Abstract
Small molecules that recognize double-stranded DNA have the capacity to modulate various cellular processes, including DNA replication and repair, gene expression, cell cycle regulation, and growth, and therefore may serve as treatments for cancers or various genetic diseases. Currently, most DNA-binding therapeutics target short sequences of DNA with rather low selectivity, causing deleterious effects in both diseased and healthy cells (1). Thus, the development of molecules that target longer, more cell-type-specific sequences of DNA is of great interest. In this chapter, a rapid solid-phase synthesis of hairpin polyamides, a promising class of minor groove binding agents developed by the Dervan group at Caltech, is described (2). The robust coupling methods of aromatic amino acids outlined facilitate the application of combinatorial methods to polyamides and their further development as pharmaceutical reagents.
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References
Lawley P. D. and Phillips D. H. (1996) DNA adducts from chemotherapeutic agents. Mutat. Res. 355, 13–40.
Dervan P. B. and Burli R. W. (1999) Sequence-specific DNA recognition by polyamides. Curr. Op. Chem. Biol. 3, 688–693, and references therein.
Trauger J. W., Baird E. E., and Dervan P. B. (1996) Recognition of DNA by designed ligands at subnanomolar concentrations. Nature 382, 559–561.
Swalley S. E., Baird E. E., and Dervan P. B. (1997) Discrimination of 5'-GGGG-3', 5'-GCGC-3', and 5'-GGCC-3' sequences in the minor groove of DNA by eightring hairpin polyamides. J. Am. Chem. Soc. 119, 6953–6961.
Trauger J. W., Baird E. E., and Dervan P. B. (1998) Recognition of 16 base pairs in the minor groove of DNA by a pyrrole-imidazole polyamide dimer. J. Am. Chem. Soc. 120, 3524–3535.
Kielkopf C. L., Baird E. E., Dervan P. B., and Rees D. C. (1998) Structural basis for G-C recognition in the DNA minor groove. Nature Struct. Biol. 5, 104–109.
Hawkins C. A., de Clairac R. P., Dominery R. N., Baird E. E., White S., Dervan P. B., and Wemmer D. E. (2000) Controlling binding orientation in hairpin polyamide DNA complexes. J. Am. Chem. Soc. 122, 5235–5243.
Satz A. L. and Bruice T. C. (1999) Synthesis of a fluorescent microgonotropen (FMGT-1) and its interactions with the dodecamer d(CCGGAATTCCGG). Bioorg. Med. Chem. Lett. 9, 3261–3266.
Filipowsky M. E., Kopka M. L., Brazil-Zison M., Lown J. W., and Dickerson R. E. (1996) Linked lexitropsins and the in vitro inhibition of HIV-1 reverse transcriptase RNA-directed DNA polymerization: A novel induced-fit of 3,5 m-pyridyl bisdistamycin to enzyme-associated template primer. Biochemistry 35, 15,397–15,410.
For review of distamycin and netropsin analogues: Bailly C. and Chaires J. B. (1998) Sequence-specific DNA minor groove binders. Design and synthesis of netropsin and distamycin analogues. Bioconjugate Chem. 9, 513–538.
Dickinson L. J., Gulizia R. J., Trauger J. W., Baird E. E., Mosier D. E., Gottesfeld J. M., and Dervan P. B. (1998) Inhibition of RNA polymerase II transcription in human cells by synthetic DNA-binding ligands. Proc. Natl. Acad. Sci. USA 95, 12,890–12,895.
Gottesfeld J. M., Neely L., Trauger J. W., Baird E. E., and Dervan P. B. (1997) Regulation of gene expression by small molecules. Nature 387, 202–205.
Janssen S., Cuvier O., Muller M., and Laemmli U. K. (2000) Specific gain-and loss-of-function phenotypes induced by satellite-specific DNA-binding drugs fed to Drosophila melanogaster. Mol. Cell 6, 1013–1024.
Janssen S., Durussel T., and Laemmli U. K. (2000) Chromatin opening of DNA satellites by targeted sequence-specific drugs. Mol. Cell 6, 999–1011.
Wurtz N. R. and Dervan P. B. (2000) Sequence specific alkylation of DNA by hairpin pyrrole-imidazole polyamide conjugates. Chemistry and Biology 7, 153–161.
Tao Z.-F., Fujiwara T., Saito I., and Sugiyama H. (1999) Rational design of sequence-specific DNA alkylating agents based on duocarmycin A and pyrroleimidazole hairpin polyamides. J. Am. Chem. Soc. 121, 4961–4967.
Nishiwaki E., Tanaka S., Lee H., and Shibuya M. (1988) Efficient synthesis of oligo-N-methylpyrrolecarboxamides and related compounds. Heterocycles 27, 1945–1952.
Xiao J., Yuan G., Huang W., Chan A. S. C., and Lee K.-L. D. (2000) A convenient method for the synthesis of DNA-recognizing polyamides in solution. J. Org. Chem. 65, 5506–5513.
Vazquez E., Caamano A. M., Castedo L., and Mascarenas J. L. (1999) An Fmoc solid phase approach to linear poly-pyrrole peptide conjugates. Tet. Lett. 40, 3621–3624.
Wurtz N. R., Turner J. M., Baird E. E., and Dervan P. B. (2001) Fmoc solid phase synthesis of polyamides containing pyrrole and imidazole amino acids. Org. Lett. 3, 1201–1203.
Baird E. E. and Dervan P. B. (1996) Solid phase synthesis of polyamides containing imidazole and pyrrole amino acids. J. Am. Chem. Soc. 118, 6141–6146.
Pitie M., Van Horn J. D., Brion D., Burrows C. J., and Meunier B. (2000) Targeting the DNA cleavage activity of copper phenanthroline and Clip-phen to A-T tracts via linkage to a poly-N-methylpyrrole. Bioconjugate Chem. 11, 892–900.
Sharma S. K., Tandon M., and Lown J. W. (2001) A general solution and solid phase synthetic procedure for incorporating three contiguous imidazole moieties into DNA sequence reading polyamides. J. Org. Chem. 66, 1030–1034.
Schnolzer M., Alewood P., Jones A., Alewood D., and Kent S. B. (1992) In situ neutralization in Boc-chemistry solid phase peptide synthesis. Int. J. Pept. Res. 40, 180–193.
Albericio F. and Carpino L. A. (1997) Coupling reagents and activation. Methods Enzymol. 289, 104–126.
Alewood P., Alewood D., Miranda L., Love S., Meutermans W., and Wilson D. (1997) Rapid in situ neutralization protocols for Boc and Fmoc solid-phase chemistries. Methods Enzymol. 289, 14–29.
Miranda L. P. and Alewood P. F. (1999) Accelerated chemical synthesis of peptides and small proteins. Proc. Natl. Acad. Sci. USA 96, 1181–1186.
Carpino L. A. and El-Faham A. (1999) The diisopropyl/1-hydroxy-7-azabenzotriazole system: segment coupling and stepwise peptide assembly. Tetrahedron 55, 6813–6830.
Lundt B. F., Johansen N. L., Volund A., and Maskussen J. (1978) Removal of t-butoxycarbonyl protecting groups with trifluoroacetic acid. Int. J. Pept. Prot. Res. 12, 258–268.
Pearson D. A., Blanchette M., Baker M. L., and Guindon C. A. (1989) Trialkylsilanes as scavengers for the trifluoroacetic acid deblocking of protecting groups in peptide synthesis. Tet. Lett. 30, 2739–2742.
Sole N. A. and Barany G. (1992) Optimization of solid-phase synthesis of [Ala8]-dynorphin A. J. Org. Chem. 57, 5399–5403.
Moore W. T. (1997) Laser desorption mass spectrometry. Methods Enzymol. 289, 520–542.
Burdick D. J. and Stults J. T. (1997) Analysis of peptide synthesis products by electrospray ionization mass spectrometry. Methods Enzymol. 289, 499–519.
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.
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Krutzik, P.O., Chamberlin, A.R. (2002). Synthesis of DNA-Binding Polyamides. In: English, L.B. (eds) Combinatorial Library. Methods in Molecular Biology™, vol 201. Springer, Totowa, NJ. https://doi.org/10.1385/1-59259-285-6:77
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DOI: https://doi.org/10.1385/1-59259-285-6:77
Publisher Name: Springer, Totowa, NJ
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