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Volumn 46, Issue 42, 2007, Pages 11661-11670

Sequence recognition in the minor groove of DNA by covalently linked formamido imidazole-pyrrole-imidazole polyamides: Effect of H-pin linkage and linker length on selectivity and affinity

Author keywords

[No Author keywords available]

Indexed keywords

BINDING AFFINITY; HIGH-AFFINITY COOPERATIVE BINDING; LINKER LENGTH;

EID: 35448948822     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi701053a     Document Type: Article
Times cited : (16)

References (52)
  • 2
    • 0022858456 scopus 로고
    • Molecular recognition between oligopeptides and nucleic acids: Novel imidazole-containing oligopeptides related to netropsin that exhibit altered DNA sequence specificity
    • Lown, J. W., Krowicki, K., Bhat, U. G., Skorobaty, A., Ward, B., and Dabrowiak, J. C. (1986) Molecular recognition between oligopeptides and nucleic acids: novel imidazole-containing oligopeptides related to netropsin that exhibit altered DNA sequence specificity, Biochemistry 25, 7408-7416.
    • (1986) Biochemistry , vol.25 , pp. 7408-7416
    • Lown, J.W.1    Krowicki, K.2    Bhat, U.G.3    Skorobaty, A.4    Ward, B.5    Dabrowiak, J.C.6
  • 4
    • 0342987251 scopus 로고
    • 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
    • Wade, W. S., Mrksich, M., and Dervan, P. B. (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, 8783-8794.
    • (1992) J. Am. Chem. Soc , vol.114 , pp. 8783-8794
    • Wade, W.S.1    Mrksich, M.2    Dervan, P.B.3
  • 5
    • 0026661689 scopus 로고
    • 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
    • Mrksich, M., Wade, W. S., Dwyer, T. W., Geierstanger, B. H., Wemmer, D. E., and Dervan, P. B. (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, 7586-7590.
    • (1992) Proc. Natl. Acad. Sci. U.S.A , vol.89 , pp. 7586-7590
    • Mrksich, M.1    Wade, W.S.2    Dwyer, T.W.3    Geierstanger, B.H.4    Wemmer, D.E.5    Dervan, P.B.6
  • 6
    • 0027445693 scopus 로고
    • Binding affinities of synthetic peptides, pyridine-2-carboxamidenetropsin and 1-methylimidazole-2- carboxamidenetropsin, that form 2:1 complexes in the minor groove of double stranded helical DNA
    • Wade, W. S., Mrksich, M., and Dervan, P. B. (1993) Binding affinities of synthetic peptides, pyridine-2-carboxamidenetropsin and 1-methylimidazole-2- carboxamidenetropsin, that form 2:1 complexes in the minor groove of double stranded helical DNA, Biochemistry 32, 11385-11389.
    • (1993) Biochemistry , vol.32 , pp. 11385-11389
    • Wade, W.S.1    Mrksich, M.2    Dervan, P.B.3
  • 7
    • 0027276389 scopus 로고
    • Antiparallel side-by-side heterodimer for sequence specific recognition in the minor groove of DNA by a distamycin/1-methylimidazole-2-carboxamide-netropsin pair
    • Mrksich, M., and Dervan, P. B. (1993) Antiparallel side-by-side heterodimer for sequence specific recognition in the minor groove of DNA by a distamycin/1-methylimidazole-2-carboxamide-netropsin pair, J. Am. Chem. Soc. 115, 2572-2576.
    • (1993) J. Am. Chem. Soc , vol.115 , pp. 2572-2576
    • Mrksich, M.1    Dervan, P.B.2
  • 8
    • 0028212564 scopus 로고
    • Structural and dynamic characterisation of the heterodimeric and homodimeric complexes of distamcyin and 1-methylimidazole-2- carboxamide-netropsin bound to the minor groove of DNA
    • Geierstanger, B. H., Jacobsen, J. P., Mrksich, M., Dervan, P. B., and Wemmer, D. E. (1994) Structural and dynamic characterisation of the heterodimeric and homodimeric complexes of distamcyin and 1-methylimidazole-2- carboxamide-netropsin bound to the minor groove of DNA, Biochemistry 33, 3055-3062.
    • (1994) Biochemistry , vol.33 , pp. 3055-3062
    • Geierstanger, B.H.1    Jacobsen, J.P.2    Mrksich, M.3    Dervan, P.B.4    Wemmer, D.E.5
  • 9
    • 0028171224 scopus 로고
    • Design of a GC specific DNA minor groove-binding peptide
    • Geierstanger, B. H., Mrksich. M., Dervan, P. B., and Wemmer, D. E. (1994) Design of a GC specific DNA minor groove-binding peptide, Science 266, 646-650.
    • (1994) Science , vol.266 , pp. 646-650
    • Geierstanger, B.H.1    Mrksich, M.2    Dervan, P.B.3    Wemmer, D.E.4
  • 10
    • 0028904198 scopus 로고
    • Recognition in the minor groove of DNA at 5′-(A,T)GCGC(A,T)-3′ by a four ring tetrapeptide dimer. Reversal of the specificity of the natural product distamycin
    • Mrksich, M., and Dervan, P. B. (1995) Recognition in the minor groove of DNA at 5′-(A,T)GCGC(A,T)-3′ by a four ring tetrapeptide dimer. Reversal of the specificity of the natural product distamycin, J. Am. Chem. Soc. 117, 3325.
    • (1995) J. Am. Chem. Soc , vol.117 , pp. 3325
    • Mrksich, M.1    Dervan, P.B.2
  • 11
    • 0031933884 scopus 로고    scopus 로고
    • Structural basis for GC recognition in the DNA minor groove
    • Kielkopf, C. L., Baird, E. E., Dervan, P. B., and Rees, D. C. (1998) Structural basis for GC recognition in the DNA minor groove, Nat. Struct. Biol. 5, 104-109.
    • (1998) Nat. Struct. Biol , vol.5 , pp. 104-109
    • Kielkopf, C.L.1    Baird, E.E.2    Dervan, P.B.3    Rees, D.C.4
  • 12
    • 0032475994 scopus 로고    scopus 로고
    • Kielkopf, C. L., White, S., Szewczyk, J. M., Turner, J. M., Baird, E. E., Dervan, P. B., and Rees, D. C. (1998) A structural basis for recognition of A. T and T. A base pairs in the minor groove of B-DNA, Science 282, 111-115.
    • Kielkopf, C. L., White, S., Szewczyk, J. M., Turner, J. M., Baird, E. E., Dervan, P. B., and Rees, D. C. (1998) A structural basis for recognition of A. T and T. A base pairs in the minor groove of B-DNA, Science 282, 111-115.
  • 13
    • 0029786013 scopus 로고    scopus 로고
    • Recognition of DNA by designed ligands at subnanomolar concentrations
    • Trauger, J. W., Baird. E. E., and Dervan, P. B. (1996) Recognition of DNA by designed ligands at subnanomolar concentrations, Nature 382, 559-561.
    • (1996) Nature , vol.382 , pp. 559-561
    • Trauger, J.W.1    Baird, E.E.2    Dervan, P.B.3
  • 17
    • 0033617408 scopus 로고    scopus 로고
    • Inhibition of ets-1 DNA binding and ternary complex formation between ets-1, NF-κb and DNA by a designed DNA-binding ligand
    • Dickinson, L. A., Trauger, J. W., Baird, E. E., Dervan, P. B., Graves, B. J., and Gottesfeld, J. M. (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, 12765-12773.
    • (1999) J. Biol. Chem , vol.274 , pp. 12765-12773
    • Dickinson, L.A.1    Trauger, J.W.2    Baird, E.E.3    Dervan, P.B.4    Graves, B.J.5    Gottesfeld, J.M.6
  • 18
    • 35448949541 scopus 로고    scopus 로고
    • Activation of gene expression by small molecule transcription factors
    • Mapp, A. K., Ansari, A. Z., Ptashne, M., and Dervan, P. B. (2000) Activation of gene expression by small molecule transcription factors, Proc. Natl. Acad. Sci. U.S.A. 18, 4359-4363.
    • (2000) Proc. Natl. Acad. Sci. U.S.A , vol.18 , pp. 4359-4363
    • Mapp, A.K.1    Ansari, A.Z.2    Ptashne, M.3    Dervan, P.B.4
  • 19
    • 0034637562 scopus 로고    scopus 로고
    • Targeting the ets-1 binding site of the her2/neu promoter with pyrrole-imidazole polyamides
    • Chiang, S. Y., Burli, R. W., Benz, C. C., Gawron, L., Scott, G. K., Dervan, P. B., and Beerman, T. A. (2000) Targeting the ets-1 binding site of the her2/neu promoter with pyrrole-imidazole polyamides, J. Biol. Chem. 275, 24246-24254.
    • (2000) J. Biol. Chem , vol.275 , pp. 24246-24254
    • Chiang, S.Y.1    Burli, R.W.2    Benz, C.C.3    Gawron, L.4    Scott, G.K.5    Dervan, P.B.6    Beerman, T.A.7
  • 20
    • 15544385574 scopus 로고    scopus 로고
    • Inhibition of DNA binding by human estrogen-related receptor 2 and estrogen receptor α with minor groove binding polyamides
    • Gearhart, M. D., Dickinson, L., Ehley, J., Melander, C., Dervan, P. B., Wright, P. E., and Gottesfeld, J. M. (2005) Inhibition of DNA binding by human estrogen-related receptor 2 and estrogen receptor α with minor groove binding polyamides, Biochemistry 44, 4196-4203.
    • (2005) Biochemistry , vol.44 , pp. 4196-4203
    • Gearhart, M.D.1    Dickinson, L.2    Ehley, J.3    Melander, C.4    Dervan, P.B.5    Wright, P.E.6    Gottesfeld, J.M.7
  • 23
    • 33746795976 scopus 로고    scopus 로고
    • DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA. TTC repeats in Friedreich's ataxia
    • Burnett, R., Melander, C., Puckett, J. W., Son, L. S., Wells, R. D., Dervan, P. B., and Gottesfeld, J. M. (2006) DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA. TTC repeats in Friedreich's ataxia, Proc. Natl. Acad. Sci. U.S.A. 103, 11497-11502.
    • (2006) Proc. Natl. Acad. Sci. U.S.A , vol.103 , pp. 11497-11502
    • Burnett, R.1    Melander, C.2    Puckett, J.W.3    Son, L.S.4    Wells, R.D.5    Dervan, P.B.6    Gottesfeld, J.M.7
  • 24
    • 33750701787 scopus 로고    scopus 로고
    • Binding of f-PIP, a pyrrole- and imidazole-containing triamide, to the inverted CCAAT box-2 of topoisomerase II alpha promoter and modulation of gene expression in cells
    • Le, N. M., Sielaff, A. M., Cooper, A. J., Mackay, H., Brown, T., Kotecha, M., O'Hare, C., Hochhauser, D., Lee, M., and Hartley, J. A. (2006) Binding of f-PIP, a pyrrole- and imidazole-containing triamide, to the inverted CCAAT box-2 of topoisomerase II alpha promoter and modulation of gene expression in cells, Bioorg. Med. Chem. Lett. 16, 6161-6164.
    • (2006) Bioorg. Med. Chem. Lett , vol.16 , pp. 6161-6164
    • Le, N.M.1    Sielaff, A.M.2    Cooper, A.J.3    Mackay, H.4    Brown, T.5    Kotecha, M.6    O'Hare, C.7    Hochhauser, D.8    Lee, M.9    Hartley, J.A.10
  • 26
    • 19944432385 scopus 로고    scopus 로고
    • Extending the language of DNA molecular recognition by polyamides: Unexpected influence of imidazole and pyrrole arrangement on binding affinity and specificity
    • Buchmueller, K. L., Staples, C. M., Howard, C. M., Horick, S. M., Uthe, P. B., Le, M., Cox, K. K., Nguyen, B., Pacheco, K. A. O., Wilson, W. D., and Lee, M. (2005) Extending the language of DNA molecular recognition by polyamides: unexpected influence of imidazole and pyrrole arrangement on binding affinity and specificity, J. Am. Chem. Soc. 127, 742-750.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 742-750
    • Buchmueller, K.L.1    Staples, C.M.2    Howard, C.M.3    Horick, S.M.4    Uthe, P.B.5    Le, M.6    Cox, K.K.7    Nguyen, B.8    Pacheco, K.A.O.9    Wilson, W.D.10    Lee, M.11
  • 29
    • 0030460191 scopus 로고    scopus 로고
    • Optimisation of cross-linked lexitropsins
    • Chen, Y-H., Yang, Y., and Lown, J. W. (1996) Optimisation of cross-linked lexitropsins, J. Biomol. Struct. Dyn. 14, 341-355.
    • (1996) J. Biomol. Struct. Dyn , vol.14 , pp. 341-355
    • Chen, Y.-H.1    Yang, Y.2    Lown, J.W.3
  • 30
    • 0027970146 scopus 로고
    • Hairpin peptide motif; a new class of oligopeptides for sequence specific recognition in the minor groove of double helical DNA
    • Mrksich, M., Parks. M. E., and Dervan, P. B. (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, 7983-7988.
    • (1994) J. Am. Chem. Soc , vol.116 , pp. 7983-7988
    • Mrksich, M.1    Parks, M.E.2    Dervan, P.B.3
  • 32
    • 0028119199 scopus 로고
    • Design of a covalent peptide heterodimer for sequence-specific recognition in the minor groove of double helical DNA
    • Mrksich, M., and Dervan, P. B. (1994) Design of a covalent peptide heterodimer for sequence-specific recognition in the minor groove of double helical DNA, J. Am. Chem. Soc. 116, 3663-3664.
    • (1994) J. Am. Chem. Soc , vol.116 , pp. 3663-3664
    • Mrksich, M.1    Dervan, P.B.2
  • 33
    • 0028142728 scopus 로고
    • A new DNA minor groove binding motif: Cross-linked lexitropsins
    • Chen, Y-H., and Lown, J. W. (1994) A new DNA minor groove binding motif: cross-linked lexitropsins, J. Am. Chem. Soc. 116, 6995-7005.
    • (1994) J. Am. Chem. Soc , vol.116 , pp. 6995-7005
    • Chen, Y.-H.1    Lown, J.W.2
  • 34
    • 0344641913 scopus 로고    scopus 로고
    • Sequence-specific recognition by polyamides
    • Dervan, P. B., and Burli, R. W. (1999) Sequence-specific recognition by polyamides, Curr. Opin. Chem. Biol. 3, 688-693.
    • (1999) Curr. Opin. Chem. Biol , vol.3 , pp. 688-693
    • Dervan, P.B.1    Burli, R.W.2
  • 35
    • 0007788984 scopus 로고
    • Design and synthesis of sequence specific DNA minor groove recognising ligands of the cross-linked lexitropsin class
    • Chen, Y-H., and Lown, J. W. (1995) Design and synthesis of sequence specific DNA minor groove recognising ligands of the cross-linked lexitropsin class, Heterocycles 41, 1691-1707.
    • (1995) Heterocycles , vol.41 , pp. 1691-1707
    • Chen, Y.-H.1    Lown, J.W.2
  • 36
    • 0028931174 scopus 로고
    • DNA minor groove binding of cross-linked lexitropsins: Experimental conditions required to observe the covalently linked WPPW (groove wall-peptide-peptide groove wall) motif
    • Chen, Y-H., and Lown, J. W. (1995) DNA minor groove binding of cross-linked lexitropsins: experimental conditions required to observe the covalently linked WPPW (groove wall-peptide-peptide groove wall) motif, Biophys. J. 68, 2041-2048.
    • (1995) Biophys. J , vol.68 , pp. 2041-2048
    • Chen, Y.-H.1    Lown, J.W.2
  • 37
    • 0037039371 scopus 로고    scopus 로고
    • DNA sequence recognition in the minor groove by crosslinked polyamides: The effect of N-terminal head group and linker length in binding affinity and specificity
    • O'Hare, C. C., Mack, D., Tandon, M., Sharma, S. K., Lown, J. W., Kopka, M. L., Dickerson, R. E., and Hartley, J. A. (2002) DNA sequence recognition in the minor groove by crosslinked polyamides: the effect of N-terminal head group and linker length in binding affinity and specificity, Proc. Natl. Acad. Sci. U.S.A. 99, 72-77.
    • (2002) Proc. Natl. Acad. Sci. U.S.A , vol.99 , pp. 72-77
    • O'Hare, C.C.1    Mack, D.2    Tandon, M.3    Sharma, S.K.4    Lown, J.W.5    Kopka, M.L.6    Dickerson, R.E.7    Hartley, J.A.8
  • 38
    • 0037070562 scopus 로고    scopus 로고
    • Influence of a terminal formamido group on the sequence recognition of DNA by polyamides
    • Lacy, E. R., Le, N. M., Price, C. A., Lee, M., and Wilson, W. D. (2002) Influence of a terminal formamido group on the sequence recognition of DNA by polyamides, J. Am. Chem. Soc. 124, 2153-2163.
    • (2002) J. Am. Chem. Soc , vol.124 , pp. 2153-2163
    • Lacy, E.R.1    Le, N.M.2    Price, C.A.3    Lee, M.4    Wilson, W.D.5
  • 39
    • 33750979299 scopus 로고    scopus 로고
    • Buchmueller, K. L., Bailey, S. L., Matthews, D. A., Taherbhai, Z. T., Register, J. K., Davis, Z. S., Bruice, C. D., O'Hare, C. C., Hartley, J. A., and Lee, M. (2006) Physical and structural basis for the strong interactions of the -ImPy- central pairing motif in the polyamide f-ImPyIm, Biochemistry 45, 13551-13565.
    • Buchmueller, K. L., Bailey, S. L., Matthews, D. A., Taherbhai, Z. T., Register, J. K., Davis, Z. S., Bruice, C. D., O'Hare, C. C., Hartley, J. A., and Lee, M. (2006) Physical and structural basis for the strong interactions of the -ImPy- central pairing motif in the polyamide f-ImPyIm, Biochemistry 45, 13551-13565.
  • 40
    • 35448944798 scopus 로고    scopus 로고
    • Biacore, 1997 BIAevaluation version 3.0: Software Handbook, Biacore AB, Uppsala, Sweden
    • Biacore. (1997) BIAevaluation version 3.0: Software Handbook, Biacore AB, Uppsala, Sweden.
  • 41
    • 0026351785 scopus 로고
    • The CD of ligand-DNA systems. 1. poly (dG-dC) B-DNA
    • Lyng, R., Rodger, A., and Norden, B. (1991) The CD of ligand-DNA systems. 1. poly (dG-dC) B-DNA, Biopolymers 31, 1709-1720.
    • (1991) Biopolymers , vol.31 , pp. 1709-1720
    • Lyng, R.1    Rodger, A.2    Norden, B.3
  • 42
    • 0026926970 scopus 로고
    • The CD of ligand-DNA systems. 2. poly (dA-dT) B-DNA
    • Lyng, R., Rodger, A., and Norden, B. (1992) The CD of ligand-DNA systems. 2. poly (dA-dT) B-DNA, Biopolymers 32, 1201-1214.
    • (1992) Biopolymers , vol.32 , pp. 1201-1214
    • Lyng, R.1    Rodger, A.2    Norden, B.3
  • 44
    • 0031848098 scopus 로고    scopus 로고
    • Extending the range of rate constants available from BIACORE: Interpreting mass transport-influenced binding data
    • Myszka, D. G., He, X., Dembo, M., Morton, T. A., and Goldstein, B. (1998) Extending the range of rate constants available from BIACORE: interpreting mass transport-influenced binding data, Biophys. J. 75, 583-594.
    • (1998) Biophys. J , vol.75 , pp. 583-594
    • Myszka, D.G.1    He, X.2    Dembo, M.3    Morton, T.A.4    Goldstein, B.5
  • 45
    • 0032702275 scopus 로고    scopus 로고
    • Affinity analysis of non-steady-state data obtained under mass transport limited conditions using BIACORE technology
    • Karlsson, R. (1999) Affinity analysis of non-steady-state data obtained under mass transport limited conditions using BIACORE technology, J. Mol. Recognit. 12, 285-292.
    • (1999) J. Mol. Recognit , vol.12 , pp. 285-292
    • Karlsson, R.1
  • 46
    • 34247533690 scopus 로고    scopus 로고
    • Biosensor-Surface Plasmon Resonance: Quantitative Analysis Of Small Molecule-Nucleic Acid Interactions
    • Nguyen, B., Tanious, F. A., and Wilson, W. D. (2007) Biosensor-Surface Plasmon Resonance: Quantitative Analysis Of Small Molecule-Nucleic Acid Interactions, Methods 42, 150-161.
    • (2007) Methods , vol.42 , pp. 150-161
    • Nguyen, B.1    Tanious, F.A.2    Wilson, W.D.3
  • 47
    • 0034581194 scopus 로고    scopus 로고
    • Kinetic, equilibrium and thermodynamic analysis of macromolecular interactions with BIACORE
    • Myszka, D. G. (2000) Kinetic, equilibrium and thermodynamic analysis of macromolecular interactions with BIACORE, Methods Enzymol. 323, 325-340.
    • (2000) Methods Enzymol , vol.323 , pp. 325-340
    • Myszka, D.G.1
  • 48
    • 0032576722 scopus 로고    scopus 로고
    • White, S., Szewczyk, Turner, J. W., Baird, E. E., and Dervan, P. B. (1998) Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands, Nature 391, 468-471.
    • White, S., Szewczyk, Turner, J. W., Baird, E. E., and Dervan, P. B. (1998) Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands, Nature 391, 468-471.
  • 49
    • 0037687485 scopus 로고    scopus 로고
    • Imidazopyridine/pyrrole and hydroxy-benimidazole/pyrrole pairs for DNA minor groove recognition
    • Renneberg, D., and Dervan, P. B. (2003) Imidazopyridine/pyrrole and hydroxy-benimidazole/pyrrole pairs for DNA minor groove recognition, J. Am. Chem. Soc. 125, 5707-5716.
    • (2003) J. Am. Chem. Soc , vol.125 , pp. 5707-5716
    • Renneberg, D.1    Dervan, P.B.2
  • 51
    • 4143091493 scopus 로고    scopus 로고
    • Expanding the repertoire of heterocycle ring pairs for programmable minor groove DNA recognition
    • Marques, M. A., Doss, R. M., Foister, S., and Dervan, P. B. (2004) Expanding the repertoire of heterocycle ring pairs for programmable minor groove DNA recognition, J. Am. Chem. Soc. 126, 10339-10349.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 10339-10349
    • Marques, M.A.1    Doss, R.M.2    Foister, S.3    Dervan, P.B.4


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