Dervan Lab Publications

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Number
Title, Authors
Journal Volume, Pages (Year)
313
"Programming Multiple Protein Patterns on a Single DNA Nanostructure," Justin D. Cohen, John P. Sadowski, Peter B. Dervan.
J. Am. Chem. Soc. 130, 402-403 (2008).
312
"The Reach of Linear Protein-DNA Dimerizers," Ryan L. Stafford, Peter B. Dervan.
J. Am. Chem. Soc. 129, 14026-14033 (2007).
311
"α-Diaminobutyric acid-linked hairpin polyamides," Michelle E. Farkas, Sherry M. Tsai, Peter B. Dervan.
Bioorg. Med. Chem. 15, 6927-6936 (2007).
310
"Recognition of "Mirror-Image" DNA by Small Molecules," Christian Dose, Dominik Ho, Hermann E. Gaub, Peter B. Dervan, Christian H. Albrecht.
Angew. Chem. Int. Ed. 46, 8384-8387 (2007).
309
"Quantitative Microarray Profiling of DNA Binding Molecules," James W. Puckett, Katy A. Muzikar, Josh Tietjen, Christopher L. Warren, Aseem Z. Ansari, Peter B. Dervan.
J. Am. Chem. Soc. 129, 12310-12319 (2007).
308
"Addressing Single Molecules on DNA Nanostructures," Justin D. Cohen, John P. Sadowski, Peter B. Dervan.
Angew. Chem. Int. Ed. 46, 7956-7959 (2007).
307
"Modulating Hypoxia-Inducible Transcription by Disrupting the HIF-1–DNA Interface," Nicholas G. Nickols, Claire S. Jacobs, Michelle E. Farkas, Peter B. Dervan.
ACS Chem. Biol. 2, 561-571 (2007).
306
"Suppression of androgen receptor-mediated gene expression by a sequence-specific DNA-binding polyamide," Nicholas G. Nickols, Peter B. Dervan.
Proc. Natl. Acad. Sci. USA 104, 10418-10423 (2007).
305
"Fluorescent Sequence-Specific dsDNA Binding Oligomers," David M. Chenoweth, Anne Viger, Peter B. Dervan.
J. Am. Chem. Soc. 129, 2216-2217 (2007).
304
"Completion of a Programmable DNA-Binding Small Molecule Library," Carey F. Hsu, John W. Phillips, John W. Trauger, Michelle E. Farkas, Jason M. Belitsky, Alexander Heckel, Bogdan Z. Olenyuk, James W. Puckett, Clay C. C. Wang, Peter B. Dervan.
Tetrahedron 63, 6146-6151 (2007).
303
"Minimization of a Protein-DNA Dimerizer," Ryan L. Stafford, Hans-Dieter Arndt, Mary L. Brezinski, Aseem Z. Ansari, Peter B. Dervan.
J. Am. Chem. Soc. 129, 2660-2668 (2007).
302
"Unanticipated Differences in the Comparison of α- versus γ-Diaminobutyric Acid-linked Hairpin Polyamide-Alkylator Conjugates," Sherry M. Tsai, Michelle E. Farkas, C. J. Chou, Joel M. Gottesfeld, Peter B. Dervan.
Nucleic Acids Res. 35, 307-316 (2007).
301
"Programmable oligomers targeting 5'-GGGG-3' in the minor groove of DNA and NF-κB binding inhibition," David M. Chenoweth, Julie A. Poposki, Michael A. Marques, Peter B. Dervan.
Bioorg. Med. Chem. 15, 759-770 (2007).
300
"Improved Nuclear Localization of DNA-binding polyamides," Nicholas G. Nickols, Claire S. Jacobs, Michelle E. Farkas, Peter B. Dervan.
Nucleic Acids Res. 35, 363-370 (2007).
299
"Exploring the limits of benzimidazole DNA-binding oligomers for the hypoxia inducible factor (HIF) site," Anne Viger, Peter B. Dervan.
Bioorg. Med. Chem. 14, 8539-8549 (2006).
298
"DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA·TTC repeats in Friedreich's ataxia," Ryan Burnett, Christian Melander, James W. Puckett, Leslie S. Son, Robert D. Wells, Peter B. Dervan, Joel M. Gottesfeld.
Proc. Natl. Acad. Sci. USA 103, 11497-11502 (2006).
297
"A two-hit mechanism for pre-mitotic arrest of cancer cell proliferation by a polyamide-alkylator conjugate," D. Alvarez, C. J. Chou, L. Latella, S. G. Zeitlin, S. Ku, P. L. Puri, Peter B. Dervan, Joel M. Gottesfeld.
Cell Cycle 5, 1537-1548 (2006).
296
"Programmable Oligomers for Minor Groove DNA Recognition," Raymond M. Doss, Michael A. Marques, Shane Foister, David M. Chenoweth, Peter B. Dervan.
J. Am. Chem. Soc. 128, 9074-9079 (2006).
295
"Defining the sequence-recognition profile of DNA-binding molecules," Christopher L. Warren, Natasha C. S. Kartochvil, Karl E. Hauschild, Shane Foister, Mary L. Brezinski, Peter B. Dervan, George N. Phillips, Jr., Aseem Z. Ansari.
Proc. Natl. Acad. Sci. USA 103, 867-872 (2006).
294
"Sequence-Specific Fluorescence Detection of DNA by Polyamide-Thiazole Orange Conjugates," Eric J. Fechter, Bogdan Olenyuk, Peter B. Dervan.
J. Am. Chem. Soc. 127, 16685-16691 (2005).
293
"Programmable DNA binding oligomers for control of transcription," Peter B. Dervan, Raymond M. Doss, Michael A. Marques.
Curr. Med. Chem.: Anti-Cancer Agents 5, 373-387 (2005).
292
"Inhibition of DNA Binding by Human Estrogen-Related Receptor 2 and Estrogen Receptor α with Minor Groove Binding Polyamides," Micah D. Gerhart, Liliane Dickinson, Jennifer Ehley, Christian Melander, Peter B. Dervan, Peter E. Wright, Joel M. Gottesfeld.
Biochemistry 44, 4196-4203 (2005).
291
"Temperature-sensitive protein-DNA dimerizers," Karl E. Hauschild, Renee E. Metzler, Hans-Dieter Arndt, Rocco Moretti, Marni Raffaelle, Peter B. Dervan, Aseem Z. Ansari.
Proc. Natl. Acad. Sci. USA 102, 5008-5013 (2005).
290
"DNA Damage Effects of a Polyamide-CBI Conjugate in SV40 Virions," Brian J. Philips, Aileen Y. Chang, Peter B. Dervan, Terry A. Beerman.
Mol. Pharmacol. 67, 877-882 (2005).
289
"Nucleosomes in Solution Exist as a Mixture of Twist-defect States," Rajeswari S. Edayathumangalam, Philipp Weyermann, Peter B. Dervan, Joel M. Gottesfeld, Karolin Luger.
J. Mol. Biol. 345, 103-114 (2005).
288
"Small Molecule Transcription Factor Mimic," Youngjoo Kwon, Hans-Dieter Arndt, Qian Mao, Yongmun Choi, Yoshinori Kawazoe, Peter B. Dervan, Motonari Uesugi.
J. Am. Chem. Soc. 126, 15940-15941 (2004).
287
"Inhibition of vascular endothelial growth factor with a sequence-specific hypoxia response element antagonist," Bogdan Z. Olenyuk, Guo-Jun Zhang, Jeffrey M. Klco, Nicholas G. Nickols, William G. Kaelin, Jr., Peter B. Dervan.
Proc. Natl. Acad. Sci. USA 101, 16768-16773 (2004).
286
"Arresting Cancer Proliferation by Small-Molecule Gene Regulation," Liliane A. Dickinson, Ryan Burnett, Christian Melander, Benjamin S. Edelson, Paramjit S. Arora, Peter B. Dervan, Joel M. Gottesfeld.
Chem. Biol. 11, 1583-1594 (2004).
285
"Paradoxical Effects of DNA Binding Polyamides on HTLV-1 Transcription," Jill A. Livengood, Eric J. Fechter, Peter B. Dervan, Jennifer K. Nyborg.
Front. Biosci. 9, 3058-3067 (2004).
284
"Expanding the Repertoire of Heterocycle Ring Pairs for Programmable Minor Groove DNA Recognition," Michael A. Marques, Raymond M. Doss, Shane Foister, Peter B. Dervan.
J. Am. Chem. Soc. 126, 10339-10349 (2004).
283
"NMR Structure of a Cyclic Polyamide-DNA Complex," Qing Zhang, Tammy J. Dwyer, Vickie Tsui, David A. Case, Junhyeong Cho, Peter B. Dervan, David E. Wemmer.
J. Am. Chem. Soc. 126, 7958-7966 (2004).
282
"Influence of structural variation on nuclear localization of DNA-binding polyamide-fluorophore conjugates," Benjamin S. Edelson, Timothy P. Best, Bogdan Olenyuk, Nicholas G. Nickols, Raymond M. Doss, Shane Foister, Alexander Heckel, Peter B. Dervan.
Nucleic Acids Res. 32, 2802-2818 (2004).
281
"Regulation of Gene Expression by Synthetic DNA-Binding Ligands," Peter B. Dervan, Adam T. Poulin-Kerstien, Eric J. Fechter, Benjamin S. Edelson.
Top. Curr. Chem. 253, 1-31 (2005).
280
"Design of a Sequence-Specific DNA Bisintercalator," Eric J. Fechter, Bogdan Olenyuk, Peter B. Dervan.
Angew. Chem. Int. Ed. 43, 3591-3594 (2004).
279
"Polyamides Reveal a Role for Repression in Latency within Resting T Cells of HIV-Infected Donors," Loyda Ylisastigui, Jason J. Coull, Victor C. Rucker, Christian Melander, Ronald J. Bosch, Scott J. Brodie, Lawrence Corey, Donald L. Sodora, Peter B. Dervan, David M. Margolis.
J. Infect. Dis. 190, 1429-1437 (2004).
278
"DNA Minor-Groove Recognition by 3-Methylthiophene/Pyrrole Pair," Raymond M. Doss, Michael A. Marques, Shane Foister, Peter B. Dervan.
Chem. Biodiversity 1, 886-899 (2004).
277
"Mechanism of Sequence-Specific Fluorescent Detection of DNA by N-Methyl-imidazole, N-Methyl-pyrrole, and β-Alanine Linked Polyamides," Victor C. Rucker, Alexander R. Dunn, Shantanu Sharma, Peter B. Dervan, Harry B. Gray.
J. Phys. Chem. B 108, 7490-7494 (2004).
276
"Molecular recognition of the nucleosomal "supergroove"," Rajeswari S. Edayathumangalam, Philipp Weyermann, Joel M. Gottesfeld, Peter B. Dervan, Karolin Luger.
Proc. Natl. Acad. Sci. USA 101, 6864-6869 (2004).
275
"Allosteric Inhibition of Zinc-Finger Binding in the Major Groove of DNA by Minor-Groove Binding Ligands," Doan H. Nguyen-Hackley, Elizabeth Ramm, Christina M. Taylor, J. Keith Joung, Peter B. Dervan, Carl O. Pabo.
Biochemistry 43, 3880-3890 (2004).
273
"DNA-Templated Dimerization of Hairpin Polyamides," Adam T. Poulin-Kerstien, Peter B. Dervan.
J. Am. Chem. Soc. 125, 15811-15821 (2003).
272
"Toward Artificial Developmental Regulators," Hans-Dieter Arndt, Karl E. Hauschild, David P. Sullivan, Kara Lake, Peter B. Dervan, Aseem Z. Ansari.
J. Am. Chem. Soc. 125, 13322-13323 (2003).
271
"Nuclear localization of pyrrole-imidazole polyamide-fluorescein conjugates in cell culture," Timothy P. Best, Benjamin S. Edelson, Nicholas G. Nickols, Peter B. Dervan.
Proc. Natl. Acad. Sci. USA 100, 12063-12068 (2003).
270
"Accessibility of Nuclear Chromatin by DNA Binding Polyamides," Brigitte A. Dudouet, Ryan Burnett, Liliane A. Dickinson, Malcolm R. Wood, Christian Melander, Jason M. Belitsky, Benjamin Edelson, Nicholas Wurtz, Christoph Briehn, Peter B. Dervan, Joel M. Gottesfeld.
Chem. Biol. 10, 859-867 (2003).
269
"Influence of β-Alanine on Hairpin Polyamide Orientation in the DNA Minor Groove," Victor C. Rucker, Christian Melander, Peter B. Dervan.
Helv. Chim. Acta 87, 1839-1851 (2003).
268
"Shape Selective Recognition of T·A Base Pairs by Hairpin Polyamides Containing N-Terminal 3-Methoxy (and 3-Chloro) Thiophene Residues," Shane Foister, Michael A. Marques, Raymond M. Doss, Peter B. Dervan.
Bioorg. Med. Chem. 11, 4333-4340 (2003).
267
"Recognition of the DNA minor groove by pyrrole-imidazole polyamides," Peter B. Dervan, Benjamin S. Edelson.
Curr. Opin. Struc. Biol. 13, 284-299 (2003).
266
"U-Pin Polyamide Motif for Recognition of the DNA Minor Groove," Alexander Heckel, Peter B. Dervan.
Chem. Eur. J. 9, 3353-3366 (2003).
265
"Allosteric Inhibition of Protein-DNA Complexes by Polyamide-Intercalator Conjugates," Eric J. Fechter, Peter B. Dervan.
J. Am. Chem. Soc. 125, 8476-8485 (2003).
264
"Inhibition of Moloney Murine Leukemia Virus Integration Using Polyamides Targeting the Long-Terminal Repeat Sequences," Fan Yang, Jason M. Belitsky, Rodrigo A. Villanueva, Peter B. Dervan, Monica J. Roth.
Biochemistry 42, 6249-6258 (2003).
263
"Imidazopyridine/Pyrrole and Hydroxybenzimidazole/Pyrrole Pairs for DNA Minor Groove Recognition," Dorte Renneberg, Peter B. Dervan.
J. Am. Chem. Soc. 125, 5707-5716 (2003).
262
"Alternative Heterocycles for DNA Recognition: The Benzimidazole/Imidazole Pair," Christoph A. Briehn, Philipp Weyermann, Peter B. Dervan.
Chem. Eur. J. 9, 2110-2122 (2003).
261
"Parallel Synthesis of H-pin Polyamides by Alkene Metathesis on Solid Phase," Bogdan Olenyuk, Cristian Jitianu, Peter B. Dervan.
J. Am. Chem. Soc. 125, 4741-4751 (2003).
260
"Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands," Robert K. Suto, Rajeswari S. Edayathumangalam, Cindy L. White, Christian Melander, Joel M. Gottesfeld, Peter B. Dervan, Karolin Luger.
J. Mol. Biol. 326, 371-380 (2003).
259
"DNA crosslinking and biological activity of a hairpin polyamide-chlorambucil conjugate," Yong-Dong Wang, Jaroslaw Dziegielewski, Nicholas R. Wurtz, Barbara Dziegielewska, Peter B. Dervan, Terry A. Beerman.
Nucleic Acids Res. 31, 1208-1215 (2003).
258
"Sequence Specific Fluorescence Detection of Double Strand DNA," Victor C. Rucker, Shane Foister, Christian Melander, Peter B. Dervan.
J. Am. Chem. Soc. 125, 1195-1202 (2003).
257
"Cell-free and Cellular Activities of a DNA Sequence Selective Hairpin Polyamide-CBI Conjugate," Yong-Dong Wang, Jaroslaw Dziegielewski, Aileen Y. Chang, Peter B. Dervan, Terry A. Beerman.
J. Biol. Chem. 277, 42431-42437 (2002).
256
"Toward an Understanding of the Chemical Etiology for DNA Minor-Groove Recognition by Polyamides," Michael A. Marques, Raymond M. Doss, Adam R. Urbach, Peter B. Dervan.
Helv. Chim. Acta 85, 4485-4517 (2002).
255
"Design of Artificial Transcriptional Activators with Rigid Poly-L-proline Linkers," Paramjit S. Arora, Aseem Z. Ansari, Timothy P. Best, Mark Ptashne, Peter B. Dervan.
J. Am. Chem. Soc. 124, 13067-13071 (2002).
254
"Analysis of Hairpin Polyamide Complexes Having DNA Binding Sites in Close Proximity," Cheryl A. Hawkins, Eldon E. Baird, Peter B. Dervan, David E. Wemmer.
J. Am. Chem. Soc. 124, 12689-12696 (2002).
253
"Targeted Derepression of the Human Immunodeficiency Virus Type 1 Long Terminal Repeat by Pyrrole-Imidazole Polyamides," Jason J. Coull, Guocheng He, Christian Melander, Victor C. Rucker, Peter B. Dervan, David M. Margolis.
J. Virol. 76, 12349-12354 (2002).
252
"Structure of a β-Alanine-linked Polyamide Bound to a Full Helical Turn of Purine Tract DNA in the 1:1 Motif," Adam R. Urbach, John J. Love, Scott A. Ross, Peter B. Dervan.
J. Mol. Biol. 320, 55-71 (2002).
251
"Recognition of Ten Base Pairs of DNA by Head-to-Head Hairpin Dimers," Philipp Weyermann, Peter B. Dervan.
J. Am. Chem. Soc. 124, 6872-6876 (2002).
250
"Blocking Transcription Through a Nucleosome with Synthetic DNA Ligands," Joel M. Gottesfeld, Jason M. Belitsky, Christian Melander, Peter B. Dervan, Karolin Luger.
J. Mol. Biol. 321, 249-263 (2002).
249
"Cellular Uptake of N-Methylpyrrole/N-Methylimidazole Polyamide-Dye Conjugates," Jason M. Belitsky, Stephanie J. Leslie, Paramjit S. Arora, Terry A. Beerman, Peter B. Dervan.
Bioorg. Med. Chem. 10, 3313-3318 (2002).
248
"Search for the Optimal Linker in Tandem Hairpin Polyamides," Inger Kers, Peter B. Dervan.
Bioorg. Med. Chem. 10, 3339-3349 (2002).
247
"Solid-Phase Synthesis of DNA Binding Polyamides on Oxime Resin," Jason M. Belitsky, Doan H. Nguyen, Nicholas R. Wurtz, Peter B. Dervan.
Bioorg. Med. Chem. 10, 2767-2774 (2002).
246
"Inhibition of DNA Binding by NF-κB with Pyrrole-Imidazole Polyamides," Nicholas R. Wurtz, Joel L. Pomerantz, David Baltimore, Peter B. Dervan.
Biochemistry 41, 7604-7609 (2002).
245
"Promoter Scanning for Transcription Inhibition with DNA-Binding Polyamides," Jennifer A. Ehley, Christian Melander, David Herman, Eldon E. Baird, Heather A. Ferguson, James A. Goodrich, Peter B. Dervan, Joel M. Gottesfeld.
Mol. Cell. Biol. 22, 1723-1733 (2002).
243
"Molecular Recognition of DNA by Small Molecules," Peter B. Dervan.
Bioorg. Med. Chem. 9, 2215-2235 (2001).
242
"Sequence-Specific Trapping of Topoisomerase I by DNA Binding Polyamide-Camptothecin Conjugates," Clay C. C. Wang, Peter B. Dervan.
J. Am. Chem. Soc. 123, 8657-8661 (2001).
241
"Inhibition of Major Groove DNA Binding bZIP Proteins by Positive Patch Polyamides," Ryan E. Bremer, Nicholas R. Wurtz, Jason W. Szewczyk, Peter B. Dervan.
Bioorg. Med. Chem. 9, 2093-2103 (2001).
240
"Towards a minimal motif for artificial transcriptional activators," Aseem Z. Ansari, Anna K. Mapp, Doan H. Nguyen, Peter B. Dervan, Mark Ptashne.
Chem. Biol. 8, 583-592 (2001).
239
"Footprinting Methods for Analysis of Pyrrole-Imidazole/DNA Complexes," John W. Trauger, Peter B. Dervan.
Methods Enzymol. 340, 450-466 (2001).
238
"Sequence-specific Recognition of DNA in the Nucleosome by Pyrrole-Imidazole Polyamides," Joel M. Gottesfeld, Christian Melander, Robert K. Suto, Holger Raviol, Karolin Luger, Peter B. Dervan.
J. Mol. Biol. 309, 615-629 (2001).
237
"Fmoc Solid Phase Synthesis of Polyamides Containing Pyrrole and Imidazole Amino Acids," Nicholas R. Wurtz, James M. Turner, Eldon E. Baird, Peter B. Dervan.
Org. Lett. 3, 1201-1203 (2001).
236
"Toward rules for 1:1 polyamide:DNA recognition," Adam R. Urbach, Peter B. Dervan.
Proc. Natl. Acad. Sci. USA 98, 4343-4348 (2001).
235
"Expanding the Recognition of the Minor Groove of DNA by Incorporation of β-Alanine in Hairpin Polyamides," Clay C. C. Wang, Ulf Ellervik, Peter B. Dervan.
Bioorg. Med. Chem. 9, 653-657 (2001).
234
"Alternative Heterocycles for DNA Recognition: An N-Methylpyrazole/N-Methylpyrrole Pair Specifies for A·T/T·A Base Pairs," Doan H. Nguyen, Jason W. Szewczyk, Eldon E. Baird, Peter B. Dervan.
Bioorg. Med. Chem. 9, 7-17 (2001).
233
"Kinetic Consequences of Covalent Linkage of DNA Binding Polyamides," Ramesh Baliga, Eldon E. Baird, David M. Herman, Christian Melander, Peter B. Dervan, Donald M. Crothers.
Biochemistry 40, 3-8 (2001).
232
"Preparation of thioesters for the ligation of peptides with non-native substrates," Anna K. Mapp, Peter B. Dervan.
Tetrahedron Lett. 41, 9451-9454 (2000).
231
"Discrimination of A/T Sequences in the Minor Groove of DNA within a Cyclic Polyamide Motif," Christian Melander, David M. Herman, Peter B. Dervan.
Chem. Eur. J. 6, 4487-4497 (2000).
230
"Hydroxybenzamide/Pyrrole Pair Distinguishes T·A from A·T Base Pairs in the Minor Groove of DNA," Ulf Ellervik, Clay C. C. Wang, Peter B. Dervan.
J. Am. Chem. Soc. 122, 9354-9360 (2000).
229
"Chemical Approaches to Control Gene Expression," Joel M. Gottesfeld, James M. Turner, Peter B. Dervan.
Gene Expression 9, 77-92 (2000).
228
"Alternative Heterocycles for DNA Recognition: A 3-Pyrazole/Pyrrole Pair Specifies for G·C Base Pairs," Zheng-Yun J. Zhan, Peter B. Dervan.
Bioorg. Med. Chem. 8, 2467-2474 (2000).
227
"Molecular Recognition of DNA by Hoechst Benzimidazoles: Exploring Beyond the Pyrrole-Imidazole-Hydroxypyrrole Polyamide-Pairing Code," Thomas G. Minehan, Konstanze Gottwald, Peter B. Dervan.
Helv. Chim. Acta 83, 2197-2213 (2000).
226
"Asymmetric DNA Binding by A Homodimeric bHLH Protein," Rachel L. Winston, Jennifer A. Ehley, Eldon E. Baird, Peter B. Dervan, Joel M. Gottesfeld.
Biochemistry 39, 9092-9098 (2000).
225
"Recognition of the Minor Groove of DNA by Hairpin Polyamides Containing α-Substituted-β-Amino Acids," Paul E. Floreancig, Susanne E. Swalley, John W. Trauger, Peter B. Dervan.
J. Am. Chem. Soc. 122, 6342-6350 (2000).
224
"Recognition of the DNA Minor Groove by Pyrrole-Imidazole Polyamides: Comparison of Desmethyl- and N-Methylpyrrole," Ryan E. Bremer, Jason W. Szewczyk, Eldon E. Baird, Peter B. Dervan.
Bioorg. Med. Chem. 8, 1947-1955 (2000).
223
"Targeting the Ets Binding Site of the HER2/neu Promoter with Pyrrole-Imidazole Polyamides," Shu-Yuan Chiang, Roland W. Bürli, Chris C. Benz, Loretta Gawron, Gary K. Scott, Peter B. Dervan, Terry A. Beerman.
J. Biol. Chem. 275, 24246-24254 (2000).
222
"Controlling Binding Orientation in Hairpin Polyamide DNA Complexes," Cheryl A. Hawkins, Rafael Peláez de Clairac, Raymond N. Dominey, Eldon E. Baird, Sarah White, Peter B. Dervan, David E. Wemmer.
J. Am. Chem. Soc. 122, 5235-5243 (2000).
221
"Strand Selective Cleavage of DNA by Diastereomers of Hairpin Polyamide-seco-CBI Conjugates," Aileen Y. Chang, Peter B. Dervan.
J. Am. Chem. Soc. 122, 4856-4864 (2000).
220
"Selective inhibition of DNA gyrase in vitro by a GC specific eight-ring hairpin polyamide at nanomolar concentration," H. Simon, L. Kittler, Eldon E. Baird, Peter B. Dervan, C. Zimmer.
FEBS Lett. 471, 173-176 (2000).
219
"Activation of gene expression by small molecule transcription factors," Anna K. Mapp, Aseem Z. Ansari, Mark Ptashne, Peter B. Dervan.
Proc. Natl. Acad. Sci. USA 97, 3930-3935 (2000).
218
"Sequence specific alkylation of DNA by hairpin pyrrole-imidazole polyamide conjugates," Nicholas R. Wurtz, Peter B. Dervan.
Chem. Biol. 7, 153-161 (2000).
217
"Structural Effects of DNA Sequence on T·A Recognition by Hydroxypyrrole/Pyrrole Pairs in the Minor Groove," Clara L. Kielkopf, Ryan E. Bremer, Sarah White, Jason W. Szewczyk, James M. Turner, Eldon E. Baird, Peter B. Dervan, Douglas C. Rees.
J. Mol. Biol. 295, 557-567 (2000).
216
"Sequence Selectivity of 3-Hydroxypyrrole/Pyrrole Ring Pairings in the DNA Minor Groove," Adam R. Urbach, Jason W. Szewczyk, Sarah White, James M. Turner, Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 121, 11621-11629 (1999).
215
"Sequence-specific DNA recognition by polyamides," Peter B. Dervan, Roland W. Bürli.
Curr. Opin. Chem. Biol. 38, 688-693 (1999).
214
"The Tax Protein-DNA Interaction is Essential for HTLV-I Transactivation in Vitro," Brian A. Lenzmeier, Eldon E. Baird, Peter B. Dervan, Jennifer K. Nyborg.
J. Mol. Biol. 291, 731-744 (1999).
213
"Anti-represion of RNA Polymerase II Transcription by Pyrrole-Imidazole Polyamides," Liliane A. Dickinson, John W. Trauger, Eldon E. Baird, Peter Ghazal, Peter B. Dervan, Joel M. Gottesfeld.
Biochemistry 38, 10801-10807 (1999).
212
"Inhibition of Ets-1 DNA Binding and Ternary Complex Formation between Ets-1, NF-κB, and DNA by a Designed DNA-binding Ligand," Liliane A. Dickinson, John W. Trauger, Eldon E. Baird, Peter B. Dervan, Barbara J. Graves, Joel M. Gottesfeld.
J. Biol. Chem. 274, 12765-12773 (1999).
211
"Minor Groove DNA-Protein Contacts Upstream of a tRNA Gene Detected with a Synthetic DNA Binding Ligand," Steven J. McBryant, Eldon E. Baird, John W. Trauger, Peter B. Dervan, Joel M. Gottesfeld.
J. Mol. Biol. 286, 973-981 (1999).
210
"NMR Characterization of the Aliphatic β/β Pairing for Recognition of A·T/T·A Base Pairs in the Minor Groove of DNA," Rafael Peláez Lamamie de Clairac, Christian J. Seel, Bernhard H. Geierstanger, Milan Mrksich, Eldon E. Baird, Peter B. Dervan, David E. Wemmer.
J. Am. Chem. Soc. 121, 2956-2964 (1999).
209
"The Thermodynamics of Polyamide-DNA Recognition: Hairpin Polyamide Binding in the Minor Groove of Duplex DNA," Daniel S. Pilch, Nataša Poklar, Eldon E. Baird, Peter B. Dervan, Kenneth J. Breslauer.
Biochemistry 38, 2143-2151 (1999).
208
"Tandem Hairpin Motif for Recognition in the Minor Groove of DNA by Pyrrole-Imidazole Polyamides," David M. Herman, Eldon E. Baird, Peter B. Dervan.
Chem. Eur. J. 5, 975-983 (1999).
207
"Cycle Polyamide Motif for Recognition of the Minor Groove of DNA," David M. Herman, James M. Turner, Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 121, 1121-1129 (1999).
206
"Effects of γ-Turn and β-Tail Amino Acids on Sequence-Specific Recognition of DNA by Hairpin Polyamides," Susanne E. Swalley, Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 121, 1113-1120 (1999).
205
"Affinity and Specificity of Multiple Hydroxypyrrole/Pyrrole Ring Pairings for Coded Recognition of DNA," Sarah White, James M. Turner, Jason W. Szewczyk, Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 121, 260-261 (1999).
204
"Inhibition of RNA polymerase II transcription in human cells by synthetic DNA-binding ligands," Liliane A. Dickinson, Richard J. Gulizia, John W. Trauger, Eldon E. Baird, Donald E. Mosier, Joel M. Gottesfeld, Peter B. Dervan.
Proc. Natl. Acad. Sci. USA 95, 12890-12895 (1998).
203
"A Structural Basis for Recognition of A·T and T·A Base Pairs in the Minor Groove of B-DNA," Clara L. Kielkopf, Sarah White, Jason W. Szewczyk, James M. Turner, Eldon E. Baird, Peter B. Dervan, Douglas C. Rees.
Science 282, 111-115 (1998).
202
"Aliphatic/Aromatic Amino Acid Pairings for Polyamide Recognition in the Minor Groove of DNA," James M. Turner, Susanne E. Swalley, Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 120, 6219-6226 (1998).
201
"Cooperative Hairpin Dimers for Recognition of DNA by Pyrrole-Imidazole Polyamides," John W. Trauger, Eldon E. Baird, Peter B. Dervan.
Angew. Chem. Int. Ed. 37, 1421-1423 (1998).
200
"Recognition of 16 Base Pairs in the Minor Groove of DNA by a Pyrrole-Imidazole Polyamide Dimer," John W. Trauger, Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 120, 3534-3535 (1998).
199
"Structure of a stereoregular phosphorothioate DNA/RNA duplex," M. Bachelin, G. Hessler, G. Kurz, J. G. Hacia, P. B. Dervan, H. Kessler.
Nat. Struct. Biol. 5, 271-276 (1998).
198
"Inhibition of major-groove-binding-proteins by pyrrole-imidazole polyamides with an Arg-Pro-Arg positive patch," Ryan E. Bremer, Eldon E. Baird, Peter B. Dervan.
Chem. Biol. 5, 119-133 (1998).
197
"A Comparison of H-Pin and Hairpin Polyamide Motifs for the Recognition of the Minor Groove of DNA," William A. Greenberg, Eldon E. Baird, Peter B. Dervan.
Chem. Eur. J. 4, 796-805 (1998).
196
"Structural basis for G·C recognition in the DNA minor groove," Clara L. Kielkopf, Eldon E. Baird, Peter B. Dervan, Douglas C. Rees.
Nat. Struct. Biol. 5, 104-109 (1998).
195
"Stereochemical Control of the DNA Binding Affinity, Sequence Specificity, and Orientation Preference of Chiral Hairpin Polyamides in the Minor Groove," David M. Herman, Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 120, 1382-1391 (1998).
194
"Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands," Sarah White, Jason W. Szewczyk, James M. Turner, Eldon E. Baird, Peter B. Dervan.
Nature 391, 468-471 (1998).
193
"Importance of Minor Groove Binding Zinc Fingers within the Transcription Factor IIIA-DNA Complex," Laura Neely, John W. Trauger, Eldon E. Baird, Peter B. Dervan, Joel M. Gottesfeld.
J. Mol. Biol. 274, 439-445 (1997).
192
"136. Triple-Helix Formation by Pyrimidine Oligonucleotides Containing Nonnatural Nucleosides with Extended Aromatic Nucleobases: Intercalation from the Major Groove as a Method for Recognizing C&mid," Thomas E. Lehmann, William A. Greenberg, David A. Liberles, Carol K. Wada, Peter B. Dervan.
Helv. Chim. Acta 80, 2002-2022 (1997).
191
"On the pairing rules for recognition in the minor groove of DNA by pyrrole-imidazole polyamides," Sarah White, Eldon E. Baird, Peter B. Dervan.
Chem. Biol. 4, 569-576 (1997).
190
"Orientation Preferences of Pyrrole-Imidazole Polyamides in the Minor Groove of DNA," Sarah White, Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 119, 8756-8765 (1997).
189
"A Pyrrole-Imidazole Polyamide Motif for Recognition of Eleven Base Pair Sequences in the Minor Groove of DNA," Susanne E. Swalley, Eldon E. Baird, Peter B. Dervan.
Chem. Eur. J. 3, 1600-1607 (1997).
188
"Recognition of Seven Base Pair Sequences in the Minor Groove of DNA by Ten-Ring Pyrrole-Imidazole Polyamide Hairpins," James M. Turner, Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 119, 7636-7644 (1997).
187
"Discrimination of 5'-GGGG-3', 5'-GCGC-3', and 5'-GGCC-3' Sequences in the Minor Groove of DNA by Eight-Ring Hairpin Polyamides," Susanne E. Swalley, Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 119, 6953-6961 (1997).
186
"Targeting the minor groove of DNA," David E. Wemmer, Peter B. Dervan.
Curr. Opin. Struc. Biol. 7, 355-361 (1997).
185
"NMR Characterization of Hairpin Polyamide Complexes with the Minor Groove of DNA," Rafael Peláez Lamamie de Clairac, Bernhard H. Geierstanger, Milan Mrksich, Peter B. Dervan, David E. Wemmer.
J. Am. Chem. Soc. 119, 7909-7916 (1997).
184
"Regulation of gene expression by small molecules," Joel M. Gottesfeld, Laura Neely, John W. Trauger, Eldon E. Baird, Peter B. Dervan.
Nature 387, 202-205 (1997).
183
"Kinetic Analysis of Sequence-Specific Alkylation of DNA by Pyrimidine Oligodeoxyribonucleotide-Directed Triple-Helix Formation," Matthew J. Taylor, Peter B. Dervan.
Bioconjugate Chem. 8, 354-364 (1997).
182
"Solution Structure of an Intramolecular DNA Triplex Containing an N7-Glycosylated Guanine Which Mimics a Protonated Cytosine," Karl M. Koshlap, Peter Schultze, Helmut Brunar, Peter B. Dervan, Juli Feigon.
Biochemistry 36, 2659-2668 (1997).
181
"Effects of the A·T/T·A Degeneracy of Pyrrole-Imidazole Polyamide Recognition in the Minor Groove of DNA," Sarah White, Eldon E. Baird, Peter B. Dervan.
Biochemistry 35, 12532-12537 (1996).
180
"Sequence-Specific Alkylation and Cleavage of DNA Mediated by Purine Motif Triple Helix Formation," Kathryn B. Grant, Peter B. Dervan.
Biochemistry 35, 12313-12319 (1996).
179
"Design of artificial sequence-specific DNA bending ligands," David A. Liberles, Peter B. Dervan.
Proc. Natl. Acad. Sci. USA 93, 9510-9514 (1996).
178
"Recognition of a 5'-(A,T)GGG(A,T)2-3' Sequence in the Minor Groove of DNA by an Eight-Ring Hairpin Polyamide," Susanne E. Swalley, Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 118, 8198-8206 (1996).
177
"Binding of a hairpin polyamide in the minor groove of DNA: Sequence-specific enthalpic discrimination," Daniel S. Pilch, Nataša Poklar, Craig A. Gelfand, Scott M. Law, Kenneth J. Breslauer, Eldon E. Baird, Peter B. Dervan.
Proc. Natl. Acad. Sci. USA 93, 8306-8311 (1996).
176
"Recognition of DNA by designed ligands at subnanomolar concentrations," John W. Trauger, Eldon E. Baird, Peter B. Dervan.
Nature 382, 559-561 (1996).
175
"Cooperative Triple-Helix Formation via a Minor Groove Dimerization Domain," Jason W. Szewczyk, Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 118, 6778-6779 (1996).
174
"Sequence-Specific Recognition of DNA by a Major and Minor Groove Binding Ligand," Jason W. Szewczyk, Eldon E. Baird, Peter B. Dervan.
Angew. Chem. Int. Ed. 35, 1487-1489 (1996).
173
"Binding site size limit of the 2:1 pyrrole-imidazole polyamide-DNA motif," James J. Kelly, Eldon E. Baird, Peter B. Dervan.
Proc. Natl. Acad. Sci. USA 93, 6981-6985 (1996).
172
"Extended hairpin polyamide motif for sequence-specific recognition in the minor groove of DNA," John W. Trauger, Eldon E. Baird, Peter B. Dervan.
Chem. Biol. 3, 369-377 (1996).
171
"Extension of Sequence-Specific Recognition in the Minor Groove of DNA by Pyrrole-Imidazole Polyamides to 9-13 Base Pairs," John W. Trauger, Eldon E. Baird, Milan Mrksich, Peter B. Dervan.
J. Am. Chem. Soc. 118, 6160-6166 (1996).
170
"Recognition of 5'-(A,T)GG(A,T)2-3' Sequences in the Minor Groove of DNA by Hairpin Polyamides," Michelle E. Parks, Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 1996, 6153-6159 (1996).
169
"Optimization of the Hairpin Polyamide Design for Recognition of the Minor Groove of DNA," Michelle E. Parks, Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 118, 6147-6152 (1996).
168
"Solid Phase Synthesis of Polyamides Containing Imidazole and Pyrrole Amino Acids," Eldon E. Baird, Peter B. Dervan.
J. Am. Chem. Soc. 118, 6141-6146 (1996).
167
"Simultaneous Binding of a Polyamide Dimer and an Oligonucleotide in the Minor and Major Grooves of DNA," Michelle E. Parks, Peter B. Dervan.
Bioorg. Med. Chem. 4, 1045-1050 (1996).
166
"Sequence composition effects on the stabilities of triple helix formation by oligonucleotiides containing N7-deoxyguanosine," Helmut Brunar, Peter B. Dervan.
Nucleic Acids Res. 24, 1987-1991 (1996).
165
"Solution Structure of a Pyrimidine·Purine·Pyrimidine Triplex Containing the Sequence-specific Intercalating Non-natural Base D3," Edmond Wang, Karl M. Koshlap, Paul Gillespie, Peter B. Dervan, Juli Feigon.
J. Mol. Biol. 257, 1052-1069 (1996).
164
"Extending the recognition site of designed minor groove binding molecules," Bernhard H. Geierstanger, Milan Mrksich, Peter B. Dervan, David E. Wemmer.
Nat. Struct. Biol. 3, 321-324 (1996).
163
"RecA·oligonucleotide filaments bind in the minor groove of double-stranded DNA," Ramesh Baliga, Jennifer W. Singleton, Peter B. Dervan.
Proc. Natl. Acad. Sci. USA 92, 10393-10397 (1995).
162
"Cyclic polyamides for recognition in the minor groove of DNA," Junhyeong Cho, Michelle E. Parks, Peter B. Dervan.
Proc. Natl. Acad. Sci. USA 92, 10389-10392 (1995).
161
"Only one of the two DNA-bound orientations of AP-1 found in solution cooperates with NFATp," Lin Chen, Martha G. Oakley, J. N. Mark Glover, Jugnu Jain, Peter B. Dervan, Patrick G. Hogan, Anjana Rao, Gregory L. Verdine.
Curr. Biol. 5, 882-889 (1995).
160
"Energetics of Formation of Sixteen Triple Helical Complexes Which Vary at a Single Position within a Purine Motif," William A. Greenberg, Peter B. Dervan.
J. Am. Chem. Soc. 117, 5016-5022 (1995).
159
"Cooperative Triple-Helix Formation at Adjacent DNA Sites: Sequence Composition Dependence at the Junction," Natalia Colocci, Peter B. Dervan.
J. Am. Chem. Soc. 117, 4781-4787 (1995).
158
"Recognition in the Minor Groove of DNA at 5'-(A,T)GCGC(A,T)-3' by a Four Ring Tripeptide Dimer. Reversal of the Specificity of the Natural Product Distamycin," Milan Mrksich, Peter B. Dervan.
J. Am. Chem. Soc. 117, 3325-3332 (1995).
157
"Sequence Composition Effects on the Energetics of Triple Helix Formation by Oligonucleotides Containing a Designed Mimic of Protonated Cytosine," E. Scott Priestley, Peter B. Dervan.
J. Am. Chem. Soc. 117, 4761-4765 (1995).
156
"Design of an N7-Glycosylated Purine Nucleoside for Recognition of GC Base Pairs by Triple Helix Formation," Jürg Hunziker, E. Scott Priestley, Helmut Brunar, Peter B. Dervan.
J. Am. Chem. Soc. 117, 2661-2662 (1995).
155
"Energetics of Formation of Sixteen Triple Helical Complexes Which Vary at a Single Position within a Pyrimidine Motif," George C. Best, Peter B. Dervan.
J. Am. Chem. Soc. 117, 1187-1193 (1994).
154
"Design of a G·C-Specific DNA Minor Groove-Binding Peptide," Bernhard H. Geierstanger, Milan Mrksich, Peter B. Dervan, David E. Wemmer.
Science 266, 646-650 (1994).
153
"Temperature Dependence of the Energetics of Oligonucleotide-Directed Triple-Helix Formation at a Single DNA Site," Scott F. Singleton, Peter B. Dervan.
J. Am. Chem. Soc. 116, 10376-10382 (1994).
152
"Weak Temperature Dependence of Electron Transfer Rates in Fixed-Distance Porphyrin-Quinone Model Systems," Lutfur R. Khundkar, Joseph W. Perry, James E. Hanson, Peter B. Dervan.
J. Am. Chem. Soc. 116, 9700-9709 (1994).
151
"Mapping RNA Regions in Eukaryotic Ribosomes That Are Accessible to Methidiumpropyl-EDTA·Fe(II) and EDTA·Fe(II)," Hogyu Han, Alanna Schepartz, Maria Pellegrini, Peter B. Dervan.
Biochemistry 33, 9831-9844 (1994).
150
"Hairpin Peptide Motif. A New Class of Oligopeptides for Sequence-Specific Recognition in the Minor Groove of Double-Helical DNA," Milan Mrksich, Michelle E. Parks, Peter B. Dervan.
J. Am. Chem. Soc. 116, 7983-7988 (1994).
149
"Different conforrmational families of pyrimidine·purine·pyrimidine triple helices depending on backbone composition," Hogyu Han, Peter B. Dervan.
Nucleic Acids Res. 22, 2837-2844 (1994).
148
"Inhibition of Klenow Fragment DNA Polymerase on Double-Helical Templates by Oligonucleotide-Directed Triple-Helix Formation," Joseph G. Hacia, Peter B. Dervan, Barbara J. Wold.
Biochemistry 33, 6192-6200 (1994).
147
"Sequence specificity of the non-natural pyrido[2,3-d]pyrimidine nucleoside in triple helix formation," Andrea B. Staubli, Peter B. Dervan.
Nucleic Acids Res. 22, 2637-2642 (1994).
146
"Visualization of RNA tertiary structure by RNA-EDTA·Fe(II) autocleavage: Analysis of tRNAPhe with uridine-EDTA·Fe(II) at position 47," Hogyu Han, Peter B. Dervan.
Proc. Natl. Acad. Sci. USA 91, 4955-4959 (1994).
145
"Phosphorothioate Oligonucleotide-Directed Triple Helix Formation," Joseph G. Hacia, Barbara J. Wold, Peter B. Dervan.
Biochemistry 33, 5367-5369 (1994).
144
"Design of a Covalent Peptide Heterodimer for Sequence-Specific Recognition in the Minor Groove of Double-Helical DNA," Milan Mrksich, Peter B. Dervan.
J. Am. Chem. Soc. 116, 3663-3664 (1994).
143
"Synthesis of a Hybrid Protein Containing the Iron-Binding Ligand of Bleomycin and the DNA-Binding Domain of Hin," Martha G. Oakley, Kenneth D. Turnbull, Peter B. Dervan.
Bioconjugate Chem. 5, 242-247 (1994).
142
"Cooperative Binding of 8-mer Oligonucleotides Containing 5-(1-Propynyl)-2'-deoxyuridine to Adjacent DNA Sites by Triple-Helix Formation," Natalia Colocci, Peter B. Dervan.
J. Am. Chem. Soc. 116, 785-786 (1994).
141
"Structural and Dynamic Characterization of the Heterodimeric and Homodimeric Complexes of Distamycin and 1-Methylimidazole-2-carboxamide-Netropsin Bound to the Minor Groove of DNA," Bernhard H. Geierstanger, Jens Peter Jacobsen, Milan Mrksich, Peter B. Dervan, David E. Wemmer.
Biochemistry 33, 3055-3062 (1994).
140
"Equilibrium Association Constants for Oligonucleotide-Directed Triple Helix Formation at Single DNA Sites: Linkage to Cation Valence and Concentration," Scott F. Singleton, Peter B. Dervan.
Biochemistry 32, 13171-13179 (1993).
139
"Structural Analysis of Covalent Peptide Dimers, Bis(pyridine-2-carboxamidonetropsin)(CH2)3-6, in Complex with 5'-TGACT-3' Sites by Two-Dimensional NMR," Tammy J. Dwyer, Bernhard H. Geierstanger, Milan Mrksich, Peter B. Dervan, David E. Wemmer.
J. Am. Chem. Soc. 115, 9900-9906 (1993).
138
"Enhanced Sequence Specific Recognition in the Minor Groove of DNA by Covalent Peptide Dimers: Bis(pyridine-2