Recognition of the DNA minor groove by pyrrole-imidazole polyamides
Tóm tắt
Từ khóa
Tài liệu tham khảo
Pelton, 1989, Structural characterization of a 2:1 distamycin A·D(CGCAAATTGGC) complex by two-dimensional NMR, Proc. Natl. Acad. Sci. U.S.A., 86, 5723, 10.1073/pnas.86.15.5723
Gottesfeld, 2000, Chemical approaches to control gene expression, Gene Expr., 9, 77, 10.3727/000000001783992696
Dervan, 2001, Molecular recognition of DNA by small molecules, Bioorg. Med. Chem., 9, 2215, 10.1016/S0968-0896(01)00262-0
White, 1998, Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands, Nature, 391, 468, 10.1038/36116
Wade, 1992, 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, 8783, 10.1021/ja00049a006
Mrksich, 1992, 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. U.S.A., 89, 7586, 10.1073/pnas.89.16.7586
Kielkopf, 1998, Structural basis for G⋅C recognition in the DNA minor groove, Nat. Struct. Biol., 5, 104, 10.1038/nsb0298-104
Pilch, 1999, The thermodynamics of polyamide-DNA recognition: hairpin polyamide binding in the minor groove of duplex DNA, Biochemistry, 38, 2143, 10.1021/bi982628g
Kielkopf, 1998, A structural basis for recognition of A·T and T·A base pairs in the minor groove of B-DNA, Science, 282, 111, 10.1126/science.282.5386.111
Kielkopf, 2000, Structural effects of DNA sequence on T⋅A recognition by hydroxypyrrole/pyrrole pairs in the minor groove, J. Mol. Biol., 295, 557, 10.1006/jmbi.1999.3364
Wellenzohn, 2003, Hydration of hydroxypyrrole influences binding of ImHpPyPy-β-Dp polyamide to DNA, J. Am. Chem. Soc., 125, 1088, 10.1021/ja0277778
Mrksich, 1994, Hairpin peptide motif. A new class of oligopeptides for sequence-specific recognition in the minor-groove of double-helical DNA, J. Am. Chem. Soc., 116, 7983, 10.1021/ja00097a004
Trauger, 1996, Recognition of DNA by designed ligands at subnanomolar concentrations, Nature, 382, 559, 10.1038/382559a0
deClairac, 1997, NMR characterization of hairpin polyamide complexes with the minor groove of DNA, J. Am. Chem. Soc., 119, 7909, 10.1021/ja964314r
White, 1997, Orientation preferences of pyrrole-imidazole polyamides in the minor groove of DNA, J. Am. Chem. Soc., 119, 8756, 10.1021/ja971569b
Urbach AR: 1:1 motif for DNA recognition by β-alanine-linked polyamides [PhD Thesis]. Pasadena: California Institute of Technology; 2002.
Herman, 1998, 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, 1382, 10.1021/ja9737228
Woods, 2002, Hairpin versus extended DNA binding of a substituted β-alanine linked polyamide, J. Am. Chem. Soc., 124, 2148, 10.1021/ja0122039
Herman, 1999, Cycle polyamide motif for recognition of the minor groove of DNA, J. Am. Chem. Soc., 121, 1121, 10.1021/ja983206x
Melander, 2000, Discrimination of A/T sequences in the minor groove of DNA within a cyclic polyamide motif, Chem. Eur. J., 6, 4487, 10.1002/1521-3765(20001215)6:24<4487::AID-CHEM4487>3.0.CO;2-C
Baliga, 2001, Kinetic consequences of covalent linkage of DNA binding polyamides, Biochemistry, 40, 3, 10.1021/bi0022339
Greenberg, 1998, A comparison of H-pin and hairpin polyamide motifs for the recognition of the minor groove of DNA, Chem. Eur. J., 4, 796, 10.1002/(SICI)1521-3765(19980515)4:5<796::AID-CHEM796>3.0.CO;2-G
Olenyuk, 2003, Parallel synthesis of H-pin polyamides by alkene metathesis on solid phase, J. Am. Chem. Soc., 125, 4741, 10.1021/ja0213221
Swalley, 1997, A pyrrole-imidazole polyamide motif for recognition of eleven base pair sequences in the minor groove of DNA, Chem. Eur. J., 3, 1600, 10.1002/chem.19970031009
Turner, 1998, Aliphatic/aromatic amino acid pairings for polyamide recognition in the minor groove of DNA, J. Am. Chem. Soc., 120, 6219, 10.1021/ja980147e
Wang, 2001, Expanding the recognition of the minor groove of DNA by incorporation of β-alanine in hairpin polyamides, Bioorg. Med. Chem., 9, 653, 10.1016/S0968-0896(00)00282-0
Kelly, 1996, Binding site size limit of the 2:1 pyrrole-imidazole polyamide-DNA motif, Proc. Natl. Acad. Sci. U.S.A., 93, 6981, 10.1073/pnas.93.14.6981
Trauger, 1998, Cooperative hairpin dimers for recognition of DNA by pyrrole-imidazole polyamides, Angew. Chem. Int. Ed. Engl., 37, 1421, 10.1002/(SICI)1521-3773(19980605)37:10<1421::AID-ANIE1421>3.0.CO;2-8
Weyermann, 2002, Recognition of ten base pairs of DNA by head-to-head hairpin dimers, J. Am. Chem. Soc., 124, 6872, 10.1021/ja020258k
Herman, 1999, Tandem hairpin motif for recognition in the minor groove of DNA by pyrrole-imidazole polyamides, Chem. Eur. J., 5, 975, 10.1002/(SICI)1521-3765(19990301)5:3<975::AID-CHEM975>3.0.CO;2-T
Kers, 2002, Search for the optimal linker in tandem hairpin polyamides, Bioorg. Med. Chem., 10, 3339, 10.1016/S0968-0896(02)00221-3
Maeshima, 2001, Specific targeting of insect and vertebrate telomeres with pyrrole and imidazole polyamides, EMBO J., 20, 3218, 10.1093/emboj/20.12.3218
Nguyen, 2001, Alternative heterocycles for DNA recognition: an N-methylpyrazole/N-methylpyrrole pair specifies for A⋅T/T⋅A base pairs, Bioorg. Med. Chem., 9, 7, 10.1016/S0968-0896(00)00219-4
Marques, 2002, Toward an understanding of the chemical etiology for DNA minor-groove recognition by polyamides, Helv. Chim. Acta., 85, 4485, 10.1002/hlca.200290024
Minehan, 2000, Molecular recognition of DNA by Hoechst benzimidazoles: exploring beyond the pyrrole-imidazole-hydroxypyrrole polyamide-pairing code, Helv. Chim. Acta., 83, 2197, 10.1002/1522-2675(20000906)83:9<2197::AID-HLCA2197>3.0.CO;2-N
Lown JW: DNA sequence recognition altered bis-benzimidazole minor-groove binders. In Advances in DNA Sequence-Specific Agents. Edited by Jones GB. London: JAI Press Inc.; 1998:67-95.
Renneberg, 2003, Imidazopyridine/pyrrole and hydroxybenzimidazole/pyrrole pairs for DNA minor groove recognition, J. Am. Chem. Soc., 125, 5707, 10.1021/ja0300158
Baird, 1996, Solid phase synthesis of polyamides containing imidazole and pyrrole amino acids, J. Am. Chem. Soc., 118, 6141, 10.1021/ja960720z
Wurtz, 2001, Fmoc solid phase synthesis of polyamides containing pyrrole and imidazole amino acids, Org. Lett., 3, 1201, 10.1021/ol0156796
Fattori, 2002, A practical approach to the synthesis of hairpin polyamide-peptide conjugates through the use of a safety-catch linker, Bioorg. Med. Chem. Lett., 12, 1143, 10.1016/S0960-894X(02)00122-1
Swalley, 1999, Effects of γ-turn and β-tail amino acids on sequence-specific recognition of DNA by hairpin polyamides, J. Am. Chem. Soc., 121, 1113, 10.1021/ja9830905
Belitsky, 2002, Solid-phase synthesis of DNA binding polyamides on oxime resin, Bioorg. Med. Chem., 10, 2767, 10.1016/S0968-0896(02)00133-5
Darnell, 2002, Transcription factors as targets for cancer therapy, Nat. Rev. Cancer, 2, 740, 10.1038/nrc906
Gottesfeld, 1997, Regulation of gene expression by small molecules, Nature, 387, 202, 10.1038/387202a0
Neely, 1997, Importance of minor groove binding zinc fingers within the transcription factor IIIA-DNA complex, J. Mol. Biol., 274, 439, 10.1006/jmbi.1997.1411
Dickinson, 1998, Inhibition of RNA polymerase II transcription in human cells by synthetic DNA-binding ligands, Proc. Natl. Acad. Sci. U.S.A., 95, 12890, 10.1073/pnas.95.22.12890
McBryant, 1999, Minor groove DNA-protein contacts upstream of a tRNA gene detected with a synthetic DNA binding ligand, J. Mol. Biol., 286, 973, 10.1006/jmbi.1999.2539
Ehley, 2002, Promoter scanning for transcription inhibition with DNA-binding polyamides, Mol. Cell Biol., 22, 1723, 10.1128/MCB.22.6.1723-1733.2002
Winston, 2000, Asymmetric DNA binding by a homodimeric bHLH protein, Biochemistry, 39, 9092, 10.1021/bi000947d
Dickinson, 1999, Inhibition of Ets-1 DNA binding and ternary complex formation between Ets-1, NF-κB, and DNA by a designed DNA-binding ligand, J. Biol. Chem., 274, 12765, 10.1074/jbc.274.18.12765
Chiang, 2000, Targeting the Ets binding site of the HER2/neu promoter with pyrrole-imidazole polyamides, J. Biol. Chem., 275, 24246, 10.1074/jbc.M000820200
Lenzmeier, 1999, The Tax protein-DNA interaction is essential for HTLV-I transactivation in vitro, J. Mol. Biol., 291, 731, 10.1006/jmbi.1999.2969
Simon, 2000, Selective inhibition of DNA gyrase in vitro by a GC specific eight-ring hairpin polyamide at nanomolar concentration, FEBS Lett., 471, 173, 10.1016/S0014-5793(00)01390-9
Wurtz, 2002, Inhibition of DNA binding by NF-κB with pyrrole-imidazole polyamides, Biochemistry, 41, 7604, 10.1021/bi020114i
Bremer, 1998, Inhibition of major-groove-binding proteins by pyrrole-imidazole polyamides with an Arg-Pro-Arg positive patch, Chem. Biol., 5, 119, 10.1016/S1074-5521(98)90057-6
Bremer, 2001, Inhibition of major groove DNA binding bZIP proteins by positive patch polyamides, Bioorg. Med. Chem., 9, 2093, 10.1016/S0968-0896(01)00122-5
Fechter EJ, Dervan PB: Allosteric inhibition of protein-DNA complexes by polyamide-intercalator conjugates. J Am Chem Soc 2003, in press.
Janssen, 2000, Specific gain- and loss-of-function phenotypes induced by satellite-specific DNA-binding drugs fed to Drosophila melanogaster, Mol. Cell, 6, 1013, 10.1016/S1097-2765(00)00100-3
Dickinson, 1999, Anti-repression of RNA polymerase II transcription by pyrrole-imidazole polyamides, Biochemistry, 38, 10801, 10.1021/bi9912847
Coull, 2002, Targeted derepression of the human immunodeficiency virus type 1 long terminal repeat by pyrrole-imidazole polyamides, J. Virol., 76, 12349, 10.1128/JVI.76.23.12349-12354.2002
Ansari, 2002, Modular design of artificial transcription factors, Curr. Opin. Chem. Biol., 6, 765, 10.1016/S1367-5931(02)00377-0
Mapp, 2000, Activation of gene expression by small molecule transcription factors, Proc. Natl. Acad. Sci. U.S.A., 97, 3930, 10.1073/pnas.97.8.3930
Ansari, 2001, Towards a minimal motif for artificial transcriptional activators, Chem. Biol., 8, 583, 10.1016/S1074-5521(01)00037-0
Arora, 2002, Design of artificial transcriptional activators with rigid poly-L-proline linkers, J. Am. Chem. Soc., 124, 13067, 10.1021/ja0208355
Gottesfeld, 2001, Sequence-specific recognition of DNA in the nucleosome by pyrrole-imidazole polyamides, J. Mol. Biol., 309, 615, 10.1006/jmbi.2001.4694
Suto, 2003, Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands, J. Mol. Biol., 326, 371, 10.1016/S0022-2836(02)01407-9
Gottesfeld, 2002, Blocking transcription through a nucleosome with synthetic DNA ligands, J. Mol. Biol., 321, 249, 10.1016/S0022-2836(02)00598-3
Belitsky, 2002, Cellular uptake of N-methylpyrrole/N-methylimidazole polyamide-dye conjugates, Bioorg. Med. Chem., 10, 3313, 10.1016/S0968-0896(02)00204-3
Crowley, 2003, Controlling the intracellular localization of fluorescent polyamide analogs in cultured cells, Bioorg. Med. Chem. Lett., 13, 1565, 10.1016/S0960-894X(03)00152-5
Gygi, 2002, Use of fluorescent sequence-specific polyamides to discriminate human chromosomes by microscopy and flow cytometry, Nucleic Acids Res., 30, 2790, 10.1093/nar/gkf406
Rucker, 2003, Sequence specific fluorescence detection of double strand DNA, J. Am. Chem. Soc., 125, 1195, 10.1021/ja021011q
Supekova, 2002, Genomic effects of polyamide/DNA interactions on mRNA expression, Chem. Biol., 9, 821, 10.1016/S1074-5521(02)00174-6
Agami, 2002, RNAi and related mechanisms and their potential use for therapy, Curr. Opin. Chem. Biol., 6, 829, 10.1016/S1367-5931(02)00378-2
Kamath, 2003, Systematic functional analysis of the Caenorhabditis elegans genome using RNAi, Nature, 421, 231, 10.1038/nature01278
Wang, 2001, Sequence-specific trapping of topoisomerase I by DNA binding polyamide-camptothecin conjugates, J. Am. Chem. Soc., 123, 8657, 10.1021/ja010392p
Malik, 2000, Transcriptional regulation through mediator-like coactivators in yeast and metazoan cells, Trends Biochem. Sci., 25, 277, 10.1016/S0968-0004(00)01596-6