Romesberg Lab Publications

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Select Year:
2009
	PCR with an expanded genetic alphabet D. Malyshev, Y.J. Seo, P. Ordoukhanian, F.E. Romesberg J. Am. Chem. Soc (2009) 131:14620-14621.
	Major groove derivatization of an unnatural base pair Y.J. Seo, F.E. Romesberg ChemBioChem (2009) 10:2394-2400. Cover Story
	The effects of unnatural base pairs and mispairs on DNA duplex stability and solvation G.T. Hwang , Y. Hari, F.E. Romesberg Nucleic Acids Res, (2009) 37:4757-4763.
	Efforts toward developing probes of protein dynamics: vibrational dephasing and relaxation of carbon-deuterium stretching modes in deuterated leucine J. Zimmermann, K. Gundogdu, M.E. Cremeens, J.N. Bandaria, G.T. Hwang, M.C. Thielges, C.M. Cheatum, F.E. Romesberg J. Phys. Chem. B (2009) 113:7991-7994.
	Synthesis and biological evaluation of penem inhibitors of bacterial signal peptidase D.A. Harris, M.E. Powers, F.E. Romesberg Bioorg. Med. Chem. Lett. (2009) 19:3787-3790.
	Direct observation of structural heterogeneity in a β-sheet M.E. Cremeens, J. Zimmermann, W. Yu, P.E. Dawson, F.E. Romesberg J. Am. Chem. Soc. (2009) 131:5726-5727.
	Direct observation of ligand dynamics in cytochrome c M.T. Thielges, J. Zimmermann, F.E. Romesberg J. Am. Chem. Soc. (2009) 131:6054-6055.
	Transcription of an expanded genetic alphabet Y.J. Seo, S. Matsuda, F.E. Romesberg J. Am. Chem. Soc. (2009) 131:5046-5047.
	The determinants of stability and folding in evolutionarily diverged cytochromes c M.C. Thielges, J. Zimmermann, P.E. Dawson, F.E. Romesberg J. Mol. Biol. (2009) 24:159-167.
	Efforts toward the direct experimental characterization of enzyme microenvironments: tyrosine100 in dihydrofolate reductase D. Groff, M.C. Thielges, S. Celliti, P.G. Schultz, F.E. Romesberg Angew. Chem., Int., Ed., (2009) 48:3478-3481 .
	Chemical frustration in the protein folding landscape: grand canonical ensemble simluations of cytochrome c P. Weinkam, F.E. Romesberg, P.G. Wolynes Biochemistry (2009) 48:2394-2402.
	C-D Modes of deuterated side chain of leucine as structural reporters via dual- frequency two-dimensional infrared spectroscopy S.R.G. Naraharisetty, V.M. Kasyanenko, J. Zimmermann, M.C. Thielges, F.E. Romesberg, I.V. Rubtsov J. Phys. Chem B, (2009) 113:4940-4946 .
	Optimization of an unnatural base pair towards natural-like replication Y.J. Seo, G.T. Hwang, P. Ordoukhanian, F.E. Romesberg J. Am. Chem. Soc. (2009) 131:3246-3252.
	Protein dynamics and the evolution of novel protein functions J. Zimmermann, M.C. Thielges, W. Yu, F.E. Romesberg in Protein Engineering Handbook, Vol. 1 (2009) S. Lutz and U.T. Bornscheuer, Eds., Wiley-VCH:Weinheim, 147-186.
	Engineering nucleobases and polymerases for an expanded genetic alphabet A.M. Leconte , F.E. Romesberg in Protein Engineering (2009) C. Köhrer and U.L. RajBhandary, Eds., Springer- Verlag:Berlin, 291-314.
Select Year:
2008
	Characterization of alkaline transitions in ferricytochrome c using carbon-deuterium infrared probes P. Weinkam, J. Zimmermann, L.B. Sagle, S. Matsuda, P.E. Dawson, P.G. Wolynes, F.E. Romesberg Biochemistry (2008) 47:13470-13480.
	Unnatural substrate repertoire of A, B, and X family DNA polymerases G.T. Hwang, F.E. Romesberg J. Am. Chem. Soc. (2008) 130:14872-14882.
	Optimization of the pyridyl nucleobase scaffold for polymerase recognition and unnatural base pair replication Y. Hari, G.T. Hwang, A.M. Leconte, N. Joubert, M. Hocek, F.E. Romesberg ChemBioChem (2008) 9:2796-2799
	Editorial overview: Next generation therapeutics A. Mapp , F.E. Romesberg Curr. Opin. Chem. Biol . (2008) 12:387-388.
	Exploring the energy landscape of antibody-antigen complexes: protein dynamics, flexibility, and molecular recognition M.C. Thielges, J. Zimmermann, W. Yu, M. Oda, F.E. Romesberg Biochemistry (2008) 47:7237-7247 [June 2008 Hot Article].
	Carbon-Deuterium bonds as probes of dihydrofolate reductase M.C. Thielges, D.A. Case, F.E. Romesberg J. Am. Chem. Soc. (2008) 130:6597-6603.
	Identification of pathways controlling DNA damage induced mutation in Saccharomyces cerevisiae E.T. Lis, B.M. O'Neill, C. Gil-Lemaignere, J.K. Chin, F.E. Romesberg DNA Repair (2008) 7:801-810.
	Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet A.M. Leconte, G.T. Hwang, S. Matsuda, P. Capek, Y. Hari, F.E. Romesberg J. Am. Chem. Soc. (2008) 130:2336-2343.
Select Year:
2007
	Phosphatases, DNA Damage Checkpoints and Checkpoint Deactivation J. Heideker, E.T. Lis, F.E. Romesberg Cell Cycle (2007) 6:3058-3064.
	Structural and initial biological analysis of synthetic arylomycin A2 T.C. Roberts, P.A. Smith, R.T. Cirz, F.E. Romesberg J. Am. Chem. Soc. (2007) 129:15830-15838.
	REVIEW: Controlling mutation: intervening in evolution as a therapeutic strategy R.T. Cirz and F.E. Romesberg Crit. Rev. Biochem. Mol. Biol. (2007) 42:341-354.
	REVIEW: Combating bacteria and drug-resistance by inhibiting mechanisms of persistence and adaptation P.A. Smith and F.E. Romesberg Nat. Chem. Biol. (2007) 3:549-556.
	Polymerase recognition and stability of fluoro substituted pyridone nucleobase analogs G.T. Hwang, A.M. Leconte, F.E. Romesberg ChemBioChem. (2007) 8:1606-1611 .
	Efforts toward expansion of the genetic alphabet: Structure and replication of unnatural base pairs S. Matsuda, J.D. Fillo, A.A. Henry, P. Rai, S. J. Wilkens, T.J. Dwyer, B.H. Geierstanger, D.E. Wemmer, P.G. Schultz, G. Spraggon, F.E. Romesberg J. Am Chem. Soc. (2007) 129:10466-10473.
	AID-initiated purposeful mutations in immunoglobulin genes M.F. Goodman, M.D. Schaarf, F.E. Romesberg Adv. Immunol. (2007) 94:127-155.
	Psy2 and Pph3 form a phosphatase complex required for Rad53 dephosphorylation and replication fork restart during recovery from DNA damage B.M. O'Neill, S.J. Szyjka, E.T. Lis, A.O. Bailey, J.R. Yates III, O.M. Aparicio, F.E. Romesberg Proc. Natl. Acad. Sci. USA (2007) 104(22):9290-9295.
	Minor groove hydrogen bonds and the replication of unnatural base pairs S. Matsuda, A.M. Leconte, F.E. Romesberg J. Am. Chem. Soc. (2007) 129(17):5551-5557.
	*The complete and SOS-mediated response of Staphylococcus aureus* to the antibiotic ciprofloxacin** R.T. Cirz, M.B. Jones, N.A. Gingles, T.D. Minogue, B. Jarrahi, S.N. Peterson, F.E. Romesberg J. Bacteriol. (2007) 189(2):531-539. [Download Supporting Information]
Select Year:
2006
	From therapeutic nucleic acids to redox hydrogels: the diverse world of biopolymers H. Bayley, F.E. Romesberg Curr. Opin. Chem. Biol., (2006) 10(6):598-600.
	Chemical Biology: a broader take on DNA A.M. Leconte, F.E Romesberg Nature, (2006) 444(7119):553-555.
	Direct and high resolution characterization of cytochrome c equilibrium folding L.B. Sagle, J. Zimmermann, P.E. Dawson, F.E. Romesberg J. Am. Chem. Soc. (Comm.) (2006) 128(44):14232-14233.
	Stability and polymerase recognition of pyridine nucleobase analogues: role of minor-groove H-bond acceptors Y. Kim, A.M. Leconte, Y. Hari, F.E.Romesberg Angew. Chem. Int. Ed , (2006) 45(46):7809-7812.
	Infrared line shape of an alpha-carbon deuterium-labeled amino acid C.S. Kinnaman, M.E. Cremeens, F.E. Romesberg, S.A. Corcelli J. Am. Chem. Soc. (Comm.) (2006) 128(41):13334-13335.
	Amplify this! DNA and RNA get a third base pair A.M. Leconte and F.E. Romesberg Nat. Methods (2006) 3:667-668.
	Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics J. Zimmermann, E.L. Oakman, I.F. Thorpe, X. Shi, P. Abbyad, C.L. Brooks, III, S.G. Boxer, F.E. Romesberg Proc. Natl. Acad. Sci. USA (2006) 103(37):13722-13727.
	*Defining the Pseudomonas aeruginosa* SOS response and its role in the global response to the antibiotic ciprofloxacin** R.T. Cirz, B.M. O'Neill, J.A. Hammond, S.R. Head, F.E. Romesberg J. Bacteriol. (2006) 188(20):7101-7110. [Download Supplemental Data]
	Side effects may include evolution R.T. Cirz, N. Gingles, F.R. Romesberg Nat. Med. (2006) 12:890-891.
	Efforts towards expansion of the genetic alphabet: pyridone and methyl pyridone nucleobases A.M. Leconte, S. Matsuda, G.T. Hwang, F.E. Romesberg Angew. Chem. Int. Ed. (2006) 45(26):4326-4329.
	Redox-coupled dynamics and folding in cytochrome c L.B. Sagle, J. Zimmermann, S. Matsuda, P.E. Dawson, F.E. Romesberg J. Am. Chem. Soc (2006) 128(24):7909-7915.
	*The role of Doa1 in the S. cerevisiae* DNA damage response** E.T. Lis and F.E. Romesberg Mol. Cell. Biol., (2006) 26(11):4122-4133.
	An efficiently extended class of unnatural base pairs A.M. Leconte, S.Matsuda, F.E.Romesberg J. Am. Chem. Soc (Comm) (2006) 128(21):6780-6781.
	Efforts toward developing direct probes of protein dynamics M.E. Cremeens, H. Fujisaki, Y. Zhang, J. Zimmermann, L.B. Sagle, S. Matsuda, P.E. Dawson, J.E. Straub, F.E. Romesberg J. Am. Chem. Soc. (Comm) (2006) 128(18):6028-6029.
	Optimization of unnatural base pair packing for polymerase recognition S. Matsuda, A.A. Henry and F.E. Romesberg J. Am. Chem. Soc., (2006) 128(19):6369-6375.
	Esc4/Rtt107 and the control of recombination during replication J. K. Chin, V. I. Bashkirov, W.-D. Heyer and F.E. Romesberg. DNA Repair, (2006) 5(5):618-628.
	Substituent effects on the pairing and polymerase recognition of simple unnatural base pairs G.T. Hwang and F.E. Romesberg. Nucleic Acids Res, (2006) 34(7):2037-2045.
	Induction and inhibition of ciprofloxacin resistance-conferring mutations in hypermutator bacteria R.T. Cirz and F.E. Romesberg Antimicrob. Agents Chemother. (2006) 50(1):220-225.
Select Year:
2005
	Differential solvation and tautomer stability of a model base pair within the minor and major grooves of DNA F.-Y. Dupradeau, D.A. Case, C. Yu, R. Jimenez, F.E. Romesberg J. Am. Chem. Soc. (2005) 127(44):15612-15617.
	Polymerase evolution: efforts toward expansion of the genetic code A.M. Leconte, L.Chen, F.E. Romesberg J. Am. Chem. Soc. (Comm.) (2005) 127(36):12470-12471.
	REVIEW: The evolution of DNA polymerases with novel activities A.A. Henry and F.E. Romesberg Curr. Opin. Biotechnol. (2005) 16(4):370-377.
	Inhibition of mutation and combating the evolution of antibiotic resistance R.T. Cirz, J.K. Chin, D.R. Andes, V. de Crécy-Lagard, W.A. Craig, F.E. Romesberg PLoS Biol. (2005) 3(6):e176.
	REVIEW: Directed evolution of novel polymerases R.C. Holmberg, A.A. Henry, F.E. Romesberg Biomol. Eng. (2005) 22(1-3):39-49.
Select Year:
2004
	*Coordinated functions of WSS1, PSY2,* and TOF1 in the DNA damage response** B.M. O'Neill, D. Hanway, E.A. Winzeler, F.E. Romesberg Nucleic Acids Res. (2004) 32(22):6519-6530.
	Optimization of interstrand hydrophobic packing interactions within unnatural base pairs S. Matsuda, F.E. Romesberg J. Am. Chem. Soc. (2004) 126(44):14419-14427.
	REVIEW: Isotope effects and quantum tunneling in enzyme-catalyzed hydrogen transfer. Part I. The experimental basis F.E. Romesberg, R.L. Schowen Adv. Phys. Org. Chem. (2004) 39:27-77.
	Efforts to expand the genetic alphabet: identification of a replicable unnatural DNA self-pair A.A. Henry, A.G. Olsen, S. Matsuda, C. Yu, B.H. Geierstanger, F.E. Romesberg J. Am. Chem. Soc. (2004) 126(22):6923-6931.
	*Preliminary characterization of light harvesting in E. coli* DNA photolyase** A.A. Henry, R. Jimenez, D. Hanway, F.E. Romesberg Chembiochem (2004) 5(8):1088-1094.
	A high-resolution probe of protein folding L.B. Sagle, J. Zimmermann, P.E. Dawson, F.E. Romesberg J. Am. Chem. Soc. (Comm.) (2004) 126(11):3384-3385.
	Protein dynamics and the immunological evolution of molecular recognition R. Jimenez, G. Salazar, J. Yin, T. Joo, F.E. Romesberg Proc. Natl. Acad. Sci. USA (2004) 101(11):3803-3808.
	Expanding the substrate repertoire of a DNA polymerase by directed evolution M. Fa, A. Radeghieri, A.A. Henry, F.E. Romesberg J. Am. Chem. Soc. (2004) 126(6):1748-1754.
Select Year:
2003
	REVIEW: Beyond A, C, G, and T: augmenting nature's alphabet A.A. Henry, F.E. Romesberg Curr. Opin. Chem. Biol. (2003) 7(6):727-733.
	Determinants of unnatural nucleobase stability and polymerase recognition. A.A. Henry, C. Yu, F.E. Romesberg J. Am . Chem. Soc. (2003) 125(32):9638-9646.
	REVIEW: Multidisciplinary experimental approaches to characterizing biomolecular dynamics F.E. Romesberg Chembiochem. (2003) 4(7):563-571.
	The effect of minor-groove hydrogen-bond acceptors and donors on the stability and replication of four unnatural base pairs S. Matsuda, A.A. Henry, P.G. Schultz, F.E. Romesberg J. Am. Chem. Soc. (2003) 125(20):6134-6139.
	Flexibility and molecular recognition in the immune system R. Jimenez, G. Salazar, K.K. Baldridge, F.E. Romesberg Proc. Natl. Acad. Sci. USA (2003) 100(1):92-97.
	Femtosecond fluorescence upconversion studies of excited-state proton-transfer dynamics in 2-(2 '-hydroxyphenyl)benzoxazole (HBO) in liquid solution and DNA H. Wang, H. Zhang, O.K. Abou-Zied, C. Yu, F.E. Romesberg, M. Glasbeek Chem. Phys. Lett. (2003) 367(5-6):599-608.
Select Year:
2002
	Enzymatic phosphorylation of unnatural nucleosides Y. Wu, M. Fa, E.L. Tae, P.G. Schultz, F.E. Romesberg J. Am. Chem. Soc. (2002) 124(49):14626-14630.
	Excited state dynamics and heterogeneity of folded and unfolded states of cytochrome c R. Jimenez, F.E. Romesberg J. Phys. Chem. B. (2002) 106(35):9172-9180.
	Polymerase recognition of unnatural base pairs C. Yu, A.A. Henry, F.E. Romesberg, P.G. Schultz Angew. Chem. Int. Ed. Engl. (2002) 41(20):3841-3844.
	REVIEW: Development of a universal nucleobase and modifed nucleobases for expanding the genetic code F.E. Romesberg, C. Yu, S. Matsuda, A.A. Henry in Current Protocols in Nucleic Acid Chemistry (2002) Unit 1.5.
	Previously uncharacterized genes in the UV- and MMS-induced DNA damage response in yeast D. Hanway, J.K. Chin, G. Xia, G. Oshiro, E.A. Winzeler, F.E. Romesberg Proc. Natl. Acad. Sci. USA (2002) 99(16):10605-10610.
	Directed evolution of novel polymerase activities: mutation of a DNA polymerase into an efficient RNA polymerase G. Xia, L. Chen, T. Sera, M. Fa, P.G. Schultz, F.E. Romesberg Proc. Natl. Acad. Sci. USA (2002) 99(10):6597-6602.
	Solvent-Dependent Photoinduced Tautomerization of 2-(2'- Hydroxyphenyl)benzoxazole O.K. Abou-Zied, R. Jimenez, E.H.Z. Thompson, D.P. Millar, F.E. Romesberg J. Phys. Chem. A. (2002) 106(15):3665-3672.
	Protein dynamics and cytochrome c: correlations between ligand vibrations and redox activity J.K. Chin, R. Jimenez, F.E. Romesberg J. Am. Chem. Soc. (Comm.) (2002) 124(9):1846-1847.
	Flexibility of an Antibody Binding Site Measured with Photon Echo Spectroscopy R. Jimenez, D.A. Case, F.E. Romesberg J. Phys. Chem. B. (2002) 106(5):1090-1103.
	Stability and selectivity of unnatural DNA with five-membered-ring nucleobase analogues M. Berger, S.D. Luzzi, A.A. Henry, F.E. Romesberg J. Am. Chem. Soc. (2002) 124(7):1222-1226.
Select Year:
2001
	Efforts toward expansion of the genetic alphabet: replication of DNA with three base pairs E.L. Tae, Y. Wu, G. Xia, P.G. Schultz, F.E. Romesberg J. Am. Chem. Soc. (Comm.) (2001) 123(30):7439-7440.
	Tautomerization dynamics of a model base pair in DNA O.K. Abou-Zied, R. Jimenez, F.E. Romesberg J. Am. Chem. Soc. (Comm.) (2001) 123(19):4613-4614.
	Direct observation of protein vibrations by selective incorporation of spectroscopically observable carbon-deuterium bonds in cytochrome c J.K. Chin, R. Jimenez, F.E. Romesberg J. Am. Chem. Soc. (Comm.) (2001) 123(10):2426-2427.
Select Year:
2000
	Chemically Reactive Immunogens Lead to Functional Convergence of the Immune Response H. Shulman, C. Makarov, A.K. Ogawa, F.E. Romesberg, E. Keinan. J. Am. Chem. Soc. (2000) 122(44):10743-10753.
	A Novel Copper-Mediated DNA Base Pair E. Meggers, P.L. Holland, W.B. Tolman, F.E. Romesberg, P.G. Schultz J. Am. Chem. Soc. (Comm.) (2000) 122(43):10714-10715.
	A Phototautomerizable Model DNA Base Pair A.K. Ogawa, O.K. Abou-Zied, V. Tsui, R. Jimenez, D.A. Case, F.E. Romesberg. J. Am. Chem. Soc. (2000) 122(41):9917-9920.
	Rational Design of an Unnatural Base Pair with Increased Kinetic Selectivity A.K. Ogawa, Y. Wu, M. Berger, P.G. Schultz, F.E. Romesberg J. Am. Chem. Soc. (Comm.) (2000) 122(36):8803-8804.
	Stable and Selective Hybridization of Oligonucleotides with Unnatural Hydrophobic Bases M. Berger, A.K. Ogawa, D.L. McMinn, Y. Wu, P.G. Schultz, F.E. Romesberg Angew. Chem. Int. Ed. Engl. (2000) 39(16):2940-2942.
	Efforts toward Expansion of the Genetic Alphabet: Optimization of Interbase Hydrophobic Interactions Y. Wu, A.K. Ogawa, M. Berger, D.L. McMinn, P.G. Schultz, F.E. Romesberg J. Am. Chem. Soc. (2000) 122(32):7621-7632.
	Efforts toward the Expansion of the Genetic Alphabet: Information Storage and Replication with Unnatural Hydrophobic Base Pairs A.K. Ogawa, Y. Wu, D.L. McMinn, J. Liu, P.G. Schultz, F.E. Romesberg J. Am. Chem. Soc. (2000) 122(14):3274-3287.
	Universal bases for hybridization, replication and chain termination M. Berger, Y. Wu, A.K. Ogawa, D.L. McMinn, P.G. Schultz, F.E. Romesberg Nucleic Acids Res. (2000) 28(15):2911-2914.
Select Year:
1999
	Efforts toward Expansion of the Genetic Alphabet: DNA Polymerase Recognition of a Highly Stable, Self-Pairing Hydrophobic Base D.L. McMinn, A.K. Ogawa, Y. Wu, J. Liu, P.G. Schultz, F.E. Romesberg J. Am. Chem. Soc. (Comm.) (1999) 121(49):11585-11586.