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Neidle S. Crystallographic insights into DNA minor groove recognition by drugs. Biopolymers. 44:1997;105-121.
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Hurley LH, Chaires JB. Advances in DNA Sequence Specific Agents. 2:1996;JAI Press Inc, Greenwich, Connecticut.
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Design of peptides that bind in the minor groove of DNA at 5'-(A,T)G(A,T)C(A,T)-3' sequences by a dimeric side-by-side motif
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Wade WS, Mrksich M, Devan PB. Design of peptides that bind in the minor groove of DNA at 5'-(A,T)G(A,T)C(A,T)-3' sequences by a dimeric side-by-side motif. J Am Chem Soc. 114:1996;8783-8794.
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Wade, W.S.1
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Devan, P.B.3
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9
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0030059085
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Solid phase synthesis of polyamides containing imidazole and pyrrole aminol acids
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Baird EE, Dervan PB. Solid phase synthesis of polyamides containing imidazole and pyrrole aminol acids. J Am Chem Soc. 118:1996;6141-6146.
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Baird, E.E.1
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10
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0030567754
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Optimization of the hairpin polyamide design for recognition of the minor groove of DNA
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Parks ME, Baird EE, Dervan PB. Optimization of the hairpin polyamide design for recognition of the minor groove of DNA. J Am Chem Soc. 118:1996;6147-6152.
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Parks, M.E.1
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11
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0030567759
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Extension of sequence-specific recognition in the minor groove of DNA by pyrrole-imidazole polyamides to 9-13 base pairs
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Trauger JW, Baird EE, Mrksich M, Dervan PB. Extension of sequence-specific recognition in the minor groove of DNA by pyrrole-imidazole polyamides to 9-13 base pairs. J Am Chem Soc. 118:1996;6160-6166.
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Trauger, J.W.1
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Mrksich, M.3
Dervan, P.B.4
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Recognition of DNA by designed ligands at subnanomolar concentrations
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Trauger JW, Baird EE, Dervan PB. Recognition of DNA by designed ligands at subnanomolar concentrations. Nature. 382:1996;559-561.
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Nature
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Trauger, J.W.1
Baird, E.E.2
Dervan, P.B.3
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13
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0029776688
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Binding of a hairpin polyamide in the minor groove of DNA: Sequence specific enthalpic discrimination
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Pilch DS, Poklar N, Gelfand CA, Law SM, Breslauer KJ, Baird EE, Dervan PB. Binding of a hairpin polyamide in the minor groove of DNA: sequence specific enthalpic discrimination. Proc Natl Acad Sci USA. 93:1996;8306-8311.
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Pilch, D.S.1
Poklar, N.2
Gelfand, C.A.3
Law, S.M.4
Breslauer, K.J.5
Baird, E.E.6
Dervan, P.B.7
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14
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0030745572
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Discrimination of 5'-GGGG-3', 5'-GCGC-3', and 5'-GGCC-3' sequences in the minor groove of DNA by eight-ring hairpin polyamides
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Swalley SE, Baird EE, Dervan PB. Discrimination of 5'-GGGG-3', 5'-GCGC-3', and 5'-GGCC-3' sequences in the minor groove of DNA by eight-ring hairpin polyamides. J Am Chem Soc. 119:1997;6953-6961.
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J Am Chem Soc
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Swalley, S.E.1
Baird, E.E.2
Dervan, P.B.3
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15
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0030953342
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Recognition of seven base pair sequences in the minor groove of DNA by ten-ring pyrrole-imidazole polyamide hairpins
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Turner JM, Baird EE, Dervan PB. Recognition of seven base pair sequences in the minor groove of DNA by ten-ring pyrrole-imidazole polyamide hairpins. J Am Chem Soc. 119:1997;7636-7644.
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J Am Chem Soc
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Turner, J.M.1
Baird, E.E.2
Dervan, P.B.3
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16
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0030813474
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Orientation preferences of pyrrole-imidazole polyamides in the minor groove of DNA
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White S, Baird EE, Dervan PB. Orientation preferences of pyrrole-imidazole polyamides in the minor groove of DNA. J Am Chem Soc. 119:1997;8756-8765.
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J Am Chem Soc
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White, S.1
Baird, E.E.2
Dervan, P.B.3
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17
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0030758956
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NMR characterization of hairpin polyamide complexed with the minor groove of DNA
-
of outstanding interest. This paper reports the first high-resolution structure of a hairpin polyamide complexed with DNA.
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Pelaez R, de Clairac L, Geierstanger BH, Mrksich M, Dervan PB, Wemmer DE. NMR characterization of hairpin polyamide complexed with the minor groove of DNA. of outstanding interest J Am Chem Soc. 119:1997;7909-7916 This paper reports the first high-resolution structure of a hairpin polyamide complexed with DNA.
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J Am Chem Soc
, vol.119
, pp. 7909-7916
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Pelaez, R.1
De Clairac, L.2
Geierstanger, B.H.3
Mrksich, M.4
Dervan, P.B.5
Wemmer, D.E.6
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18
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0030951207
-
Regulation of gene expression by small molecules
-
of outstanding interest. A triumph in the structure-based design of DNA-binding agents is described. A hairpin polyamide that was designed to bind to the transcription factor IIIA binding site was shown to readily permeate cells, enter the nucleus, and specifically inhibit the expression of the 5S RNA gene. This success reveals the outstanding potential of the hairpin polyamides as economical regulators of gene expression.
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Gottesfeld JM, Neely L, Trauger JW, Baird EE, Dervan PB. Regulation of gene expression by small molecules. of outstanding interest Nature. 387:1997;202-205 A triumph in the structure-based design of DNA-binding agents is described. A hairpin polyamide that was designed to bind to the transcription factor IIIA binding site was shown to readily permeate cells, enter the nucleus, and specifically inhibit the expression of the 5S RNA gene. This success reveals the outstanding potential of the hairpin polyamides as economical regulators of gene expression.
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(1997)
Nature
, vol.387
, pp. 202-205
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Gottesfeld, J.M.1
Neely, L.2
Trauger, J.W.3
Baird, E.E.4
Dervan, P.B.5
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19
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0031045487
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Structure-based design of a new bisintercalating anthracycline antibiotic
-
of outstanding interest. A structure-based design strategy for the production of a new type of bisintercalator is described and shown to succeed. A bisanthracycline antibiotic was produced with an ultratight DNA-binding affinity, and interesting, if unexpected, biological activity.
-
Chaires JB, Leng F, Przewloka T, Fokt I, Ling YH, Perez-Soler R, Priebe W. Structure-based design of a new bisintercalating anthracycline antibiotic. of outstanding interest J Med Chem. 40:1997;261-266 A structure-based design strategy for the production of a new type of bisintercalator is described and shown to succeed. A bisanthracycline antibiotic was produced with an ultratight DNA-binding affinity, and interesting, if unexpected, biological activity.
-
(1997)
J Med Chem
, vol.40
, pp. 261-266
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-
Chaires, J.B.1
Leng, F.2
Przewloka, T.3
Fokt, I.4
Ling, Y.H.5
Perez-Soler, R.6
Priebe, W.7
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20
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0032539641
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Ultratight DNA binding of a new bisintercalating anthracycline antibiotic
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Leng F, Priebe W, Chaires JB. Ultratight DNA binding of a new bisintercalating anthracycline antibiotic. Biochemistry. 37:1998;1743-1753.
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(1998)
Biochemistry
, vol.37
, pp. 1743-1753
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Leng, F.1
Priebe, W.2
Chaires, J.B.3
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21
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0030958485
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Structure of a DNA-bisdaunomycin complex
-
of outstanding interest. The high-resolution structure of a new type of bisintercalator bound to DNA is reported, revealing details of an interaction that will permit structure-based optimization of the linker design.
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Hu GG, Shui X, Leng F, Priebe W, Chaires JB, Williams LD. Structure of a DNA-bisdaunomycin complex. of outstanding interest Biochemistry. 36:1997;5940-5946 The high-resolution structure of a new type of bisintercalator bound to DNA is reported, revealing details of an interaction that will permit structure-based optimization of the linker design.
-
(1997)
Biochemistry
, vol.36
, pp. 5940-5946
-
-
Hu, G.G.1
Shui, X.2
Leng, F.3
Priebe, W.4
Chaires, J.B.5
Williams, L.D.6
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22
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0030840016
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Binding of two novel bisdaunorubicins to DNA studied by NMR spectroscopy
-
of outstanding interest. The solution structures of two new bisintercalators bound to DNA are described. A comparison of the two complexes shows the dramatic effect of subtle changes in the linker geometry.
-
Robinson H, Priebe W, Chaires JB, Wang AH. Binding of two novel bisdaunorubicins to DNA studied by NMR spectroscopy. of outstanding interest Biochemistry. 36:1997;8663-8670 The solution structures of two new bisintercalators bound to DNA are described. A comparison of the two complexes shows the dramatic effect of subtle changes in the linker geometry.
-
(1997)
Biochemistry
, vol.36
, pp. 8663-8670
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-
Robinson, H.1
Priebe, W.2
Chaires, J.B.3
Wang, A.H.4
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23
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0030805823
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A new class of polyintercalating molecules
-
of special interest. An interesting series of new polyintercalating molecules is described, including the first reported tetraintercalator.
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Lokey RS, Kwok Y, Guelev V, Pursell CJ, Hurley LH, Iverson BL. A new class of polyintercalating molecules. of special interest J Am Chem Soc. 119:1997;7202-7210 An interesting series of new polyintercalating molecules is described, including the first reported tetraintercalator.
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(1997)
J Am Chem Soc
, vol.119
, pp. 7202-7210
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Lokey, R.S.1
Kwok, Y.2
Guelev, V.3
Pursell, C.J.4
Hurley, L.H.5
Iverson, B.L.6
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25
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0031575419
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Solution structure of the calicheamicin γ1-DNA complex
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Kumar RA, Ikemoto N, Patel DJ. Solution structure of the calicheamicin γ1-DNA complex. J Mol Biol. 265:1997;187-201.
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(1997)
J Mol Biol
, vol.265
, pp. 187-201
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Kumar, R.A.1
Ikemoto, N.2
Patel, D.J.3
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26
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0030003572
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Parsing the free energy of anthracycline antibiotic binding to DNA
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Chaires JB, Satyanarayana S, Suh D, Fokt I, Przewloka T, Priebe W. Parsing the free energy of anthracycline antibiotic binding to DNA. Biochemistry. 35:1996;2047-2053.
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(1996)
Biochemistry
, vol.35
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Chaires, J.B.1
Satyanarayana, S.2
Suh, D.3
Fokt, I.4
Przewloka, T.5
Priebe, W.6
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27
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0030465221
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Dissecting the free energy of drug binding to DNA
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Chaires JB. Dissecting the free energy of drug binding to DNA. Anticancer Drug Des. 11:1996;569-580.
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Anticancer Drug des
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, pp. 569-580
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Chaires, J.B.1
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28
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0031571628
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2 duplex: Calorimetric and spectroscopic studies
-
of outstanding interest. The authors describe a detailed and ambitious attempt at parsing the DNA binding free energy into its components. The results of the analysis reveal that the hydrophobic transfer process is the overwhelming driving force for Hoechst 33258 binding to a specific DNA sequence. The change in the solvent-accessible surface area, computed from the known X-ray structure, was shown to correlate well with the experimentally determined heat capacity change for the binding reaction, providing a direct link between structure and energetics.
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2 duplex: calorimetric and spectroscopic studies. of outstanding interest J Mol Biol. 271:1997;244-257 The authors describe a detailed and ambitious attempt at parsing the DNA binding free energy into its components. The results of the analysis reveal that the hydrophobic transfer process is the overwhelming driving force for Hoechst 33258 binding to a specific DNA sequence. The change in the solvent-accessible surface area, computed from the known X-ray structure, was shown to correlate well with the experimentally determined heat capacity change for the binding reaction, providing a direct link between structure and energetics.
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(1997)
J Mol Biol
, vol.271
, pp. 244-257
-
-
Haq, I.1
Ladbury, J.E.2
Chowdhry, B.Z.3
Jenkins, T.C.4
Chaires, J.B.5
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29
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0031472259
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A terbenzimidazole that preferentially binds and conformationally alters structurally distinct DNA duplex domains: A potential mechanism for topoisomerase I poisoning
-
of outstanding interest. A detailed thermodynamic characterization of structure-specific recognition of DNA by a small molecule is described. The results and analysis suggest a key role for the coupling of binding to DNA hydration.
-
Pilch DS, Xu S, Sun Q, LaVoie EJ, Liu LF, Breslauer KJ. A terbenzimidazole that preferentially binds and conformationally alters structurally distinct DNA duplex domains: a potential mechanism for topoisomerase I poisoning. of outstanding interest Proc Natl Acad Sci USA. 94:1997;13565-13570 A detailed thermodynamic characterization of structure-specific recognition of DNA by a small molecule is described. The results and analysis suggest a key role for the coupling of binding to DNA hydration.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 13565-13570
-
-
Pilch, D.S.1
Xu, S.2
Sun, Q.3
Lavoie, E.J.4
Liu, L.F.5
Breslauer, K.J.6
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30
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0029130871
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Macromolecules and water: Probing with osmotic stress
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Parsegian VA, Rand RP, Rau DC. Macromolecules and water: probing with osmotic stress. Methods Enzymol. 259:1995;43-94.
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(1995)
Methods Enzymol
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Parsegian, V.A.1
Rand, R.P.2
Rau, D.C.3
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31
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0028931707
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The osmotic sensitivity of netropsin analog binding to DNA
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Sidorova NY, Rau DC. The osmotic sensitivity of netropsin analog binding to DNA. Biopolymers. 35:1995;377-384.
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Biopolymers
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Sidorova, N.Y.1
Rau, D.C.2
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32
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0029026601
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Criteria for the mode of binding of DNA binding agents
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Suh D, Chaires JB. Criteria for the mode of binding of DNA binding agents. Bioorganic Med Chem. 3:1995;723-728.
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(1995)
Bioorganic Med Chem
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, pp. 723-728
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Suh, D.1
Chaires, J.B.2
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34
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0029861327
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A novel assay for drug-DNA binding mode, affinity, and exclusion number: Scanning force microscopy
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Coury JE, McFail-Isom L, Williams LD, Bottomley LA. A novel assay for drug-DNA binding mode, affinity, and exclusion number: scanning force microscopy. Proc Natl Acad Sci USA. 93:1996;12283-12286.
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Proc Natl Acad Sci USA
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Coury, J.E.1
McFail-Isom, L.2
Williams, L.D.3
Bottomley, L.A.4
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35
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0030910837
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Scanning force microscopy of small ligand - Nucleic acid complexes: Tris(o-phenanthroline)ruthenium(II) as a test for a new assay
-
of outstanding interest. An interesting application of a powerful new method for investigating the mode of action of DNA-binding agents. The controversy over the binding mode of tris(phenanthroline)Ru(II) enantiomers is laid to rest by the demonstration here that neither isomer lengthens DNA, and therefore can not intercalate.
-
Coury JE, Anderson JR, McFail-Isom L, Williams LD, Bottomley LA. Scanning force microscopy of small ligand - nucleic acid complexes: tris(o-phenanthroline)ruthenium(II) as a test for a new assay. of outstanding interest J Am Chem Soc. 119:1997;3792-3796 An interesting application of a powerful new method for investigating the mode of action of DNA-binding agents. The controversy over the binding mode of tris(phenanthroline)Ru(II) enantiomers is laid to rest by the demonstration here that neither isomer lengthens DNA, and therefore can not intercalate.
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(1997)
J Am Chem Soc
, vol.119
, pp. 3792-3796
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Coury, J.E.1
Anderson, J.R.2
McFail-Isom, L.3
Williams, L.D.4
Bottomley, L.A.5
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36
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0027538012
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Tris(phenanthroline)ruthenium(II) enatiomer interactions with DNA: Mode and specificity of binding
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Satyanarayana S, Dabrowiak JC, Chaires JC. Tris(phenanthroline)ruthenium(II) enatiomer interactions with DNA: mode and specificity of binding. Biochemistry. 32:1993;2573-2584.
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(1993)
Biochemistry
, vol.32
, pp. 2573-2584
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Satyanarayana, S.1
Dabrowiak, J.C.2
Chaires, J.C.3
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37
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0029914981
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Sequence specificity of triplex DNA formation: Analysis by a combinatorial approach, restriction endonuclease protection selection and amplification
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Hardenbol P, Van Dyke MW. Sequence specificity of triplex DNA formation: analysis by a combinatorial approach, restriction endonuclease protection selection and amplification. Proc Natl Acad Sci USA. 93:1996;2811-2816.
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Proc Natl Acad Sci USA
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Hardenbol, P.1
Van Dyke, M.W.2
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38
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0031238638
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Identification of preferred distamycin-DNA binding sites by the combinatorial method REPSA
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of special interest. A powerful new combinatorial method for the investigation of the sequence specificty of DNA-binding agents is described. The REPSA method complements and extends existing footprinting methodologies.
-
Hardenbol P, Wang JC, Van Dyke MW. Identification of preferred distamycin-DNA binding sites by the combinatorial method REPSA. of special interest Bioconjug Chem. 8:1997;617-620 A powerful new combinatorial method for the investigation of the sequence specificty of DNA-binding agents is described. The REPSA method complements and extends existing footprinting methodologies.
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(1997)
Bioconjug Chem
, vol.8
, pp. 617-620
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Hardenbol, P.1
Wang, J.C.2
Van Dyke, M.W.3
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39
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0029120464
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Structural-perturbation approaches to thermodynamics of site-specific protein-DNA interactions
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Jen-Jacobson L. Structural-perturbation approaches to thermodynamics of site-specific protein-DNA interactions. Methods Enzymol. 259:1995;305-344.
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(1995)
Methods Enzymol
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Jen-Jacobson, L.1
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40
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0028032864
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The purine 2-amino group as a critical recognition element for binding of small molecules to DNA
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Waring MJ, Bailly C. The purine 2-amino group as a critical recognition element for binding of small molecules to DNA. Gene. 149:1994;69-79.
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(1994)
Gene
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Waring, M.J.1
Bailly, C.2
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41
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0029007481
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The influence of the 2-amino group of guanine on DNA conformation. Uranyl and DNase(I) probing of inosine/diaminopurine substituted DNA
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Bailly C, Mollegaard NE, Nielsen PE, Waring MJ. The influence of the 2-amino group of guanine on DNA conformation. Uranyl and DNase(I) probing of inosine/diaminopurine substituted DNA. EMBO J. 14:1995;2121-2131.
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Bailly, C.1
Mollegaard, N.E.2
Nielsen, P.E.3
Waring, M.J.4
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42
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0030450388
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PCR-based development of DNA substrates containing modified bases: An efficient system for investigating the role of the exocyclic groups in chemical and structural recognition by minor groove binding drugs and proteins
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Bailly C, Payet D, Travers AA, Waring MJ. PCR-based development of DNA substrates containing modified bases: an efficient system for investigating the role of the exocyclic groups in chemical and structural recognition by minor groove binding drugs and proteins. Proc Natl Acad Sci USA. 93:1996;13623-13628.
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Proc Natl Acad Sci USA
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Bailly, C.1
Payet, D.2
Travers, A.A.3
Waring, M.J.4
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43
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0030847848
-
Footprinting of echinomycin and actinomycin D on DNA molecules asymmetrically substituted with inosine and/or 2,6-diaminopurine
-
of special interest. The paper describes an important extension of the structural perturbation approach that allows a single strand of a long DNA fragment to be selectively modified. The effects of substituent changes in the DNA minor groove upon drug binding may then be investigated.
-
Jennewein S, Waring MJ. Footprinting of echinomycin and actinomycin D on DNA molecules asymmetrically substituted with inosine and/or 2,6-diaminopurine. of special interest Nucleic Acids Res. 25:1997;1502-1510 The paper describes an important extension of the structural perturbation approach that allows a single strand of a long DNA fragment to be selectively modified. The effects of substituent changes in the DNA minor groove upon drug binding may then be investigated.
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(1997)
Nucleic Acids Res
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Jennewein, S.1
Waring, M.J.2
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44
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0032576722
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Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands
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White S, Szewczyk JW, Turner JM, David EE, Dervan PB. Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands. Nature. 391:1998;468-471.
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(1998)
Nature
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White, S.1
Szewczyk, J.W.2
Turner, J.M.3
David, E.E.4
Dervan, P.B.5
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