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1 1. Olsen, C. A., and Ghadiri, M. R. "Discovery of potent and selective histone deacetylase inhibitors via focused combinatorial libraries of cyclic alpha-3-betatetrapeptides." J. Med. Chem. 2009, 52, Ura, Y., Al-Sayah, M., Montenegro, J., Beierle, J. M., Leman, L. J., and Ghadiri, M. R. "Dynamic polythioesters via ring-opening polymerization of 1,4-thiazine- 2,5-diones." Org. Biomol. Chem. 2009, 7, Ura, Y., Beierle, J. M., Leman, L. J., Orgel, L. E., and Ghadiri, M. R. "Selfassembling sequence-adaptive peptide nucleic acids." Science 2009, 325, Motiei, L., Rahimipour, S., Thayer, D. A., Wong, C.-H., and Ghadiri, M. R. "Antibacterial cyclic DL-alpha-glycopeptides." Chem. Commun. 2009, Horne, W. S., Olsen, C. A., Beierle, J. M., Montero, A., and Ghadiri, M. R. "Probing the bioactive conformation of an archetypal natural product HDAC inhibitor with conformationally homogeneous triazole-modified cyclic tetrapeptides." Angew. Chem., Int. Ed. 2009, 48, Beierle, J. M., Horne, W. S., van Maarseveen, J. H., Waser, B., Reubi, J. C., and Ghadiri, M. R. "Conformationally homogeneous heterocyclic pseudotetrapeptides as three-dimensional scaffolds for rational drug design: receptor-selective somatostatin analogues." Angew. Chem., Int. Ed. 2009, 48, Picuri, J. M., Frezza, B. M., and Ghadiri, M. R. "Universal translators for nucleic acid diagnosis." J. Am. Chem. Soc. 2009, 131, Montero, A., Beierle, J. M., Olsen, C. A., and Ghadiri, M. R. "Design, synthesis, biological evaluation, and structural characterization of potent histone deacetylase inhibitors based on cyclic alpha/beta-tetrapeptide architectures." J.

2 Am. Chem. Soc. 2009, 131, Voelcker, N. H., Alfonso, I., and Ghadiri, M. R. "Catalyzed oxidative corrosion of porous silicon used as an optical transducer for ligand-receptor interactions." ChemBioChem 2008, 9, Voelcker, N. H., Guckian, K. M., Saghatelian, A., and Ghadiri, M. R. "Sequenceaddressable DNA logic." Small 2008, 4, Cheng, G., Montero, A., Gastaminza, P., Whitten-Bauer, C., Wieland, S. F., Isogawa, M., Fredericksen, B., Selvarajah, S., Gallay, P. A., Ghadiri, M. R., and Chisari, F. V. "A virocidal amphipathic alpha-helical peptide that inhibits hepatitis C virus infection in vitro." Proc. Natl. Acad. Sci. U. S. A. 2008, 105, Huang, Z.-Z., Leman, L. J., and Ghadiri, M. R. "Biomimetic catalysis of diketopiperazine and dipeptide syntheses." Angew. Chem., Int. Ed. 2008, 47, Cockroft, S. L., Chu, J., Amorin, M., and Ghadiri, M. R. "A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution." J. Am. Chem. Soc. 2008, 130, Frezza, B. M., Cockroft, S. L., and Ghadiri, M. R. "Modular multi-level circuits from immobilized DNA-based logic gates." J. Am. Chem. Soc. 2007, 129, Gianneschi, N. C., and Ghadiri, M. R. "Design of molecular logic devices based on a programmable DNA-regulated semisynthetic enzyme." Angew. Chem., Int. Ed. 2007, 46,

3 Fletcher, J. T., Finlay, J. A., Callow, M. E., Callow, J. A., and Ghadiri, M. R. "A combinatorial approach to the discovery of biocidal six-residue cyclic D,L-alphapeptides against the bacteria methicillin-resistant Staphylococcus aureus (MRSA) and E. coli and the biofouling algae ulva linza and Navicula perminuta." Chem.--Eur. J. 2007, 13, Leman, L. J., Weinberger, D. A., Huang, Z.-Z., Wilcoxen, K. M., and Ghadiri, M. R. "Functional and mechanistic analyses of biomimetic aminoacyl transfer reactions in de novo designed coiled coil peptides via rational active site engineering." J. Am. Chem. Soc. 2007, 129, Wilcoxen, K. M., Leman, L. J., Weinberger, D. A., Huang, Z.-Z., and Ghadiri, M. R. "Biomimetic catalysis of intermodular aminoacyl transfer." J. Am. Chem. Soc. 2007, 129, Yadav, M. K., Leman, L. J., Price, D. J., Brooks, C. L., III, Stout, C. D., and Ghadiri, M. R. "Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution." Biochemistry 2006, 45, Ashkenasy, N., Horne, W. S., and Ghadiri, M. R. "Design of self-assembling peptide nanotubes with delocalized electronic states." Small 2006, 2, Leman, L. J., Orgel, L. E., and Ghadiri, M. R. "Amino acid dependent formation of phosphate anhydrides in water mediated by carbonyl sulfide." J. Am. Chem. Soc. 2006, 128,

4 22. Nicolaou, K. C., Zak, M., Rahimipour, S., Estrada, A. A., Lee, S. H., O'Brate, A., Giannakakou, P., and Ghadiri, M. R. "Discovery of a biologically active thiostrepton fragment." J. Am. Chem. Soc. 2005, 127, Van Maarseveen, J. H., Horne, W. S., and Ghadiri, M. R. "Efficient route to C2 symmetric heterocyclic backbone modified cyclic peptides." Org. Lett. 2005, 7, Dartois, V., Sanchez-Quesada, J., Cabezas, E., Chi, E., Dubbelde, C., Dunn, C., Granja, J., Gritzen, C., Weinberger, D., Ghadiri, M. R., and Parr, T. R., Jr. "Systemic antibacterial activity of novel synthetic cyclic peptides." Antimicrob. Agents Chemother. 2005, 49, Horne, W. S., Wiethoff, C. M., Cui, C., Wilcoxen, K. M., Amorin, M., Ghadiri, M. R., and Nemerow, G. R. "Antiviral cyclic D, L-alpha-peptides: Targeting a general biochemical pathway in virus infections." Bioorg. Med. Chem. 2005, 13, h&_orig=browse&_srch=docinfo(%23toc%235220%232005% % %23fla%23di splay%23volume)&_cdi=5220&_sort=d&_docanchor=&_ct=42&_acct=c &_version=1&_urlVersion=0&_userid= &md5=72bd55cd f4dd27a7b70f9e6ad0988ed Yadav, M. K., Redman, J. E., Leman, L. J., Alvarez-Gutierrez, J. M., Zhang, Y., Stout, C. D., and Ghadiri, M. R. "Structure-based engineering of internal cavities in coiled-coil peptides." Biochemistry 2005, 44, Ashkenasy, N., Sanchez-Quesada, J., Bayley, H., and Ghadiri, M. R. "Recognizing a single base in an individual DNA strand: A step toward DNA sequencing in nanopores." Angew. Chem., Int. Ed. 2005, 44,

5 28. Horne, W. S., Ashkenasy, N., and Ghadiri, M. R. "Modulating charge transfer through cyclic D,L-alpha-peptide self-assembly." Chem.--Eur. J. 2005, 11, Horne, W. S., Yadav, M. K., Stout, C. D., and Ghadiri, M. R. "Heterocyclic peptide backbone modifications in an alpha-helical coiled coil." J. Am. Chem. Soc. 2004, 126, Leman, L., Orgel, L., and Ghadiri, M. R. "Carbonyl sulfide-mediated prebiotic formation of peptides." Science 2004, 306, Ashkenasy, G., and Ghadiri, M. R. "Boolean logic functions of a synthetic peptide network." J. Am. Chem. Soc. 2004, 126, Ashkenasy, G., Jagasia, R., Yadav, M., and Ghadiri, M. R. "Design of a directed molecular network." Proc. Natl. Acad. Sci. U. S. A. 2004, 101, Sanchez-Quesada, J., Saghatelian, A., Cheley, S., Bayley, H., and Ghadiri, M. R. "Single DNA rotaxanes of a transmembrane pore protein." Angew. Chem., Int. Ed. 2004, 43, Horne, W. S., Stout, C. D., and Ghadiri, M. R. "A heterocyclic peptide nanotube." J. Am. Chem. Soc. 2003, 125, Saghatelian, A., Voelcker, N. H., Guckian, K. M., Lin, V. S. Y., and Ghadiri, M. R. "DNA-based photonic logic gates: AND, NAND, and INHIBIT." J. Am. Chem. Soc. 2003, 125,

6 36. Saghatelian, A., Guckian, K. M., Thayer, D. A., and Ghadiri, M. R. "DNA detection and signal amplification via an engineered allosteric enzyme." J. Am. Chem. Soc. 2003, 125, Redman, J. E., Wilcoxen, K. M., and Ghadiri, M. R. "Automated mass spectrometric sequence determination of cyclic peptide library members." J. Comb. Chem. 2003, 5, Redman, J. E., and Ghadiri, M. R. "Synthesis of photoactive p- azidotetrafluorophenylalanine containing peptide by solid-phase Fmoc methodology." Org. Lett. 2002, 4, Sanchez-Quesada, J., Isler, M. P., and Ghadiri, M. R. "Modulating ion channel properties of transmembrane peptide nanotubes through heteromeric supramolecular assemblies." J. Am. Chem. Soc. 2002, 124, Fernandez-Lopez, S., Kim, H.-S., Choi, E. C., Delgado, M., Granja, J. R., Khasanov, A., Kraehenbuehl, K., Long, G., Weinberger, D. A., Wilcoxen, K. M., and Ghadiri, M. R. "Antibacterial agents based on the cyclic D,L-alpha-peptide architecture." Nature 2001, 412, Sanchez-Quesada, J., Kim, H. S., and Ghadiri, M. R. "A synthetic pore-mediated transmembrane transport of glutamic acid." Angew. Chem., Int. Ed. 2001, 40, Bong, D. T., and Ghadiri, M. R. "Chemoselective Pd(0)-catalyzed peptide coupling in water." Org. Lett. 2001, 3, Bong, D. T., and Ghadiri, M. R. "Self-assembling cyclic peptide cylinders as nuclei for crystal engineering." Angew. Chem., Int. Ed. 2001, 40,

7 44. Bong, D. T., Clark, T. D., Granja, J. R., and Ghadiri, M. R. "Self-assembling organic nanotubes." Angew. Chem., Int. Ed. 2001, 40, Saghatelian, A., Yokobayashi, Y., Soltani, K., and Ghadiri, M. R. "A chiroselective peptide replicator." Nature 2001, 409, Kennan, A. J., Haridas, V., Severin, K., Lee, D. H., and Ghadiri, M. R. "A de novo designed peptide ligase: a mechanistic investigation." J. Am. Chem. Soc. 2001, 123, Sanchez-Quesada, J., Ghadiri, M. R., Bayley, H., and Braha, O. "Cyclic Peptides as Molecular Adapters for a Pore-Forming Protein." J. Am. Chem. Soc. 2000, 122, Bong, D. T., Janshoff, A., Steinem, C., and Ghadiri, M. R. "Membrane partitioning of the cleavage peptide in flock house virus." Biophys. J. 2000, 78, Bong, D. T., Steinem, C., Janshoff, A., Johnson, J. E., and Ghadiri, M. R. "A highly membrane-active peptide in Flock House virus: implications for the mechanism of nodavirus infection." Chem. Biol. 1999, 6, Vollmer, M. S., Clark, T. D., Steinem, C., and Ghadiri, M. R. "Photoswitchable hydrogen-bonding in self-organized cylindrical peptide systems." Angew. Chem., Int. Ed. 1999, 38, Granja, J. R., and Ghadiri, M. R. "Self-assembling peptide nanotubes." NATO ASI Ser., Ser. C 1999, 526, Steinem, C., Janshoff, A., Vollmer, M. S., and Ghadiri, M. R. "Reversible photoisomerization of self-organized cylindrical peptide assemblies at air-water and solid interfaces." Langmuir 1999, 15, Janshoff, A., Bong, D. T., Steinem, C., Johnson, J. E., and Ghadiri, M. R. "An

8 animal virus-derived peptide switches membrane morphology: possible relevance to nodaviral transfection processes." Biochemistry 1999, 38, Clark, T. D., Kobayashi, K., and Ghadiri, M. R. "Covalent capture and stabilization of cylindrical beta-sheet peptide assemblies." Chem.--Eur. J. 1999, 5, Rapaport, H., Kim, H. S., Kjaer, K., Howes, P. B., Cohen, S., Als-Nielsen, J., Ghadiri, M. R., Leiserowitz, L., and Lahav, M. "Crystalline cyclic peptide nanotubes at interfaces." J. Am. Chem. Soc. 1999, 121, Mutz, M. W., Case, M. A., Wishart, J. F., Ghadiri, M. R., and McLendon, G. L. "De novo design of protein function: predictable structure-function relationships in synthetic redox proteins." J. Am. Chem. Soc. 1999, 121, Janshoff, A., Dancil, K.-P. S., Steinem, C., Greiner, D. P., Lin, V. S. Y., Gurtner, C., Motesharei, K., Sailor, M. J., and Ghadiri, M. R. "Macroporous p-type silicon Fabry-Perot layers. Fabrication, characterization, and applications in biosensing." J. Am. Chem. Soc. 1998, 120, Hartgerink, J. D., Clark, T. D., and Ghadiri, M. R. "Peptide nanotubes and beyond." Chem.--Eur. J. 1998, 4, Clark, T. D., Buriak, J. M., Kobayashi, K., Isler, M. P., McRee, D. E., and Ghadiri, M. R. "Cylindrical beta-sheet peptide assemblies." J. Am. Chem. Soc. 1998, 120, Kim, H. S., Hartgerink, J. D., and Ghadiri, M. R. "Oriented self-assembly of cyclic peptide nanotubes in lipid membranes." J. Am. Chem. Soc. 1998, 120, Severin, K., Lee, D. H., Martinez, J. A., Vieth, M., and Ghadiri, M. R. "Dynamic error correction in autocatalytic peptide networks." Angew. Chem., Int. Ed. 1998, 37,

9 62. Lee, D. H., Severin, K., and Ghadiri, M. R. "Autocatalytic networks: the transition from molecular self-replication to molecular ecosystems." Curr. Opin. Chem. Biol. 1997, 1, KRT5-2H&_user= &_coverDate=12%2F31%2F1997&_rdoc=12&_fmt=hi gh&_orig=browse&_srch=docinfo(%23toc%236246%231997% % %23flp%23di splay%23volume)&_cdi=6246&_sort=d&_docanchor=&_ct=28&_acct=c &_version=1&_urlVersion=0&_userid= &md5=934484bd dd3210fd12ef1f4d772ed7ba Case, M. A., Ghadiri, M. R., Mutz, M. W., and McLendon, G. L. "Stereoselection in designed three-helix bundle metalloproteins." Chirality 1998, 10, Clark, T. D., Buehler, L. K., and Ghadiri, M. R. "Self-assembling cyclic beta-3- peptide nanotubes as artificial transmembrane ion channels." J. Am. Chem. Soc. 1998, 120, Lee, D. H., Severin, K., Yokobayashi, Y., and Ghadiri, M. R. "Emergence of symbiosis in peptide self-replication through a hypercyclic network." Nature 1997, 390, Motesharei, K., and Ghadiri, M. R. "Diffusion-limited size-selective ion sensing based on SAM-supported peptide nanotubes." J. Am. Chem. Soc. 1997, 119, Lin, V. S. Y., Motesharei, K., Dancil, K.-P. S., Sailor, M. J., and Ghadiri, M. R. "A porous silicon-based optical interferometric biosensor." Science 1997, 278, Severin, K., Lee, D. H., Kennan, A. J., and Ghadiri, M. R. "A synthetic peptide ligase." Nature 1997, 389, Severin, K., Lee, D. H., Martinez, J. A., and Ghadiri, M. R. "Peptide self-

10 replication via template-directed ligation." Chem.--Eur. J. 1997, 3, Buriak, J. M., and Ghadiri, M. R. "Self-assembly of peptide based nanotubes." Mater. Sci. Eng., C 1997, C4, VSKFS2- G&_user= &_coverDate=04%2F30%2F1997&_rdoc=2&_fmt=high &_orig=browse&_srch=docinfo(%23toc%235590%231997% % %23flp%23dis play%23volume)&_cdi=5590&_sort=d&_docanchor=&_ct=18&_acct=c &_version=1&_urlVersion=0&_userid= &md5=778c3c5ae bc9b1f1ce4a9439f1d4714e 71. Dawson, P. E., Churchill, M., Ghadiri, M. R., and Kent, S. B. H. "Modulation of reactivity in native chemical ligation through the use of thiol additives." J. Am. Chem. Soc. 1997, 119, Lee, D. H., and Ghadiri, M. R. "Control of peptide architecture via self-assembly and self-organization processes." Compr. Supramol. Chem. 1996, 9, Lee, D. H., Granja, J. R., Martinez, J. A., Severin, K., and Ghadiri, M. R. "A selfreplicating peptide." Nature 1996, 382, Hartgerink, J. D., Granja, J. R., Milligan, R. A., and Ghadiri, M. R. "Selfassembling peptide nanotubes." J. Am. Chem. Soc. 1996, 118, Clark, T. D., and Ghadiri, M. R. "Supramolecular design by covalent capture. Design of a peptide cylinder via hydrogen-bond- promoted intermolecular olefin metathesis." J. Am. Chem. Soc. 1995, 117, Engels, M., Bashford, D., and Ghadiri, M. R. "Structure and dynamics of selfassembling peptide nanotubes and the channel-mediated water organization and self-diffusion. A molecular dynamics study." J. Am. Chem. Soc. 1995, 117, Kobayashi, K., Granja, J. R., and Ghadiri, M. R. "Beta-sheet peptide architecture: measuring the relative stability of parallel vs. antiparallel beta-sheets." Angew. Chem., Int. Ed. Engl. 1995, 34,

11 78. Ghadiri, M. R., Kobayashi, K., Granja, J. R., Chadha, R. K., and McRee, D. E. "The structural and thermodynamic basis for the formation of self-assembled peptide nanotubes." Angew. Chem., Int. Ed. Engl. 1995, 34, Granja, J. R., and Ghadiri, M. R. "Channel-mediated transport of glucose across lipid bilayers." J. Am. Chem. Soc. 1994, 116, Ghadiri, M. R., Granja, J. R., and Buehler, L. K. "Artificial transmembrane ion channels from self-assembling peptide nanotubes." Nature 1994, 369, Khazanovich, N., Granja, J. R., McRee, D. E., Milligan, R. A., and Ghadiri, M. R. "Nanoscale tubular ensembles with specified internal diameters. Design of a selfassembled nanotube with a 13-angstrom pore." J. Am. Chem. Soc. 1994, 116, Ghadiri, M. R., and Case, M. A. "De novo design of a novel hetero dinuclear metalloprotein with three parallel (bundled) helixes." Angew. Chem., Int. Ed. Engl. 1993, 32, Ghadiri, M. R., Granja, J. R., Milligan, R. A., McRee, D. E., and Khazanovich, N. "Self-assembling organic nanotubes based on a cyclic peptide architecture." Nature 1993, 366, Ghadiri, M. R., Soares, C., and Choi, C. "Design of an artificial four-helix bundle metalloprotein via a novel ruthenium(ii)-assisted self-assembly process." J. Am. Chem. Soc. 1992, 114, Ghadiri, M. R., Soares, C., and Choi, C. "A convergent approach to protein design. Metal ion-assisted spontaneous self-assembly of a polypeptide into a triple-helix bundle protein." J. Am. Chem. Soc. 1992, 114, Ghadiri, M. R., Choi, C., Fernholz, A. K., Ruan, F., Chen, Y., Hopkins, P. B., and Aube, J. "Peptide architecture: design of stabilized alpha-helical metallopeptides." Chemtracts Org. Chem. 1991, 4, Ghadiri, M. R., and Fernholz, A. K. "Peptide architecture. Design of stable alpha-

12 helical metallopeptides via a novel exchange-inert ruthenium(iii) complex." J. Am. Chem. Soc. 1990, 112, Ghadiri, M. R., and Choi, C. "Secondary structure nucleation in peptides. Transition metal ion stabilized alpha-helices." J. Am. Chem. Soc. 1990, 112,