",
      "DOI": "10.1021/ja0753546",
      "article-title": "Dynamics of B-DNA on the microsecond time scale",
      "volume": "129",
      "author": "P\u00e9rez",
      "year": "2007",
      "journal-title": "J. Am. Chem Soc."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B69",
      "doi-asserted-by": "crossref",
      "first-page": "3615",
      "DOI": "10.1093/nar/gkf472",
      "article-title": "Effect of a neutralized phosphate backbone on the minor groove of B-DNA: molecular dynamics simulation studies",
      "volume": "30",
      "author": "Hamelberg",
      "year": "2002",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "key\n\t\t\t\t20170512092921_gkt357-B70",
      "doi-asserted-by": "crossref",
      "first-page": "2379",
      "DOI": "10.1093/nar/gkn082",
      "article-title": "Towards a molecular dynamics consensus view of B-DNA flexibility",
      "volume": "36",
      "author": "P\u00e9rez",
      "year": "2008",
      "journal-title": "Nucleic Acids Res."
    }
  ],
  "container-title": "Nucleic Acids Research",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "http://academic.oup.com/nar/article-pdf/41/13/6750/16947887/gkt357.pdf",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2024,
        5,
        10
      ]
    ],
    "date-time": "2024-05-10T12:18:18Z",
    "timestamp": 1715343498000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkt357"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2013,
        5,
        9
      ]
    ]
  },
  "references-count": 70,
  "journal-issue": {
    "issue": "13",
    "published-online": {
      "date-parts": [
        [
          2013,
          5,
          9
        ]
      ]
    },
    "published-print": {
      "date-parts": [
        [
          2013,
          7
        ]
      ]
    }
  },
  "URL": "http://dx.doi.org/10.1093/nar/gkt357",
  "relation": {},
  "ISSN": [
    "1362-4962",
    "0305-1048"
  ],
  "subject": [],
  "published": {
    "date-parts": [
      [
        2013,
        5,
        9
      ]
    ]
  }
}