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Second structural motif for recognition of DNA by oligonucleotide-directed triple-helix formation
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The molecular origin of DNA drug specificity in netropsin and distamycin
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0342987251
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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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Structural characterization of a 2:1 distamycin A•d(CGCAAATTGGC) complex by two dimensional NMR
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On the pairing rules for recognition in the minor groove of DNA by pyrrole-imidazole polyamides
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Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin
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Mrksich M., Wade W.S., Dwyer T.J., Geierstranger B.H., Wemmer D.E., Dervan P.B. Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin. Proc Natl Acad Sci USA. 89:1992;7586-7590.
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14
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0031933884
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Structural basis for G•C recognition in the DNA minor groove
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The high resolution X-ray crystal structure of an Im-Py-containing polyamide, binding in an antiparallel 2:1 motif to DNA is described. Three hydrogen bonds between the Im/Py pair and the G•C bp have been observed
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Kielkopf C.L., Baird E.E., Dervan P.B., Rees D.C. Structural basis for G•C recognition in the DNA minor groove. Nat Struc Biol. 5:1998;104-109. The high resolution X-ray crystal structure of an Im-Py-containing polyamide, binding in an antiparallel 2:1 motif to DNA is described. Three hydrogen bonds between the Im/Py pair and the G•C bp have been observed.
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0029662190
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Effects of the A•T/T•A degeneracy of pyrrole-imidazole polyamide recognition in the minor groove of DNA
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White S., Baird E.E., Dervan P.B. Effects of the A•T/T•A degeneracy of pyrrole-imidazole polyamide recognition in the minor groove of DNA. Biochemistry. 35:1996;12532-12537.
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16
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0032576722
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Recognition of the four Watson-Crick base pairs in the minor groove by synthetic ligands
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This is a key report on the Hp/Py pair which specifies for T•A and completes the four bp code for targeting the minor groove of DNA
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White S., Szewczyk J.W., Turner J.M., Baird E.E., Dervan P.B. Recognition of the four Watson-Crick base pairs in the minor groove by synthetic ligands. Nature. 391:1998;468-471. This is a key report on the Hp/Py pair which specifies for T•A and completes the four bp code for targeting the minor groove of DNA.
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Nature
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White, S.1
Szewczyk, J.W.2
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Dervan, P.B.5
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17
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0032475994
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A structural basis for recognition of A•T and T•A base pairs in the minor groove of B-DNA
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The high resolution X-ray crystal structure of Hp/Py bound to a T•A bp reveals three specific hydrogen bonds as well as an example of shape selective recognition by the complementarity of the Hp/Py edge and the edge of a T•A bp
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Kielkopf C.L., White S., Szewczyk J.W., Turner J.M., Baird E.E., Dervan P.B., Rees D.C. A structural basis for recognition of A•T and T•A base pairs in the minor groove of B-DNA. Science. 282:1998;111-115. The high resolution X-ray crystal structure of Hp/Py bound to a T•A bp reveals three specific hydrogen bonds as well as an example of shape selective recognition by the complementarity of the Hp/Py edge and the edge of a T•A bp.
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Science
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Kielkopf, C.L.1
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Dervan, P.B.6
Rees, D.C.7
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18
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0027970146
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Hairpin peptide motif. A new class of oligopeptides for sequence-specific recognition in the minor groove of double-helical DNA
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Mrksich M., Parks M.E., Dervan P.B. Hairpin peptide motif. A new class of oligopeptides for sequence-specific recognition in the minor groove of double-helical DNA. J Am Chem Soc. 1165:1994;7983-7988.
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Mrksich, M.1
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19
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0030758956
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NMR characterization of hairpin polyamide complexes with the minor groove of DNA
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de Clairac R.P.L., Geierstanger B.H., Mrksich M., Dervan P.B., Wemmer D.E. NMR characterization of hairpin polyamide complexes with the minor groove of DNA. J Am Chem Soc. 119:1997;7909-7916.
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20
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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 E.E., Dervan P.B. Orientation preferences of pyrrole-imidazole polyamides in the minor groove of DNA. J Am Chem Soc. 119:1997;8756-8765.
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White, S.1
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21
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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 J.W., Baird E.E., Mrksich M., Dervan P.B. 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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0029786013
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Recognition of DNA by designed ligands at subnanomolar concentrations
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Trauger J.W., Baird E.E., Dervan P.B. Recognition of DNA by designed ligands at subnanomolar concentrations. Nature. 382:1996;559-561.
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Trauger, J.W.1
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23
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0033577001
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Effects of γ-turn and β-tail amino acids on the sequence-specific recognition of the minor groove of DNA by hairpin polyamides
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Swalley S.E., Baird E.E., Dervan P.B. Effects of γ-turn and β-tail amino acids on the sequence-specific recognition of the minor groove of DNA by hairpin polyamides. J Am Chem Soc. 121:1999;1113-1120.
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Swalley, S.E.1
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24
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0030059085
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Solid phase synthesis of polyamides containing imidazole and pyrrole amino acids
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Baird E.E., Dervan P.B. Solid phase synthesis of polyamides containing imidazole and pyrrole amino acids. J Am Chem Soc. 118:1996;6141-6146.
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Baird, E.E.1
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25
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0029957034
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Binding site size limit of the 2:1 pyrrole-imidazole polyamide-DNA
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Kelly J.J., Baird E.E., Dervan P.B. Binding site size limit of the 2:1 pyrrole-imidazole polyamide-DNA. Proc Natl Acad Sci USA. 93:1996;6981-6985.
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Kelly, J.J.1
Baird, E.E.2
Dervan, P.B.3
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26
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0032486215
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Cooperative hairpin dimers for recognition of DNA by pyrrole-imidazole polyamides
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A cooperatively binding hairpin polyamide shows how long DNA sequences can be recognized by molecules of relatively small molecular weight
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Trauger J.W., Baird E.E., Dervan P.B. Cooperative hairpin dimers for recognition of DNA by pyrrole-imidazole polyamides. Angew Chem Int Ed. 37:1998;1421-1423. A cooperatively binding hairpin polyamide shows how long DNA sequences can be recognized by molecules of relatively small molecular weight.
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Angew Chem Int Ed
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Trauger, J.W.1
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27
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0030847647
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A pyrrole-imidazole polyamide motif for recognition of eleven base pair sequences in the minor groove of DNA
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Swalley S.E., Baird E.E., Dervan P.B. A pyrrole-imidazole polyamide motif for recognition of eleven base pair sequences in the minor groove of DNA. Chem Eur J. 3:1997;1600-1607.
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28
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0000739713
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Recognition of 16 base pairs in the minor groove of DNA by a pyrrole-imidazole polyamide dimer
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This paper describes a DNA sequence of 16 contiguous base pairs recognized by dimeric polyamides
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Trauger J.W., Baird E.E., Dervan P.B. Recognition of 16 base pairs in the minor groove of DNA by a pyrrole-imidazole polyamide dimer. J Am Chem Soc. 120:1998;3534-3535. This paper describes a DNA sequence of 16 contiguous base pairs recognized by dimeric polyamides.
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J Am Chem Soc
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Trauger, J.W.1
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29
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0033531640
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NMR characterization of the aliphatic beta/beta pairing for recognition of a A•T/T•A base pairs in the minor groove of DNA
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de Clairac R.P.L., Seel C.J., Geierstanger B.H., Mrksich M., Baird E.E., Dervan P.B., Wemmer D.E. NMR characterization of the aliphatic beta/beta pairing for recognition of a A•T/T•A base pairs in the minor groove of DNA. J Am Chem Soc. 121:1999;2956-2964.
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De Clairac, R.P.L.1
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Baird, E.E.5
Dervan, P.B.6
Wemmer, D.E.7
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30
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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 S.E., Baird E.E., Dervan P.B. 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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Swalley, S.E.1
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Dervan, P.B.3
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31
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0032126854
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Aliphatic/aromatic amino acid pairings for polyamide recognition in the minor groove of DNA
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Turner J.M., Swalley S.E., Baird E.E., Dervan P.B. Aliphatic/aromatic amino acid pairings for polyamide recognition in the minor groove of DNA. J Am Chem Soc. 120:1998;6219-6226.
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Turner, J.M.1
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32
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0032564881
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Stereochemical control of the DNA binding affinity, sequence specificity, and orientation preference of chiral hairpin polyamides in the minor groove
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Herman D.M., Baird E.E., Dervan P.B. Stereochemical control of the DNA binding affinity, sequence specificity, and orientation preference of chiral hairpin polyamides in the minor groove. J Am Chem Soc. 120:1998;1382-1391.
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Herman, D.M.1
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33
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0032986773
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Tandem hairpin motif for recognition in the minor groove of DNA by pyrrole-imidazole polyamides
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D) and excellent specificify to long DNA sequences (11 bp).
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Chem Eur J
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Herman, D.M.1
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Dervan, P.B.3
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34
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0033576975
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Cycle polyamide motif for recognition of the minor groove of DNA
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Cyclic polyamides show enhanced binding affinity compared with their hairpin analogs
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Herman D.M., Turner J.M., Baird E.E., Dervan P.B. Cycle polyamide motif for recognition of the minor groove of DNA. J Am Chem Soc. 121:1999;1121-1129. Cyclic polyamides show enhanced binding affinity compared with their hairpin analogs.
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Herman, D.M.1
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0000831664
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Enhanced sequence-specific recognition in the minor-groove of DNA by covalent peptide dimers
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Mrksich M., Dervan P.B. Enhanced sequence-specific recognition in the minor-groove of DNA by covalent peptide dimers. J Am Chem Soc. 115:1993;9892-9899.
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Mrksich, M.1
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36
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0031782431
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Comparison of H-pin and hairpin polyamide motifs for recognition of the minor groove of DNA
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Greenberg W.A., Baird E.E., Dervan P.B.A. comparison of H-pin and hairpin polyamide motifs for recognition of the minor groove of DNA. Chem Eur J. 4:1998;796-805.
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Chem Eur J
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Greenberg, W.A.1
Baird, E.E.2
Dervan, P.B.A.3
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37
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0030951207
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Regulation of gene expression by small molecules
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Gottesfeld J.M., Neely L., Trauger J.W., Baird E.E., Dervan P.B. Regulation of gene expression by small molecules. Nature. 387:1997;202-205.
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Nature
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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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38
-
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0032573224
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Inhibition of RNA polymerase II transcription in human cells by synthetic DNA-binding ligands
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This paper describes inhibition of gene expression mediated by RNA polymerase II in human cells. A key aspect is the synergy found for combinations of polyamides
-
Dickinson L.A., Gulizia R.J., Trauger J.W., Baird E.E., Mosier D.E., Gottesfeld J.M., Dervan P.B. Inhibition of RNA polymerase II transcription in human cells by synthetic DNA-binding ligands. Proc Natl Acad Sci USA. 95:1998;12890-12895. This paper describes inhibition of gene expression mediated by RNA polymerase II in human cells. A key aspect is the synergy found for combinations of polyamides.
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Proc Natl Acad Sci USA
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Dickinson, L.A.1
Gulizia, R.J.2
Trauger, J.W.3
Baird, E.E.4
Mosier, D.E.5
Gottesfeld, J.M.6
Dervan, P.B.7
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39
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0033550509
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Affinity and specificity of multiple hydroxypyrrole/pyrrole ring pairings for coded recognition of DNA
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White S., Turner J.M., Szewczyk J.W., Baird E.E., Dervan P.B. Affinity and specificity of multiple hydroxypyrrole/pyrrole ring pairings for coded recognition of DNA. J Am Chem Soc. 121:1999;260-261.
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J Am Chem Soc
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White, S.1
Turner, J.M.2
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40
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0033573863
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The thermodynamics of polyamide-DNA recognition: Hairpin polyamide binding in the minor groove of duplex DNA
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Pilch D.S., Poklar N., Baird E.E., Dervan P.B., Breslauer K.J. The thermodynamics of polyamide-DNA recognition: hairpin polyamide binding in the minor groove of duplex DNA. Biochemistry. 38:1999;2143-2151.
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Biochemistry
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Pilch, D.S.1
Poklar, N.2
Baird, E.E.3
Dervan, P.B.4
Breslauer, K.J.5
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41
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0033516311
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Rational design of sequence-specific DNA alkylating agents based on duocarmycin A and pyrrole-imidazole hairpin polyamides
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Tao Z.F., Fujiwara T., Saito I., Sugiyama H. Rational design of sequence-specific DNA alkylating agents based on duocarmycin A and pyrrole-imidazole hairpin polyamides. J Am Chem Soc. 121:1999;4961-4967.
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Tao, Z.F.1
Fujiwara, T.2
Saito, I.3
Sugiyama, H.4
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42
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0032033739
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Inhibition of major-groove-binding proteins by pyrrole-imidazole polyamides with an Arg-Pro-Arg positive patch
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Bremer R.E., Baird E.E., Dervan P.B. Inhibition of major-groove-binding proteins by pyrrole-imidazole polyamides with an Arg-Pro-Arg positive patch. Chem Biol. 5:1998;119-133.
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Chem Biol
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Bremer, R.E.1
Baird, E.E.2
Dervan, P.B.3
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43
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0029762862
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