throbber

`Synthorx
`11099 N. Torrey Pines Rd.
`Suite 200
`La Jolla, CA 92037
`
`
`
`
`
`
`Education
`Date
`Description
`Postdoctoral Studies 1994–
`1998
`1994
`1990
`1988
`
`Curriculum Vitae
`Floyd Eric Romesberg
`
`Updated May 2020
`
`Ph: (858) 750-4811 (office)
`Ph: (858) 349-1932 (mobile)
`fromesberg@synthorx.com
`
`
`
`
`Location
`UC Berkeley, Berkeley, CA
`
`Advisor
`Professor Peter G. Schultz
`
`Cornell University, Ithaca, NY
`Cornell University, Ithaca, NY
`Ohio State University, Columbus, OH
`
`Professor David B. Collum
`Professor David B. Collum
`Professor Matthew S. Platz
`
`
`Professional Experience
`2014 – 2019
`Synthorx, La Jolla, CA (Scientific Founder, Consultant, Board of Directors);
`2010 – 2013
`RQx Pharmaceuticals, Inc., La Jolla, CA (Scientific Founder, Consultant, SAB
`member); Acquired by Genentech in 2013
`Achaogen Inc., South San Francisco, CA (Scientific Founder, Consultant, SAB
`member); NASDAQ: AKAO
`
`Distinguished Fellow, Synthorx
`Professor, Department of Chemistry, The Scripps Research Institute
`Associate Professor, Department of Chemistry, The Scripps Research Institute
`Assistant Professor, Department of Chemistry, The Scripps Research Institute
`
`Fellow, National Academy of Inventors
`ACS San Diego Section Distinguished Scientist Award
`Royal Society of Chemistry Bioorganic Chemistry Award
`ACS Nobel Laureate Signature Award for Graduate Education in Chemistry
`Member, Institute for Defense Analysis, Defense Science Study Group
`World Technology Award Nominee in Biotechnology
`Discover Magazine Technology Innovation Award
`NSF CAREER Award
`Camille Dreyfus Teacher Scholar Award
`Susan B. Komen Breast Cancer Foundation Award
`The Baxter Foundation Award
`NIH National Research Service Award Postdoctoral Fellowship
`The Mac Nevin Award
`
`Ph.D. in Chemistry
`M.S. in Chemistry
`B.S. in Chemistry
`
`
`
`
`Appointments
`2019 – present
`2014 – 2019
`2006 – 2014
`1998 – 2006
`
`
`
`2005 – 2011
`
`
`Honors
`2020
`2018
`2018
`2015
`2008 – 2009
`2005
`2004
`2004
`2003
`2003
`2002
`1994 –1996
`1987
`
`
`
`
`
`Illumina Ex. 1097
`IPR Petition - USP 10,435,742
`
`

`

`Curriculum Vitae – Floyd E. Romesberg (Page 2 of 16)
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`5.
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`6.
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`Publications, electronic list via PubMed: http://bit.ly/2uEWtff
`
`Publications: Principal Investigator, Primary Research Articles
`1. EC Fischer, K Hashimoto, Y Zhang, AW Feldman, VT Dien, RJ Karadeema, R Adhikary, MP Ledbetter,
`R Krishnamurthy, FE Romesberg (2020) New codons for efficient production of unnatural proteins in
`a semi-synthetic organism, Nat Chem Biol 16:570–576.
`2. MP Ledbetter, JM Craig, RJ Karadeema, MT Noakes, HC Kim, SJ Abell, JR Huang, BA Anderson, R
`Krishnamurthy, JH Gundlach, FE Romesberg (2020) Nanopore sequencing of an expanded genetic
`alphabet reveals high-fidelity replication of a predominantly hydrophobic unnatural base pair, J Am Chem
`Soc 142:2110–2114.
`3. Q Shao, T Chen, K Sheng, Z Liu, Z Zhang, FE Romesberg (2020) Selection of aptamers with large
`hydrophobic 2’-substituents, J Am Chem Soc 142:2125–2128.
`4. AX Zhou, K Sheng, AW Feldman, FE Romesberg (2019) Progress toward eukaryotic semisynthetic
`organisms: translation of unnatural codons, J Am Chem Soc 141:20166–20170.
`SI Walsh, DS Peters, PA Smith, A Craney, MM Dix, BF Cravatt, FE Romesberg (2019) Inhibition of
`protein secretion in Escherichia coli and sub-MIC effects of arylomycin antibiotics, Antimicrob Agents
`Chemother 63:e01253-18.
`R Adhikary, J Zimmermann, RL Stanfield, IA Wilson, W Yu, M Oda, FE Romesberg (2019) Structure
`and dynamics of stacking interactions in an antibody binding site, Biochemistry 58:2987-2995.
`7. AW Feldman, VT Dien, RJ Karadeema, EC Fischer, Y You, BA Anderson, R Krishnamurthy, JS Chen,
`L Li, FE Romesberg (2019) Optimization of replication, transcription, and translation in a semi-synthetic
`organism. J Am Chem Soc 27:10644-10653.
`8. VT Dien, M Holcomb, AW Feldman, EC Fischer, TJ Dwyer, FE Romesberg (2018) Progress toward a
`semi-synthetic organism with an unrestricted expanded genetic alphabet, J Am Chem Soc 140:16115-16123
`CH Yeh, SI Walsh, A Craney, MG Tabor, AF Voica, R Adhikary, SE Morris, FE Romesberg (2018)
`Optimization of a b-lactam scaffold for antibacterial activity via the inhibition of bacterial type I signal
`peptidase, ACS Med Chem Lett 4:376-380
`10. AW Feldman, EC Fischer, MP Ledbetter, J-Y Liao, JC Chaput, FE Romesberg (2018) A tool for the
`import of natural and unnatural nucleoside triphosphates into bacteria, J Am Chem Soc 140:1447-1454
`11. DS Peters, FE Romesberg, PS Baran (2018) Scalable access to arylomycins via C-H functionalization
`logic, J Am Chem Soc 140:2072-2075
`12. M Holcomb, R Adhikary, J Zimmermann, FE Romesberg (2018) Topological evidence of previously
`overlooked Ni+1–H…Ni H-bonds and their contribution to protein structure and stability, J Phys Chem A
`122:446-450
`13. MP Ledbetter, RJ Karadeema, FE Romesberg (2018) Reprogramming the replisome of a semisynthetic
`organism for the expansion of the genetic alphabet, J Am Chem Soc 140:758-765
`14. Y Zhang, JL Ptacin, EC Fischer, HR Aerni, CE Caffaro, K San Jose, AW Feldman, CR Turner, FE
`Romesberg (2017) A semi-synthetic organism that stores and retrieves increased genetic information,
`Nature 551:644-647
`15. A Craney, FE Romesberg (2017) Stable signal peptides and the response to secretion stress in
`Staphylococcus aureus, mBio 8:e01507-17
`16. Z Liu, T Chen, FE Romesberg (2017) Evolved polymerases facilitate selection of fully 2’OMe-modified
`aptamers, Chem Sci 8:8179-8182
`17. T Chen, FE Romesberg (2017) Enzymatic synthesis, amplification, and application of DNA with a
`functionalized backbone, Angew Chem Int Ed 56:14046-14051
`18. AW Feldman, FE Romesberg (2017) In vivo structure-activity relationships and optimization of an
`unnatural base pair for replication in a semi-synthetic organism, J Am Chem Soc 139:11427-11433
`19. T Chen, FE Romesberg (2017) Polymerase chain transcription: exponential synthesis of RNA and
`modified RNA, J Am Chem Soc 139:9949-9954
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`Curriculum Vitae – Floyd E. Romesberg (Page 3 of 16)
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`20. SE Morris, AW Feldman, FE Romesberg (2017) Synthetic biology parts for the storage of increased
`genetic information in cells, ACS Synth Biol, 6:1834-1840
`21. R Adhikary, YX Tan, J Liu, J Zimmermann, M Holcomb, C Yvellez, PE Dawson, FE Romesberg (2017)
`Conformational heterogeneity ad DNA recognition by the morphogen bicoid, Biochemistry (ACS Editors’
`Choice) 56:2787-2793
`22. D Thirunavukarasu, T Chen, Z Liu, N Hongdilokkul, FE Romesberg (2017) Selection of 2’-fluoro-
`modified aptamers with optimized properties, J Am Chem Soc (Comm) 139:2892-2895
`23. AW Feldman, VT Dien, FE Romesberg (2017) Chemical stabilization of unnatural nucleotide
`triphosphates for the in vivo expansion of the genetic alphabet, J Am Chem Soc 139:2464-2647
`24. Y Zhang, BM Lamb, AW Feldman, AX Zhou, T Lavergne, L Li, FE Romesberg (2017) A semisynthetic
`organism engineered for the stable expansion of the genetic alphabet, Proc Natl Acad Sci USA 114:1317-
`1322
`25. R Adhikary, J Zimmermann, FE Romesberg (2017) Transparent window vibrational probes for the
`characterization of proteins with high structural and temporal resolution, Chem Rev 117:1927-1969
`26. T Chen, N Hongdilokkul, Z Liu, D Thirunavukarasu, FE Romesberg (2016) The expanding world of
`DNA and RNA, Curr Op Chem Biol 34:80-87
`27. T Chen, N Hongdilokkul, Z Liu, R Adhikary, SS Tsuen, FE Romesberg (2016) Evolution of
`thermophilic DNA polymerases for the recognition and amplification of C2’-modified DNA, Nat Chem
`8:556-562
`28. T Lavergne, R Lamichhane, DA Malyshev, Z Li, L Li, E Sperling, JR Williamson, DP Millar, FE
`Romesberg (2016) FRET characterization of complex conformational changes in a large 16S ribosomal
`RNA fragment site-specifically labeled using unnatural base pairs, ACS Chem Biol 11:1347-1353
`29. R Adhikary, J Zimmermann, PE Dawson, FE Romesberg (2015) The temperature dependence of CN
`and SCN IR absorptions facilitates their interpretation and use as probes of proteins, Anal. Chem.
`87:11561-11567
`30. A Craney, MM Dix, R Adhikary, BF Cravatt, FE Romesberg (2015) An alternative terminal step of the
`general secretory pathway in Staphylococcus aureus, mBio. 6:e01178-15
`31. DB Steed, J Liu, E Wasbrough, L Miller, S Halasohoris, J Miller, B Somerville, JR Hershfield, FE
`Romesberg (2015) Origins of Y. pestis sensitivity to the arylomycin antibiotics and the inhibition of type
`I signal peptidase, Antimicrob. Agents Chemother. 59:3887-3898
`32. A Craney, FE Romesberg (2015) A putative Cro-like repressor contributes to arylomycin resistance in
`Staphylococcus aureus, Antimicrob. Agents Chemother. 59:3066-3074
`33. RA Adhikary, W Yu, M Oda, T Chen, R Walker, R Stanfield, I Wilson, J Zimmermann, FE Romesberg
`(2015) Adaptive mutations alter antibody structure and dynamics during affinity maturation, Biochemistry
`54:2085-2093
`34. RA Rodriguez, DB Steed, Y Kawamata, S Su, PA Smith, TC Steed, FE Romesberg, PS Baran (2014)
`Axinellamines as broad-spectrum antibacterial agents: scalable synthesis and biology, J Am Chem Soc
`136:15403-15413
`35. R Adhikary, J Zimmermann, J Liu, RP Forrest, TD Janicki, PE Dawson, SA Corcelli, FE Romesberg
`(2014) Evidence of an unusual N–H…N hydrogen bond in proteins, J Am Chem Soc 136:13474-13477
`36. K Dhami, DA Malyshev, P Ordoukhanian, T Kubelka, M Hocek, FE Romesberg (2014) Systematic
`exploration of a class of hydrophobic unnatural base pairs yields multiple new candidates for the
`expansion of the genetic alphabet, Nucleic Acids Res 42:10235–10244
`37. DA Malyshev, K Dhami, T Lavergne, T Chen, N Dai, JM Foster, IR Corrêa, FE Romesberg (2014) A
`semi-synthetic organism with an expanded genetic alphabet, Nature 509:385-388 [featured on the cover]
`38. R Adhikary, J Zimmermann, PE Dawson, FE Romesberg (2014) IR probes of protein
`microenvironments: utility and potential for perturbation, ChemPhysChem 15:849-853
`39. L Li, M Degardin, T Lavergne, DA Malyshev, K Dhami, P Ordoukhanian, FE Romesberg (2014)
`Natural-like replication of an unnatural base pair for the expansion of the genetic alphabet and
`biotechnology applications, J Am Chem Soc 136:826-829 [cover story]
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`Curriculum Vitae – Floyd E. Romesberg (Page 4 of 16)
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`40. K Betz, DA Malyshev, T Lavergne, W Welte, K Diederichs, FE Romesberg, A Marx (2013) Structural
`insights into DNA replication without hydrogen bonds, J Am Chem Soc 135:18637-18643
`J Liu, PA Smith, DB Steed, FE Romesberg (2013) Efforts toward broadening the spectrum of
`arylomycin antibiotic activity, Bioorg Med Chem Lett 23:5654-5659
`42. Z Li, T Lavergne, DA Malyshev, J Zimmermann, R Adhikary, K Dhami, P Ordoukhanian, Z Sun, J Xiang,
`FE Romesberg (2013) Site-specifically arraying small molecules or proteins on DNA using an expanded
`genetic alphabet, Chem Eur J 19:14205-14209
`43. R Adhikary, J Zimmermann, J Liu, PE Dawson, FE Romesberg (2013) Experimental characterization
`of electrostatic and conformational heterogeneity in an SH3 domain, J Phys Chem B 117:13082-13089
`44. T Lavergne, M Degardin, DA Malyshev, HT Quach, K Dhami, P Ordoukhanian, FE Romesberg (2013)
`Expanding the scope of replicable unnatural DNA: stepwise optimization of a predominantly
`hydrophobic base pair, J Am Chem Soc 135:5408-5419
`45. D Quinto-Alemany, A Canerina-Amaro, LG Hernandez-Abad, F Machin, FE Romesberg, C Gil-
`Lamaignere (2012) Yeasts acquire resistance secondary to antifungal drug treatment by adaptive
`mutagenesis, PLoS One, 7:e42279
`46. DA Malyshev, K Dhami, HT Quach, T Lavergne, P Ordoukhanian, A Torkamani, FE Romesberg
`(2012) Efficient and sequence-independent replication of DNA containing a third base pair establishes a
`functional six letter genetic alphabet, Proc Natl Acad Sci USA, 109:12005-12010
`47. PA Smith, FE Romesberg (2012) Mechanism of action of the arylomycin antibiotics and the effects of
`signal peptidase I inhibition Antimicrob Agents Chemother, 56:5054-5060
`48. R Adhikary, W Yu, M Oda, J Zimmermann, FE Romesberg (2012) Protein dynamics and the diversity
`of an antibody response, J Biol Chem 287:27139-27147
`49. K Betz, DA Malyshev, T Lavergne, W Welte, K Diederichs, TJ Dwyer, P Ordoukahanian, FE
`Romesberg, A Marx (2012) KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-
`Crick geometry, Nat Chem Biol, 8:612-614
`50. W Yu, PE Dawson, J Zimmermann, FE Romesberg (2012) Carbon-deuterium bonds as probes of
`protein thermal unfolding, J Phys Chem B, 116:6397-6403
`51. MA Schallenberger, S Niessen, C Shao, B J Fowler, FE Romesberg (2012) Type I signal peptidase and
`protein secretion in Staphylococcus aureus, J Bacteriol 194:2677-2686
`52. T Lavergne, DA Malyshev, FE Romesberg (2012) Major groove substituents and polymerase
`recognition of a class of unnatural base pairs, Chem Eur J 18:1231-1239
`53. YJ Seo, DA Malyshev, T Lavergne, P Ordoukhanian, FE Romesberg (2011) Site-specific labeling of
`DNA and RNA using an efficiently replicated and transcribed class of unnatural base pairs, J Am Chem
`Soc 133:19878-19888
`J Liu, C Luo, PA Smith, JK Chin, MGP Page, M Paetzel, FE Romesberg (2011) Synthesis and
`characterization of the arylomycin lipoglycopeptide antibiotics and the crystallographic analysis of their
`complex with signal peptidase, J Am Chem Soc 133:17869-17872
`55. KC Nicolaou, SP Ellery, F Rivas, K Saye, E Rogers, TJ Workinger, M Schallenberger, R Tawatao, A
`Montero, A Hessell, F Romesberg, D Carson, D Burton (2011) Synthesis and biological evaluation of
`2’,4’- and 3’,4’- bridged nucleoside analogues, Bioor Med Chem 19:5648-5669
`J Zimmermann, MC Thielges, YJ Seo, PE Dawson, FE Romesberg (2011) Cyano groups as probes of
`protein microenvironments and dynamics, Angew Chem Int Ed 50:8333-8337
`57. TC Roberts, M Schallenberger, J Liu, PA Smith, FE Romesberg (2011) Initial efforts toward the
`optimization of arylomycins for antibiotic activity, J Med Chem 54:4954-4963
`58. TC Roberts, PA Smith, FE Romesberg, (2011) Synthesis and Biological characterization of arylomycin
`B natural product antibiotics, J Nat Prod 74:956-961
`J Zimmermann, MC Thielges, W Yu, PE Dawson, FE Romesberg (2011) Carbon-deuterium bonds as
`site-specific and non-perturbative probes for time-resolved studies of protein dynamics and folding, J Phys
`Chem Lett 2:412-416
`60. PA Smith, ME Powers, TC Roberts, FE Romesberg (2011) In vitro activities of arylomycin natural-
`product antibiotics against Staphylococcus epidermidis and other coagulase-negative Staphylococci, Antimicrob
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`Curriculum Vitae – Floyd E. Romesberg (Page 5 of 16)
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`Agents Chemother 55:1130-1134
`61. ME Powers, PA Smith, TC Roberts, BJ Fowler, CC King, SA Trauger, G Siuzdak, FE Romesberg
`(2011) Type I signal peptidase and protein secretion in S epidermidis, J Bacteriol 193:340-343
`62. PA Smith, TC Roberts, FE Romesberg (2010) Broad spectrum antibiotic activity of the arylomycin
`natural products is masked by natural target mutations, Chem Biol 17:1223-1231
`63. MA Schallenberger, T Newhouse, PS Baran, FE Romesberg (2010) The psychotrimine natural products
`have antibacterial activity against Gram-positive bacteria and act via membrane disruption, J Antibiot
`(Tokyo) 63:685-687
`64. DA Malyshev, DA Pfaff, SI Ippoliti, GT Hwang, TJ Dwyer, FE Romesberg (2010) Solution structure,
`mechanism of replication, and optimization of an unnatural base pair, Chem Eur J 16:12650-12659
`65. B Li, P Smith, DJ Horvath, Jr, FE Romesberg, SS Justice (2010) SOS regulatory elements are essential
`for UPEC pathogenesis, Microbes Infect 12:662-668
`66. AM Leconte, MP Patel, LE Sass, P McInerney, M Jarosz, L Kung, J L Bowers, PR Buzby, JW Efcavitch,
`FE Romesberg (2010) Directed evolution of DNA polymerases for next-generation sequencing, Angew
`Chem Int Ed Engl 49:5921-5924
`67. D Chen, L Lei, C Lu, R Flores, MP DeLisa, TC Roberts, FE Romesberg, G Zhong (2010) Secretion of
`the chlamydial virulence factor CPAF requires the Sec-dependent pathway, Microbiology 156:3031-3040
`J Zimmermann, FE Romesberg, CL Brooks, 3rd, IF Thorpe (2010) Molecular description of flexibility
`in an antibody combining site, J Phys Chem B 114:7359-7370
`69. P Weinkam, J Zimmermann, FE Romesberg, PG Wolynes (2010) The folding energy landscape and free
`energy excitations of cytochrome c, Acc Chem Res 43:652-660
`70. D Malyshev, YJ Seo, P Ordoukhanian, FE Romesberg (2009) PCR with an expanded genetic alphabet,
`J Am Chem Soc 131:14620-14621
`71. YJ Seo, FE Romesberg (2009) Major groove derivatization of an unnatural base pair, ChemBioChem
`10:2394-2400 [cover story]
`72. GT Hwang, Y Hari, FE Romesberg (2009) The effects of unnatural base pairs and mispairs on DNA
`duplex stability and solvation Nucleic Acids Res 37:4757-4763
`J Zimmermann, K Gundogdu, ME Cremeens, JN Bandaria, GT Hwang, MC Thielges, CM Cheatum, FE
`Romesberg (2009) Efforts toward developing probes of protein dynamics: vibrational dephasing and
`relaxation of carbon-deuterium stretching modes in deuterated leucine J Phys Chem B 113:7991-7994
`74. DA Harris, M E Powers, FE Romesberg (2009) Synthesis and biological evaluation of penem inhibitors
`of bacterial signal peptidase Bioorg Med Chem Lett 19:3787-3790
`75. ME Cremeens, J Zimmermann, W Yu, PE Dawson, FE Romesberg (2009) Direct observation of
`structural heterogeneity in a β-sheet, J Am Chem Soc 131:5726-5727
`76. MC Thielges, J Zimmermann, FE Romesberg (2009) Direct observation of ligand dynamics in
`cytochrome c, J Am Chem Soc 131:6054-6055
`77. YJ Seo, S Matsuda, FE Romesberg (2009) Transcription of an expanded genetic alphabet, J Am Chem
`Soc 131:5046-5047
`78. MC Thielges, J Zimmermann, PE Dawson, FE Romesberg (2009) The determinants of stability and
`folding in evolutionarily diverged cytochromes c, J Mol Biol 24:159-167
`79. D Groff, MC Thielges, S Celliti, PG Schultz, FE Romesberg (2009) Efforts toward the direct
`experimental characterization of enzyme microenvironments: tyrosine 100 in dihydrofolate reductase,
`Angew Chem, Int, Ed 48:3478-3481
`80. P Weinkam, FE Romesberg, PG Wolynes (2009) Chemical frustration in the protein folding
`landscape: grand canonical ensemble simulations of cytochrome c, Biochemistry, 48:2394-2402
`81. SRG Naraharisetty, VM Kasyanenko, J Zimmermann, MC Thielges, FE Romesberg, IV Rubtsov (2009)
`C-D Modes of deuterated side chain of leucine as structural reporters via dual-frequency two-dimensional
`infrared spectroscopy, J Phys Chem B 113:4940-4946
`82. YJ Seo, G T Hwang, P Ordoukhanian, FE Romesberg (2009) Optimization of an unnatural base pair
`towards natural-like replication, J Am Chem Soc 131:3246-3252
`83. P Weinkam, J Zimmermann, LB Sagle, S Matsuda, PE Dawson, PG Wolynes, FE Romesberg (2008)
`Characterization of alkaline transitions in ferricytochrome c using carbon-deuterium infrared probes,
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`Curriculum Vitae – Floyd E. Romesberg (Page 6 of 16)
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`Biochemistry 47:13470-13480
`84. Y Hari, GT Hwang, AM Leconte, N Joubert, M Hocek, FE Romesberg (2008) Optimization of the
`pyridyl nucleobase scaffold for polymerase recognition and unnatural base pair replication, ChemBioChem
`9:2796-2799
`85. GT Hwang, FE Romesberg (2008) The unnatural substrate repertoire of A, B, and X family DNA
`polymerases, J Am Chem Soc 130:14872-14882
`86. MC Thielges, J Zimmermann, W Yu, M Oda, FE Romesberg (2008) Exploring the energy landscape of
`antibody-antigen complexes: protein dynamics, flexibility, and molecular recognition, Biochemistry 47:7237-
`7247 [Hot Article]
`87. MC Thielges, DA Case, FE Romesberg (2008) Carbon-deuterium bonds as probes of dihydrofolate
`reductase, J Am Chem Soc 130:6597-6603
`88. ET Lis, BM O’Neill, C Gil-Lemaignere, JK Chin, FE Romesberg (2008) Identification of pathways
`controlling DNA damage induced mutation in Saccharomyces cerevisiae, DNA Repair 7:801-810
`89. AM Leconte, GT Hwang, S Matsuda, P Capek, Y Hari, FE Romesberg (2008) Discovery,
`characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet, J Am
`Chem Soc 130:2336-2343
`90. TC Roberts, PA Smith, FE Romesberg (2007) Structural and initial biological analysis of synthetic
`arylomycin A2, J Am Chem Soc 129:15830-15838
`91. GT Hwang, AM Leconte, FE Romesberg (2007) Polymerase recognition and stability of fluoro
`substituted pyridone nucleobase analogs, ChemBioChem 8:1606-1611
`92. S Matsuda, JD Fillo, AA Henry, P Rai, SJ Wilkens, TJ Dwyer, BH Geierstanger, DE Wemmer, PG
`Schultz, G Spraggon, FE Romesberg (2007) Efforts toward expansion of the genetic alphabet: structure
`and replication of unnatural base pairs, J Am Chem Soc 129:10466-10473
`93. MF Goodman, MD Scharrf, FE Romesberg (2007) AID-initiated purposeful mutations in
`immunoglobulin genes, Adv Immunol 94:127-155
`94. BM O’Neill, SJ Szyjka, ET Lis, AO Bailey, JR Yates, III, OM Aparicio, FE Romesberg (2007) Psy2 and
`Pph3 form a phosphatase complex required for Rad53 dephosphorylation and replication form restart
`during recovery from DNA damage, Proc Natl Acad Sci USA 104:9290-9295
`95. S Matsuda, AM Leconte, FE Romesberg (2007) Minor groove hydrogen-bonds and the replication of
`unnatural base pairs, J Am Chem Soc 129:5551-5557
`96. RT Cirz, MB Jones, NA Gingles, TD Minogue, B Jarrahi, SN Peterson, FE Romesberg (2007) The
`complete and SOS-mediated response of Staphylococcus aureus to the antibiotic ciprofloxacin, J Bacteriol
`189:531-519
`97. Y Kim, AM Leconte, Y Hari, FE Romesberg (2006) Stability and polymerase recognition of pyridine
`nucleobase analogues: role of minor-groove H-bond acceptors, Angew Chem Int Ed 45:7809-7912
`98. LB Sagle, J Zimmermann, PE Dawson, FE Romesberg (2006) Direct and high resolution
`characterization of cytochrome c equilibrium folding, J Am Chem Soc (Comm) 128:14232-14233
`99. CS Kinnaman, ME Cremeens, FE Romesberg, SA Corcelli (2006) Infrared line shape of an alpha-carbon
`deuterium-labeled amino acid, J Am Chem Soc (Comm) 128:13334-13335
`100. J Zimmermann, EL Oakman, IF Thorpe, X Shi, P Abbyad, CL Brooks, III, SG Boxer, FE Romesberg
`(2006) Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics, Proc
`Natl Acad Sci USA 103:13722-13727
`101. AM Leconte, S Matsuda, GT Hwang, FE Romesberg (2006) Efforts toward expansion of the genetic
`alphabet: pyridone and methyl pyridone, Angew Chem Int Engl 45:4326-4329
`102. RT Cirz, BM O’Neill, JA Hammond, SR Head, FE Romesberg (2006) Defining the Pseudomonas aeruginosa
`SOS response and its role in the global response to the antibiotic ciprofloxacin, J Bacteriol 188:7101-7110
`103. ME Cremeens, H Fujisaki, Y Zhang, J Zimmermann, LB Sagle, S Matsuda, PE Dawson, JE Straub, FE
`Romesberg (2006) Efforts toward developing direct probes of protein dynamics, J Am Chem Soc (Comm)
`128:6028-6029
`104. AM Leconte, S Matsuda, FE Romesberg (2006) An efficiently extended class of unnatural heterobase
`pairs, J Am Chem Soc (Comm) 128:6780-6781
`105. LB Sagle, J Zimmermann, S Matsuda, PE Dawson, FE Romesberg (2006) Redox-coupled dynamics and
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`Curriculum Vitae – Floyd E. Romesberg (Page 7 of 16)
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`folding in cytochrome c, J Am Chem Soc 128:7909-7915
`106. E Lis and FE Romesberg (2006) The role of Doa1 in the S. cerevisiae DNA damage response, Mol Cell
`Biol 26:4122-4133
`107. JK Chin, VI Bashkirov, W-D Heyer, FE Romesberg (2006) Esc4 and the control of recombination
`during replication, DNA Repair 5:618-628
`108. S Matsuda, AA Henry, FE Romesberg (2006) Optimization of unnatural base pair packing for
`polymerase recognition, J Am Chem Soc 128:6369-6375
`109. GT Hwang and FE Romesberg (2006) Substituent effects on the pairing and polymerase recognition of
`simple unnatural base pairs, Nucleic Acids Res 34:2037-2045
`110. RT Cirz and FE Romesberg (2006) Induction and inhibition of ciprofloxacin resistance-conferring
`mutations in hypermutator bacteria, Antimicrob Agents Chemother 50:220-225
`111. F-Y Dupradeau, DA Case, C Yu, R Jimenez, FE Romesberg (2005) Differential solvation and tautomer
`stability of a model base pair within the major and minor grooves of DNA, J Am Chem Soc 127:15612-
`15617
`112. AM Leconte, L Chen, FE Romesberg (2005) Polymerase evolution: efforts toward expansion of the
`genetic code, J Am Chem Soc 127:12470-12471
`113. RT Cirz, JK Chin, DR Andes, V de Crécy-Lagard, WA Craig, FE Romesberg (2005) The molecular
`mechanism of mutation underlying the evolution of antibiotic resistance, PLoS Biology 3:e176
`114. BM O’Neill, D Hanway, EA Winzeler, FE Romesberg (2004) Coordinated functions of WSS1, PSY2,
`and TOF1 in the DNA damage response, Nucleic Acids Res 32:6519-6530
`115. S Matsuda and FE Romesberg (2004) Optimization of interstrand hydrophobic packing interactions
`within unnatural DNA base pairs. J Am Chem Soc 126, 14419-14427
`116. AA Henry, R Jimenez, D Hanway, FE Romesberg (2004) Preliminary characterization of light harvesting
`in E coli DNA photolyase, ChemBioChem 4:563-571
`117. AA Henry, AG Olsen, S Matsuda, C Yu, B Geierstanger, FE Romesberg (2004) Efforts to expand the
`genetic alphabet: identification of a stable and replicable unnatural DNA self pair, J Am Chem Soc
`126:6923-6931
`118. R Jimenez, G Salazar, J Yin, T Joo, FE Romesberg (2004) Protein dynamics and the immunological
`evolution of molecular recognition, Proc Natl Acad Sci USA, 101:3803-3808
`119. LB Sagle, J Zimmermann, PE Dawson and FE Romesberg (2004) A high resolution probe of protein
`folding, J Am Chem Soc (Comm), 126:3384-3385
`120. M Fa, A Radeghieri, AA Henry, FE Romesberg (2004) Expanding the substrate repertoire of a DNA
`polymerase by directed evolution, J Am Chem Soc, 126:1748-1754
`121. AA Henry, C Yu and FE Romesberg (2003) Determinants of unnatural nucleobase stability and
`polymerase recognition, J Am Chem Soc, 125:9638-9346
`122. S Matsuda, AA Henry, PE Schultz, FE Romesberg (2003) The effect of minor groove hydrogen-bond
`acceptors and donors on the stability and replication of four unnatural base pairs, J Am Chem Soc,
`125:6134-6138
`123. R Jimenez, G Salazar, KK Baldridge, FE Romesberg (2003) Flexibility and molecular recognition in the
`immune system, Proc Natl Acad Sci, 100:92-97
`124. H Wang, H Zhang, OK Abou-Zied, C Yu, FE Romesberg, M Glasbeek (2002) Femtosecond
`fluorescence upconversion
`studies of
`excited-state proton
`transfer dynamics
`in 2-(2’-
`hydroxyphenyl)benzoxazole (HBO) in liquid solution and DNA, Chem Phys Lett 367:599-608
`125. Y Wu, M Fa, E L Tae, P G Schultz, FE Romesberg (2002) Enzymatic phosphorylation of unnatural
`nucleobases, J Am Chem Soc 124:14626-14630
`126. C Yu, AA Henry, P G Schultz, FE Romesberg (2002) Polymerase recognition of unnatural base pairs,
`Angew Chem Int Ed 41:3841-3944
`127. R Jimenez and FE Romesberg (2002) Excited state dynamics and heterogeneity of folded and unfolded
`states of cytochrome c, J Phys Chem B 106:9172-9180
`128. D Hanway, JK Chin, G Xia, G Oshiro, EA Winzler, FE Romesberg (2002) Previously uncharacterized
`genes in the UV- and MMS-induced DNA damage response in yeast Proc Natl Acad Sci USA, 99:10605-
`10610
`
`
`
`

`

`Curriculum Vitae – Floyd E. Romesberg (Page 8 of 16)
`
`.
`
`
`129. G Xia, L J Chen, T Sera, M Fa, P G Schultz and FE Romesberg (2002) Directed evolution of novel
`polymerase activities: Mutation of a DNA polymerase into an efficient RNA polymerase Proc Natl Acad
`Sci USA, 99:6597-6602
`130. M Berger, S D Luzzi, AA Henr, FE Romesberg (2002) Stability and selectivity of unnatural DNA with
`five-membered-ring nucleobase analogs, J Am Chem Soc 124:1222-1226
`131. JK Chin, R Jimenez, FE Romesberg (2002) Protein dynamics and cytochrome c: correlations between
`ligand vibrations and redox activity, J Am Chem Soc (Comm) 124:1846-1847
`132. R Jimenez, DA Case, FE Romesberg (2002) Flexibility of an antibody binding site measured with photon
`echo spectroscopy, J Phys Chem B 106:1090-1103
`133. OK Abou-Zied, R Jimenez, EK Thompson, DP Millar, FE Romesberg (2002) Solvent-dependent
`photoinduced tautomerization of 2-(2’hydroxyphenyl)benzoxazole, J Phys Chem A, 106:3665-3672
`134. EL Tae, Y Wu, G Xia, PG Schultz, FE Romesberg (2001) Efforts toward expansion of the genetic
`alphabet: replication of DNA with three base pairs, J Am Chem Soc 12:7439-7440
`135. OK Abou-Zied, R Jimenez, FE Romesberg (2001) Tautomerization dynamics of a model base-pair in
`DNA, J Am Chem Soc 123:4613-4614
`136. JK Chin, R Jimenez, FE Romesberg (2001) Direct observation of protein vibrations by selective
`incorporation of spectroscopically observable carbon-deuterium bonds in cytochrome c, J Am Chem Soc
`(Comm), 123:2426-2427
`137. H Shulman, C Makarov, AK Ogawa, FE Romesberg, E Keinan (2000) Chemically reactive immunogens
`lead to functional convergence of the immune response, J Am Chem Soc 122:10743-10753
`138. AK Ogawa, OK Abou-Zied, V Tsui, R Jimenez, DA Case and FE Romesberg (2000) A photo-
`tautomerizable model DNA base pair, J Am Chem Soc 122:9917-9920
`139. A K Ogawa, Y Wu, M Berger, P G Schultz and FE Romesberg (2000) Rational design of an unnatural
`base pair with increased kinetic selectivity J Am Chem Soc (Comm) 122:8803-8804
`140. M Berger, Y Wu, AK Ogawa, DL McMinn, PG Schultz, FE Romesberg (2000) Universal bases for
`hybridization, replication, or chain termination, Nucleic Acids Res 28:2911-2914
`141. Y Wu, AK Ogawa, M Berger, DL McMinn, PG Schultz, FE Romesberg (2000) Efforts toward the
`expansion of the genetic alphabet: optimization of interbase hydrophobic interactions, J Am Chem Soc
`122:7621-7632
`142. M Berger, AK Ogawa, DL McMinn, PG Schultz, FE Romesberg (2000) Stable and selective
`hybridization of oligonucleotides using unnatural hydrophobic bases, Angew Chem Int Ed 39:2940-2942
`143. AK Ogawa, Y Wu, DL McMinn, J Liu, J-Q, PG Schultz, FE Romesberg (2000) Efforts toward the
`expansion of the genetic alphabet: information storage and replication with unnatural hydrophobic base
`pairs, J Am Chem Soc 12:3274-3287
`144. E Meggers, PL Holland, WB Tolman, FE Romesberg, PG Schultz (2000) A novel copper-mediated
`DNA Base Pair, J Am Chem Soc (Comm) 122:10714-10715
`145. DL McMinn, AK Ogawa, Y Wu, J Liu, PG Schultz, FE Romesberg (1999) Efforts toward expansion of
`the genetic alphabet: DNA polymerase recognition of a highly stable, self-pairing hydrophobic base, J Am
`Chem Soc (Comm) 121:11585-11586
`
`.
`Publications: Principal Investigator, Invited Reviews.
`146. VT Dien, M Holcomb, FE Romesberg (2019) Eight-letter DNA, Biochemistry 58:2581–2583.
`147. MP Ledbetter, DA Malyshev, FE Romesberg (2019) Site-specific labeling of DNA via PCR with an
`expanded genetic alphabet, Methods Mol Biol 1973:193–212.
`148. VT Dien, SE Morris, RJ Karadeema, FE Romesberg (2018) Expansion of the genetic code via expansion
`of the genetic alphabet, Curr Opin Chem Biol 46:196–202
`149. Y Zhang, FE Romesberg (2018) Semisynthetic organisms with expanded genetic codes, Biochemistry
`57:2177–2178
`150. A Feldman, FE Romesberg (2018) Expansion of the genetic alphabet: a chemist’s approach to synthetic
`biology, Acc Chem Res (ACS Editors’ Choice) 51:394–403
`151. T Chen, FE Romesberg (2017) A method for the exponential synthesis of RNA: introducing the
`
`
`

`

`Curriculum Vitae – Floyd E. Romesberg (Page 9 of 16)
`
`
`polymerase chain transcription (PCT) reaction, Biochemistry 56:5227–5228
`152. R Adhikary, J Zimmermann, FE Romesberg (2017) Transparent window vibrational probes for the
`characterization of proteins with high structural and temporal resolution, Chem Rev 117:1927–1969
`153. AW Feldman, MP Ledbetter, Y Zhang, FE Romesberg (2017) Reply to Hettinger: Hydrophobic
`unnatural base pairs and the expansion of the genetic alphabet, Proc Natl Acad Sci USA 114:E6478-E6479
`154. A Craney, FE Romesberg (2016) Discovery of novel antibacterials, Bioorg Med Chem 24:6225-6226
`155. SI Walsh, A Craney, FE Romesberg (2016) Not just an antibiotic target: Exploring the role of type I
`signal peptidase in bacterial virulence, Bioorg Med Chem 24:6370-6378
`156. T Chen, N Hongdilokkul, Z Liu, D Thirunavukarasu, FE Romesberg (2016) The Expanding World of
`DNA and RNA, Curr Op Chem Biol 34:80-87
`157. A Craney, FE Romesberg (2015) The inhibition of type I bacterial signal peptidase: Biological
`consequences and therapeutic potential, Bioorg. Med. Chem. Lett. 25:4761-4766
`158. DA Malyshev, FE Romesberg (2015) An expanded genetic alphabet, Chem Int. Ed. 54:11930-11944
`159. T Chen and FE Romesberg (2014) Directed polymerase evolution, FEBS Lett 588:219-229
`160. J Zimmermann and FE Romesberg (2014) Carbon-deuterium bonds as non-perturbative infrared
`probes of protein dynamics, electrostatics, heterogeneity, and folding, Methods Mol Biol 1084:101-119
`161. DA Harris and FE Romesberg (2012) SpsB signal pept

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