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Publications of Loren Williams
  • 153) Glass, JB, Elbon, CE, and Williams, LD "Something Old, Something New, Something Borrowed, Something Blue: The Anaerobic Microbial Ancestry of Aerobic Respiration", Trends Microbiol (2022) (pdf)
  • 152) Biesiada, M, Hu, MY, Williams, LD, Purzycka, KJ, and Petrov, AS "rRNA Expansion Segment 7 in Eukaryotes: From Signature Fold to Tentacles", Nucleic Acids Res. 50, 10717–10732 (2022) (pdf)
  • 151) Alvarez-Carreño, C, Gupta, R, Petrov, AS, and Williams, LD "Protein Fold Evolution by Creative Destruction", Proc Nat Acad Sci, USA 119, e2207897119 (2022) (pdf)
  • 150) Müller, UF, Elsila, J, Trail, D, DasGupta, S, Giese, C-C, Walton, CR, Cohen, ZR, Stolar, T, Krishnamurthy, R, Lyons, TW, Rogers, KL, and Williams, LD "Frontiers in Prebiotic Chemistry and Early Earth Environments" Orig Life Evol Biosph, 52, 165-181 (2022) (pdf)
  • 149) C, M, Frenkel-Pinter, M., Smith, K.H., Rivera-Santana, V.F., Sargon, A.B., Jacobson, K.C., Guzman-Martinez, A., Williams, L.D., Leman, L.J., Liotta, C.L., Martha A. Grover, and Hud, N.V. "Water-Based Dynamic Depsipeptide Chemistry: Building Block Recycling and Oligomer Distribution Control Using Hydration–Dehydration Cycles", JACS Au 2, 1395-1404 (2022) (pdf)
  • 148) Frenkel-Pinter, M, Bouza, M, Fernández, FM, Leman, LJ, Williams, LD, Hud, NV, and Guzman-Martinez, A "Thioesters Provide a Plausible Prebiotic Path to Proto-Peptides" Nature Commun 13, 1-8 (2022) (pdf)
  • 147) Frenkel-Pinter, M, Jacobson, KC, Eskew-Martin, J, Forsythe, JG, Grover, MA, Williams, LD, and Hud, NV "Differential Oligomerization of Alpha Versus Beta Amino Acids and Hydroxy Acids in Abiotic Proto-Peptide Synthesis Reactions" Life 12, 265-280 (2022) (pdf)
  • 146) Frenkel-Pinter, M, Petrov, AS, Matange, K, Travisano, M, Glass, JB, and Williams, LD "Adaptation and Exaptation: From Small Molecules to Feathers" J Mol Evol 90, 166-175 (2022) (pdf)
  • 145) Penev, PI, Alvarez-Carreño, C, Smith, E, Petrov, AS, and Williams, LD "TwinCons: Conservation Score for Uncovering Deep Sequence Similarity and Divergence" PLoS Comp Biol 17, e1009541 (2021) (pdf)
  • 144) Alvarez-Carreño, C, Penev, PI, Petrov, AS, and Williams, LD "Fold Evolution Before LUCA: Common Ancestry of SH3 Domains and OB Domains" Mol Biol Evol 38, 5134-5143 (2021) (pdf)
  • 143) Sweeney, BA, Hoksza, D, Nawrocki, EP, Ribas, CE, Madeira, F, Cannone, JJ, Gutell, R, Maddala, A, Meade, CD, Williams, LD, Petrov, AS, Chan,, Lowe, TM, Finn, RD, and Petrov, AI "R2DT Is a Framework for Predicting and Visualising RNA Secondary Structure Using Templates" Nature Commun 12, 1-12 (2021) (pdf)
  • 142) Goldman, A, Fournier, G, Gogarten, JP, Petrov, AS, Rothschild, L, Segrè, D, Smith, E, and Williams, LD "Understanding the Early Major Transitions in Evolutionary History Part 1: Stages in the Emergence of Complex Life" Bull Am Astro Soc 53, 247 (2021) (pdf)
  • 141) Fournier, G, Gogarten, JP, Goldman, AD, Petrov, AS, Rothschild, L, Segrè, D, Smith, E, and Williams, LD, "Understanding the Early Major Transitions in Evolutionary History Part 2: Ancient Evolution of Biological Systems and the Biosphere" Bull Am Astro Soc 53, 253 (2021) (pdf)
  • 140) Penev, PI, McCann, HM, Meade, CD, Maddala, A, Bernier, CR, Chivukula, VL, Ahmad, M, Gulen, B, Sharma, A, Alvarez-Carreño, C, Williams, LD, Petrov AS “ProteoVision: Web Server for Advanced Visualization of Ribosomal Proteins”, Nucleic Acids Res (2021) (pdf)
  • 139) Frenkel-Pinter, M, Sargon, AB, Glass, JB, Hud, NV, and Williams, LD "Transition Metals Enhance Prebiotic Depsipeptide Oligomerization Reactions Involving Histidine" RSC Advances 11, 3534-3538 (2021) (pdf)
  • 138) Frenkel-Pinter, M, Rajaei, V, Glass, JB, Hud, NV, and Williams, LD "Water and Life: the Medium Is the Message" J Mol Evo 89, 2–11 (2021) (pdf)
  • 137) Mestre-Fos, S, Moore, CM, Reddi, AR, and Williams, LD "Human Ribosomal G-quadruplexes Regulate Heme Bioavailability" J Biol Chem 295, 14855–14865 (2020) (pdf)
  • 136) Penev, PI, Fakhretaha-Aval, S, Patel, VJ, Cannone, JJ, Petrov, AS, Williams, LD, and Glass, JB "Supersized Ribosomal RNA Expansion Segments in Asgard Archaea" Genome Biol Evol 12, 1694–1710 (2020) (pdf)
  • 135) Mascuch, S, Fakhretaha-Aval, S, Bowman, J, Ma, M, Thomas, G, Bommarius, B, Ito, C, Zhao, L, Newnam, G, Matange, K, Thapa, H, Barlow, B, Donegan, R, Nguyen, N, Saccuzzo, E, Obianyor, C, Karunakaran, S, Pollet, P, Rothschild-Mancinelli, B, Mestre-Fos, S, Guth-Metzler, R, Bryksin, A, Petrov, A, Hazell, M, Ibberson, C, Penev, P, Mannino, R, Lam, W, García, A, Kubanek, J, Agarwal, V, Hud, N, Glass, J, Williams, LD, and Lieberman, R "A Blueprint for Academic Labs to Produce SARS-CoV-2 RT-qPCR Test Kits" J Biol Chem 295, 15438-15453 (2020) (pdf)
  • 134) Guth-Metzler, R, Bray, MS, Suttapitugsakul, S, Montllor-Albalate, C, Bowman, JC, Wu, R, Reddi, AR, Okafor, CD, Glass, JB, and Williams, LD "Cutting in-Line with Iron: Ribosomal Function and Non-Oxidative RNA Cleavage" Nucleic Acids Res 48, 8663–8674 (2020) (pdf)
  • 133) Frenkel-Pinter, M, Haynes, JW, Mohyeldin, AM, Martin, C, Sargon, AB, Petrov, AS, Krishnamurthy, R, Hud, NV, Williams, LD, and Leman, LJ "Mutually Stabilizing Interactions between Proto-Peptides and RNA" Nature Commun 11, 1-14 (2020) (pdf)
  • 132) Bowman, JC, Petrov, AS, Frenkel-Pinter, M, Penev, PI, and Williams, LD "Root of the Tree: The Significance, Evolution, and Origins of the Ribosome" Chem Rev 120, 4848-4878 (2020) (pdf)
  • 131) Ghosh, A, Williams, LD, Pestov, DG, and Shcherbik, N "Proteotoxic Stress Promotes Entrapment of Ribosomes and Misfolded Proteins in a Shared Cytosolic Compartment" Nucleic Acids Res 48, 3888-3905 (2020) (pdf)
  • 130) Mestre-Fos S, Penev PI, Richards JC, Dean WL, Gray RD, Chaires JB, and Williams, LD "Profusion of G-quadruplexes on both subunits of metazoan ribosomes" PLoS One 14, e0226177 (2019) (pdf)
  • 129) Frenkel-Pinter, M, Haynes, JW, C, M, Petrov, AS, Burcar, BT, Krishnamurthy, R, Hud, NV, Leman, LJ and Williams, LD "Selective Incorporation of Proteinaceous over Nonproteinaceous Cationic Amino Acids in Model Prebiotic Oligomerization Reactions" Proc Nat Acad Sci, USA 116, 16338-16346 (2019) (pdf)
  • 128) Mestre-Fos, S, Penev, PI, Suttapitugsakul, S, Ito, C, Petrov, AS, Wartell, RM, Wu, R, and Williams, LD "G-quadruplexes in Human Ribosomal RNA" J Mol Biol 431, 1940-1955 (2019) (pdf)
  • 127) Bowman, JC, Petrov, AS, and Williams, LD "Role of Cations in RNA Folding and Function, in Handbook of Astrobiology (Kolb, V M, Ed), CRC Press, New York, NY (2019) (pdf)
  • 126) Runnels, C, Lanier, KA, WIlliams, JK, Bowman, JC, Petrov, AS, Hud, NV, and Williams, LD "Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers" J Mol Evol 86, 598–610 (2018) (pdf)
  • 125) Bray, MS, Lenz, TK, Haynes, JW, Bowman, JC, Petrov, AS, Reddi, AR, Hud, NV, Williams, LD, and Glass, JB "Multiple Prebiotic Metals Mediate Translation" Proc Nat Acad Sci, USA 115, 12164-12169 (2018) doiorg/101073/pnas1803636115 (pdf)
  • 124) Kovacs, NA, Penev, PI, Venapally, A, Petrov, AS, and Williams, LD "Circular Permutation Obscures Universality of a Ribosomal Protein" J Mol Evol, 1-12 (2018) (pdf)
  • 123) Okafor, CD, Bowman, JC, Hud, NV, Glass, JB, and Williams, LD "Folding and Catalysis near Life’s Origin: Su"pp"ort for Fe2+ as a Dominant Divalent Cation, in Prebiotic Chemistry and Chemical Evolution of Nucleic Acids" (Cesar Menor-Salván, ed), [Review], 227-243, (2018) Springer International Publishing AG (pdf)
  • 122) Fang, P-Y, Bowman, JC, Gómez Ramos, L, Hsiao, C, and Williams, LD "RNA: Packaged and Protected by VLPs" RSC Advances 8, 21399-21406 (2018) doiorg/101039/c8ra02084a (pdf)
  • 121) Bernier, CR, Petrov, AS, Kovacs, NA, Penev, PI, and Williams, LD "Translation: The Universal Structural Core of Life" Mol Biol Evol 34, 2065–2076 (2018) doiorg/101093/molbev/msy101 (pdf)
  • 120) Lenz, TK, Norris, AM, Hud, NV, and Williams, LD "Protein-Free Ribosomal RNA Folds to a near-Native State in the Presence of Mg2+" RSC Advances 7, 54674-54681, (2017) (pdf)
  • 119) Gomez Ramos, LM, Degtyareva, NN, Kovacs, NA, Holguin, SY, Jiang, L, Petrov, AS, Biesiada, M, Hu, MY, Purzycka, KJ, Arya, DP, and Williams, LD "Eukaryotic Ribosomal Expansion Segments as Antimicrobial Targets" Biochemistry 56, 5288-5299 (2017) (pdf)
  • 118) Lanier, KA, Petrov, AS, and Williams, LD "The Central Symbiosis of Molecular Biology" J Mol Evol 85, 8-13 (2017) (pdf)
  • 117) Lanier, KA, Roy, P, Schneider, DM, and Williams, LD "Ancestral Interactions of Ribosomal RNA and Ribosomal Proteins" Biophys J 13, 268-276 (2017) (pdf)
  • 116) Okafor, CD, Lanier, KA, Petrov, AS, Athavale, SS, Bowman, JC, Hud, NV, and Williams, LD "Iron Mediates Catalysis of Nucleic Acid Processing Enzymes: Support for Fe(II) as a Cofactor before the Great Oxidation Event" Nucleic Acids Res 45, 3634-3642 (2017) (pdf)
  • 115) Kovacs, NA, Petrov, AS, Lanier, KA, and Williams, LD "Frozen in Time: The History of Proteins" Mol Biol Evol 34, 1252-1260 (2017) (pdf)
  • 114) Lanier, KA, and Williams, LD "The Origin of Life: Models and Data" J Mol Evol 84, 85-92 (2017) (pdf)
  • 113) Jones, BL, Walker, CL, Azizi, B, Tolbert, L, Williams, LD, and Snell, TW "Conservation of Estrogen Receptor Function in Invertebrate Reproduction" BMC Evol Biol 17, 65-75 (2017) (pdf)
  • 112) Fang, P-Y, Gomez Ramos, LM, Holguin, YS, Hsiao, C, Bowman, JC, Yang, H-W, and Williams, LD "Functional RNAs: Combined Assembly and Packaging in VLPs" Nucleic Acids Res, (2016) (pdf)
  • 111) Gomez Ramos, LM, Smeekens, JM, Kovacs, NA, Bowman, JC, Wartell, RM, Wu, R, and Williams, LD "Yeast rRNA Expansion Segments: Folding and Function" J Mol Biol 428, 4048-4059 (2016) (pdf)
  • 110) Lanier, KA, Athavale, SS, Petrov, AS, Wartell, R, and Williams, LD "Imprint of Ancient Evolution on rRNA Folding" Biochemistry 55, 4603-4613 (2016) (pdf)
  • 109) Komeda, S, Qu, Y, Mangrum, JB, Hegmans, A, Williams, LD, and Farrell, NP "The Phosphate Clamp as Recognition Motif in Platinum-DNA Interactions" Inorg Chim Acta 452, 25-33 (2016) (pdf)
  • 108) Gulen, B, Petrov, AS, Okafor, CD, Vander Wood, D, O'Neill, EB, Hud, NV, and Williams, LD "Ribosomal Small Subunit Domains Radiate from a Central Core" Sci Reports 6, 20885 (2016) (pdf)
  • 107) Petrov, AS, Gulen, B, Norris, AM, Kovacs, NA, Bernier, CR, Lanier, KA, Fox, GE, Harvey, SC, Wartell, RM, Hud, NV, and Williams, LD "History of the Ribosome and the Origin of Translation" Proc Nat Acad Sci, USA 112, 15396-15401 (2015) (pdf)
  • 106) Petrov, AS, and Williams, LD "The Ancient Heart of the Ribosomal Large Subunit: A Response to Caetano-Anolles" J Mol Evol 80 166-170 (2015) (pdf)
  • 105) Bowman, JC, Hud, NV, and Williams, LD "The Ribosome Challenge to the RNA World" J Mol Evol 80, 143-161 (2015) (pdf)
  • 104) Ma, Z, Chen, W, Johnson, M, Schmidt-Krey, I, Williams, LD, and Schuster, GB "Modular-DNA Programmed Molecular Construction of "Fixed" 2D and 3D-Au Nanoparticle Arrays" Chem Mater 26, 5499-5505 (2015) (pdf)
  • 103) Petrov, AS, Bernier, CR, Gulen, B, Waterbury, CC, Hershkovitz, E, Hsiao, C, Harvey, SC, Hud, NV, Fox, GE, Wartell, RM, and Williams, LD "Secondary Structures of rRNAs from All Three Domains of Life" PLoS One 9, e88222 (2014) (pdf)
  • 102) Petrov, AS, Bernier, CR, Hsiao, C, Norris, AM, Kovacs, NA, Waterbury, CC, Stepanov, VG, Harvey, SC, Fox, GE, Wartell, RM, Hud, NV, and Williams, LD "Evolution of the Ribosome at Atomic Resolution" Proc Nat Acad Sci, USA 111, 10251-10256 (2014) (pdf)
  • 101) Harris, LA, Williams, LD, and Koudelka, GB "Specific Minor Groove Solvation Is a Crucial Determinant of DNA Binding Site Recognition" Nucleic Acids Res 42, 14053-14059 (2014) (pdf)
  • 100) Bernier, C, Petrov, AS, Waterbury, C, Jett, J, Li, F, Freil, LE, Xiong, b, Wang, L, Le, A, Milhouse, BL, Hershkovitz, E, Grover, M, Xue, Y, Hsiao, C, Bowman, JC, Harvey, SC, Wartel, JZ, and Williams, LD "Ribovision: Visualization and Analysis of Ribosomes" Faraday Discuss 169, 1-12 (2014) (pdf)
  • 99) Jones, BL, VanLoozen, J, Kim, MH, Miles, SJ, Dunham, CM, Williams, LD, and Snell, TW "Stress Granules Form in Brachionus Manjavacas (Rotifera) in Response to a Variety of Stressors" Comparative biochemistry and physiology Part A, Molecular and integrative physiology 166, 375-384 (2013) (pdf)
  • 98) Petrov, AS, Bernier, CR, Hershkovitz, E, Xue, Y, Waterbury, CC, Grover, MA, C, HS, Hud, NV, Wartell, RM, and Williams, LD "Secondary Structure and Domain Architecture of the 23S rRNA" Nucleic Acids Res 41, 7522-7535 (2013) (pdf)
  • 97) Hsiao, C, Chou, I-C, Okafor, CD, Bowman, JC, O'Neill, EB, Athavale, SS, Petrov, AS, Hud, NV, Wartell, RM, Harvey, SC, and Williams, LD "Iron(II) Plus RNA Can Catalyze Electron Transfer" Nature Chem 5, 525-528 (2013) (pdf)
  • 96) Hud, NV, Cafferty, BJ, Krishnamurthy, R, and Williams, LD "The Origin of RNA and "My Grandfather's Axe"" Chem Biol 20, 466-474 (2013) (pdf)
  • 95) Hsiao, C, Lenz, TK, Peters, JK, Fang, PY, Schneider, DM, Anderson, EJ, Preeprem, T, Bowman, JC, O'Neill, EB, Lie, L, Athavale, SS, Gossett, JJ, Trippe, C, Murray, J, Petrov, AS, Wartell, RM, Harvey, SC, Hud, NV, and Williams, LD "Molecular Paleontology: A Biochemical Model of the Ancestral Ribosome" Nucleic Acids Res 41, 3373-3385 (2013) (pdf)
  • 94) Athavale, SS, Gossett, JJ, Bowman, JC, Hud, NV, Williams, LD, and Harvey, SC "In Vitro Secondary Structure of the Genomic RNA of Satellite Tobacco Mosaic Virus" PLoS One 8, e54384 (2013) (pdf)
  • 93) Harris, LA, Watkins, D, Williams, LD, and Koudelka, GB "Indirect Readout of DNA Sequence by P22 Repressor: Roles of DNA and Protein Functional Groups in Modulating DNA Conformation" J Mol Biol 425, 133-143 (2013) (pdf)
  • 92) Williams, LD "Yin and Yang: Polypeptide and Polynucleotide" Origins of LIfe Community Page (2012) (pdf)
  • 91) Peters, JW, and Williams, LD "The Origin of Life: Look up and Look Down" Astrobiology 12, 1087-1092 (2012) (pdf)
  • 90) Bowman, JC, Azizi, B, Lenz, TK, Roy, P, and Williams, LD Preparation of Long Templates for RNA in Vitro Transcription by Recursive PCR, in Recombinant and in Vitro RNA Synthesis: Methods and Protocols, Methods in Molecular Biology (Conn, G L, Ed), 19-41, Springer Science, LLC (2012) (pdf)
  • 89) Petrov, AS, Bernier, CR, Hsiao, CL, Okafor, CD, Tannenbaum, E, Stern, J, Gaucher, E, Schneider, D, Hud, NV, Harvey, SC, and Williams, LD "RNA-Magnesium-Protein Interactions in Large Ribosomal Subunit" J Phys Chem B 116, 8113-8120 (2012) (pdf)
  • 88) Bowman, JC, Lenz, TK, Hud, NV, and Williams, LD "Cations in Charge: Magnesium Ions in RNA Folding and Catalysis " Cur Op Struct Biol 22, 262-272 (2012) (pdf)
  • 87) Engelhart, AE, Cafferty, BJ, Okafor, CD, Chen, MC, Williams, LD, Lynn, DG, and Hud, NV "Nonenzymatic Ligation of DNA with a Reversible Step and a Final Linkage That Can Be Used in PCR" ChemBioChem 13, 1121-1124 (2012) (pdf)
  • 86) Athavale, SS, Petrov, AS, Hsiao, C, Watkins, D, Prickett, CD, Gossett, JJ, Lie, L, Bowman, JC, O'Neill, E, Bernier, CR, Hud, NV, Wartell, RM, Harvey, SC, and Williams, LD "RNA Folding and Catalysis Mediated by Iron (II)" PLoS ONE 7, e38024 (2012) (pdf)
  • 85) Athavale, SS, Gossett, JJ, Hsiao, C, Bowman, JC, O'Neill, E, Hershkovitz, E, Preeprem, T, Hud, NV, Wartell, RM, Harvey, SC, and Williams, LD "Domain III of the T thermophilus 23S rRNA Folds Independently to a near-Native State" RNA 18, 752-758 (2012) (pdf)
  • 84) Maehigashi, T, Hsiao, C, Kruger Woods, K, Moulaei, T, Hud, NV, and Williams, LD "B-DNA Structure Is Intrinsically Polymorphic: Even at the Level of Base Pair Positions" Nucleic Acids Res 8, 3714-3722 (2012) (pdf)
  • 83) Bowman, JC, and Williams, LD Nucleic Acids, in Encyclodedia of Astrobiology (Gargaud, M, Cernicharo, J, Viso, M, Cleaves II, H J, Pinti, D, Amils, R, and Kobayashi, K, Eds), Springer, New York, NY (2011)
  • 82) Watkins , D, Harris , L-A, Koudelka , G, B, and Williams, LD "Protein: Feeling the Groove of DNA" in Frontiers in Nucleic Acids (Sheardy, R D, and Winkle, S A, Eds), 133-145, American Chemical Society (2011) (pdf)
  • 81) Buckley, R, Enekwa, CD, Williams, LD, and Hud, NV "Molecular Recognition of Watson-Crick-Like Purine-Purine Base Pairs" ChemBioChem 12, 2155-2158 (2011) (pdf)
  • 80) Petrov, AS, Bowman, JC, Harvey, SC, and Williams, LD "Bidentate RNA-Magnesium Clamps: On the Origin of the Special Role of Magnesium in RNA Folding" RNA, 17, 291-297 (2011) (pdf)
  • 79) Schneider, DM, and Williams, LD "You Can't Change That: Arsenic, Phosphorus and Life" J Cosmology 13, 3627-3630 (2010) (commentary)
  • 78) Komeda, S, Moulaei, T, Chikuma, M, Odani, A, Kipping, R, Farrell, NP, and Williams, LD "The Phosphate Clamp: A Small and Independent Motif for Nucleic Acid Backbone Recognition" Nucleic Acids Research, 24, 1-12 (2010) (pdf)
  • 77) Mohan, S, Hsiao, C, Bowman, JC, Wartell, R, and Williams, LD "RNA Tetraloop Folding Reveals Tension between Backbone Restraints and Molecular Interactions J Am Chem Soc, 132, 12679-12689 (2010) (pdf)
  • 76) Watkins, D, Mohan, S, Koudelka, GB and Williams, LD "Sequence Recognition of DNA by Protein-Induced Conformational Transitions" J Mol Biol, 396, 1145-1164 (2010) (pdf)
  • 75) Watkins, D, Moulaei, T, Komeda, S, and Williams, LD "Application of Anomalous Diffraction Methods to the Study of DNA and DNA-Complexes" Methods in Enzymology, (Fox, K, Ed) 133-152 (2010)
  • 74) Hsiao, C, Mohan, S, Kalahar, BK, and Williams, LD "Peeling the Onion: Ribosomes are Ancient Molecular Fossils" Mol Bio Evol, 26, 2415-2425 (2009) (pdf)
  • 73) Hsiao, C and Williams, LD "A Recurrent Magnesium-Binding Motif Provides a Framework for the Ribosomal Peptidyl Transferase Center" Nucleic Acids Res, 37, 3134-3142 (2009) (pdf)
  • 72) Apostolico, A, Ciriello, G, Guerra, C, Heitsch, C E, Hsiao, C, and Williams, LD "Finding 3D Motifs in Ribosomal RNA Structures" Nucleic Acids Res, 37, e29 (2009) (pdf)
  • 71) Mohan, S, Hsiao, C, VanDeusen, H, Gallagher, R, Krohn, E, Kalahar, B, Wartell, R M, and Williams, LD "Mechanism of RNA Double Helix-Propagation at Atomic-Resolution" J Phys Chem B, 113, 2614-2623 (2009) (pdf)
  • 70) Hsiao, C, Tannenbaum, M, VanDeusen, H, Hershkovitz, E, Perng, G, Tannenbaum, A, and Williams, LD "Complexes of Nucleic Acids with Group I and II Cations" in Nucleic Acid Metal Ion Interactions (Hud, N, ed) The Royal Society of Chemistry: London, 1-35 (2008) (pdf)
  • 69) Richardson, JS, Schneider, B, Murray, LW, Kapral, GJ, Immormino, RM, Headd, JJ, Richardson, DC, Ham, D, Hershkovits, E, Williams, LD, Keating, KS, Pyle, AM, Micallef, D, Westbrook, J, and Berman, HM "RNA Backbone: Consensus All-angle Conformers and Modular String Nomenclature" RNA, 14, 1-17 (2008) (pdf)
  • 68) Watkins, D, Hsiao, C, Woods, KK, Koudelka, GB, and Williams, LD "P22 C2 Repressor-Operator Complex: Mechanisms of Direct and Indirect Readout" Biochemistry, 47, 2325-2338 (2008) (pdf)
  • 67) Gold, B, Marky, L M, Stone, MP and Williams, LD "A Review of the Role of the Sequence-Dependent Electrostatic Landscape in DNA Alkylation Patterns" Chem Res Toxicol, 19, 1402-1414 (2006) (pdf)
  • 66) Komeda, S, Moulaei, T, Woods, KK, Chikuma, M, Farrell, NP, and Williams, LD "A Third Mode of DNA Binding: Phosphate Clamps by a Polynuclear Platinum Complex" J Am Chem Soc 128, 16092-16103, (2006) (pdf)
  • 65) Hsiao, C, Mohan, S, Hershkovitz, E, Tannenbaum, A, and Williams, LD "Single Nucleotide RNA Choreography" Nucleic Acids Research 34, 1481-1491 (2006) (pdf)
  • 64) Hershkovitz, E, Sapiro, G, Tannenbaum, A and Williams, LD "Statistical Analysis of RNA Backbone" IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3, 33-46 (2006) (pdf)
  • 63) Williams, LD "Revised Periodic Table of the Elements" Skeptical Inquirer, 29, 68 (2005)
  • 62) Moulaei, T, Maehigashi, T, Lountos, G T, Komeda, S, Watkins, D, Stone, M P, Marky, LA, Li, J-S, Gold, B and Williams, LD "Structure of B-DNA with Cations Tethered in the Major Groove" Biochemistry, 44, 7458-7468, (2005) (pdf)
  • 61) Williams, LD "Between Objectivity and Whim: Nucleic Acid Structural Biology" in Topics in Current Chemistry, (Chaires, J B andamp; Waring, M, eds) 77-88 (2005) (pdf)
  • 60) Woods, KK, Maehigashi, T, Howerton, SB, Sines, CC, Tannenbaum, S and Williams, LD "High-Resolution Structure of an Extended A-Tract: [d(CGCAAATTTGCG)]2" J Am Chem Soc, 126, 15330-15331 (2004) (pdf)
  • 59) Hershkovitz, E, Tannenbaum, E, Howerton, SB, Sheth, A, Tannenbaum, A, and Williams, LD "Automated Identification of RNA Conformational Motifs: Theory and Application to the HM LSU 23S rRNA" Nucleic Acids Research 31, 6249-6257 (2003) (pdf)
  • 58) Razskazovskiy, Y, Debije, M G, Howerton, SB, Williams, LD and Bernhard, WA "Strand Breaks in X-Irradiated Crystalline DNA: Alternating CG Oligomers" Radiation Research, 160, 334-339 (2003) (pdf)
  • 57) Howerton, SB, Nagpal, A, and Williams, LD "Surprising Roles of Electrostatic Interactions in DNA-Ligand Complexes" Biopolymers, 69, 87-99 (2003) (pdf)
  • 56) Reynisson, J, Schuster, GB, Howerton, SB, Williams, LD, Barnett, RN, Cleveland, CL, Landman, U, Harrit, N and Chaires, JB "Intercalation of Trioxatriangulenium Ion in DNA: Binding, Electron Transfer, X-Ray Crystallography, and Electronic Structure" J Am Chem Soc, 125, 2072-2083 (2003) (pdf)
  • 55) Woods, KK, Lan, T, McLaughlin, LW and Williams, LD "The Role of Minor Groove Functional Groups in DNA Hydration" Nucleic Acids Research, 31, 1536-1540 (2003) (pdf)
  • 54) Hamelberg, D, Williams, LD and Wilson, WD "Effect of a Neutralized Phosphate Backbone on the Minor Groove of B-DNA: Molecular Dymanics Simulation Studies" Nucleic Acids Research, 30, 3615-3623 (2002) (pdf)
  • 53) Hamelberg, D, Williams, LD and Wilson, WD "Influence of the Dynamic Positions of Cations on the Structure of the DNA Minor Groove: Sequence-Dependent Effects" J Am Chem Soc, 123, 7745-7755 (2001) (pdf)
  • 52) Howerton, SB, Sines, CC, VanDerveer, D and Williams, LD "Locating Monovalent Cations in the Grooves of B-DNA" Biochemistry, 40, 10023-10031 (2001) (pdf)
  • 51) Peek, ME and Williams, LD "X-Ray Crystallography of DNA-Drug Complexes" Methods in Enzymology, 340, 282-290 (2001) (pdf)
  • 50) Sines, CC, McFail-Isom, L, Howerton, SB, VanDerveer, D and Williams, LD "Cations Mediate B-DNA Conformational Heterogeneity" J Am Chem Soc, 122, 11048-11056 (2000) (pdf)
  • 49) Hamelberg, D, McFail-Isom, L, Williams, LD and Wilson, WD "Flexible Structure of DNA: Ion Dependence of Minor-Groove Structure and Dynamics" J Am Chem Soc, 122, 10513-10520 (2000) (pdf)
  • 48) Williams, LD and Maher, LJ "Electrostatic Mechanisms of DNA Deformation" Annual Review of Biophysics and Biomolecular Structure, 29, 497-521 (2000) (pdf)
  • 47) Woods, KK, McFail-Isom, L, Sines, CC, Howerton, SB, Stephens, RK and Williams, LD "Monovalent Cations Sequester within the A-Tract Minor Groove of [d(CGCGAATTCGCG)]2" J Am Chem Soc, 122, 1546-1547 (2000) (pdf)
  • 46) Shui, X, Peek, ME, Lipscomb, LA, Gao, Q, Ogata, C, Roques, BP, Garbay-Jaureguiberry, C, Wilkinson, A P and Williams, LD " Effects of Cationic Charge on Three-Dimensional Structures of Intercalative Complexes: Structure of a bis-Intercalated DNA Complex Solved by MAD Phasing" Current Medicinal Chemistry, 7, 59-71 (2000) (pdf)
  • 45) McFail-Isom, L, Sines, CC and Williams, LD "DNA Structure: Cations in Control?" Current Opinion in Structural Biology, 9, 298-304 (1999) (pdf)
  • 44) Zhang, Y, Ghasemzadeh, S, Kotliar, AM, Kumar, S Presnell, S and Williams, LD "Fibers from Soybean Protein and Poly(vinyl alcohol)" Journal of Applied Polymer Science, 71, 11-19 (1999) (pdf)
  • 43) Gasper, S M, Armitage, B, Shui, X, Hu, GG, Yu, C, Schuster, GB and Williams, LD "Three-Dimensional Structure and Reactivity of a Photochemical Cleavage Agent Bound to DNA" J Am Chem Soc, 120, 12402-12409 (1998) (pdf)
  • 42) McFail-Isom, L, Shui, X and Williams, LD "Divalent Cations Stabilize Unstacked Conformations of DNA and RNA by Interacting with Base andPi; Systems" Biochemistry, 37, 17105-17111 (1998) (pdf)
  • 41) Shui, X, McFail-Isom, L, Sines, C, VanDerveer, D and Williams, LD "Structure of the Potassium Form of CGCGAATTCGCG: DNA Deformation by Electrostatic Collapse around Inorganic Cations" Biochemistry, 37, 16877-16887 (1998) (pdf)
  • 40) Shui, X, McFail-Isom, L, Hu, GG and Williams, LD "The B-DNA Dodecamer at High Resolution Reveals a Spine of Water on Sodium" Biochemistry, 37, 8541-8555 (1998) (pdf)
  • 39) Presnell, SR, Patil, GS, Mura, C, Jude, KM, Conley, JM, Bertrand, JA, Kam, C-M, Powers, JC and Williams, LD "Oxyanion-Mediated Inhibition of Serine Proteases" Biochemistry, 37, 17068-17081 (1998) (pdf)
  • 38) Milano, MT, Hu, GG, Williams, LD and Bernhard, WA "Migration of Electrons and Holes in Crystalline d(CGATCG)-anthracycline Complexes X-Irradiated at 4K" Radiation Research, 150, 101-114 (1998) (abstract)
  • 37) Davis, TM, McFail-Isom, L, Keane, E and Williams, LD "Melting of a DNA Hairpin without Hyperchromism" Biochemistry, 37, 6975-6978 (1998) (pdf)
  • 36) Breslin, DT, Coury, JE, Anderson, JR, McFail-Isom, L, Kan, Y, Williams, LD, Bottomley, LA and Schuster, GB "Anthraquinone Photonuclease Structure Determines Its Mode of Binding to DNA and the Cleavage Chemistry Observed" J Am Chem Soc, 119, 5043-5044 (1997) (pdf)
  • 35) Hu, GG, Shui, X, Leng, F, Preibe, W, Chaires, JB and Williams, LD "Structure of a DNA-Bisdaunmycin Complex" Biochemistry, accelerated publication, 36, 5940-5946 (1997) (pdf)
  • 34) Coury, JE, Anderson, JR, McFail-Isom, L, Williams, LD and Bottomley, LA "Scanning Force Microscopy of Small Ligand-Nucleic Acid Complexes: Tris(o-phenanthroline)ruthenium(II) as a Test for a New Assay" J Am Chem Soc, 119, 3792-3796, (1997) (pdf)
  • 33) Coury, JE, McFail-Isom, L, Williams, LD and Bottomley, LA "A Novel Assay for Drug-DNA Binding Mode, Affinity, and Exclusion Number: Scanning Force Microscopy" Proceedings of the National Academy of Sciences, USA, 93, 12283-12286 (1996) (pdf)
  • 32) Gao, Q, Sood, A, Shaw, BR and Williams, LD "2'-Deoxycytidine-N3-cyanoborane" Acta Cryst, C52, 1823-1825 (1996) (pdf)
  • 31) Lipscomb, LA, Zhou, F X, Presnell, SR, Woo, RJ, Peek, ME, Plaskon, RR and Williams, LD "Structure of a DNA-Porphyrin Complex" Biochemistry, accelerated publication, 35, 2818-2823 (1996) (pdf)
  • 30) Lipscomb, LA, Zhou, FX and Williams, LD "Clathrate Hydrates are Poor Models for Biomolecule Hydration" Bioploymers, 38, 177-181 (1996) (pdf)
  • 29) Bertrand, JA, Oleksyszyn, J, Kam, C-M, Boduszek, B, Presnell, S, Plaskon, RR, Suddath, FL, Powers, JC and Williams, LD "Inhibition of Trypsin and Thrombin by Amino(4-amidinophenyl)methanephosphonate Diphenyl Ester Derivatives: X-ray Structures and Molecular Models" Biochemistry, 35, 3147-3155 (1996) (pdf)
  • 28) Coury, JE, McFail-Isom, L, Presnell, S, Williams, LD and Bottomley, LA "Scanning Probe Visualization of Electrostatically Immobilized Intercalating Drug-Nucleic Acid Complexes" J Vac Sci and Technol, 13, 1746-1751 (1995) (pdf)
  • 27) Lipscomb, LA, Peek, ME, Morningstar, ML, Verghis, SM, Miller, EM, Rich, A, Essigmann, JM and Williams, LD "X-ray Structure of a DNA Decamer Containing 7,8-Dihydro-8-oxoguanine" Proceedings of the National Academy of Sciences, USA, 92, 719-723 (1995) (pdf)
  • 26) Peek, ME, Lipscomb, LA, Haseltine, J, Gao, Q, Roques, BP, Garbay-Jaureguiberry, C and Williams, LD "Asymmetry and Dynamics in Bis-Intercalated DNA" J Bioorg and Med Chem, 3, 693-699 (1995) (pdf)
  • 25) Lipscomb, LA, Peek, ME, Zhou, F X, Bertrand, J A, VanDerveer, D and Williams, LD "Water Ring Structure at DNA Interfaces: Hydration and Dynamics of DNA-Anthracycline Complexes" Biochemistry, 33, 3649-3659 (1994) (pdf)
  • 24) Peek, ME, Lipscomb, LA, Bertrand, JA, Gao, Q, Roques, BP, Garbay-Jaureguiberry, C and Williams, LD "DNA Distortion in bis-Intercalated Complexes" Biochemistry, accelerated publication, 33, 3794-3800 (1994) (pdf)
  • 23) Bancroft, D, Williams, LD, Rich, A and Egli, M "The Low-Temperature Crystal Structure of the Pure-Spermine Forms of Z-DNA Reveals Binding of a Spermine Molecule in the Minor Groove" Biochemistry, 33, 1073-1086 (1994) (pdf)
  • 22) MacPhail, RA, Williams, LD, Jones, DA and Shaw, BR "Variable Temperature Infrared Spectroscopy of Cytosine-Guanine Base Pairs: Tautomerism versus Polarization" J Biomol Struct Dynam, 9, 881-898 (1992)
  • 21) Williams, LD and Gao, Q "DNA-Ditercalinium Interactions: Implications for Recognition of Damaged DNA" Biochemistry, 31, 4315-4324 (1992) (pdf)
  • 20) Williams, LD and Rich, A "Understanding DNA Interactions and Deformations from 3-Dimensional Structures" in Molecular Structure and Life, (Kyogoku, Y andamp; Nishimura, N, eds) 3-27 (1992)
  • 19) Williams, LD, Egli, M, Gao, Q and Rich, A "DNA Intercalation: Helix Unwinding and Neighbor Exclusion" in Structure andamp; Function, Volume I: Nucleic Acids, (Sarma, R H andamp; Sarma, M H, eds) 107-125 (1992) (pdf)
  • 18) Williams, LD, Frederick, CA, Gessner, RV and Rich, A "Molecular Structures of Spermine: Nucleic Acid Complexes" in Molecular Conformation and Biological Interactions, (Balaram, P and Ramaseshan, S, eds) 295-309 (1991)
  • 17) Gao, Q, Williams, LD, Egli, M, Rabinovich, D, Chen, S-H, Quigley, GJ and Rich, A "Drug-Induced DNA Repair: X-Ray Structure of a DNA-Ditercalinium Complex" Proc Nat Acad Sci, USA, 88, 2422-2426 (1991) (pdf)
  • 16) Egli, M, Williams, LD, Frederick, CA and Rich, A "DNA-Nogalamycin Interactions" Biochemistry, 30, 1364-1372 (1991) (pdf)
  • 15) Egli, M, Williams, LD, Gao, Q and Rich, A "Structure of the Pure-Spermine Form of Z-DNA (Magnesium Free) at 1-andAring Resolution" Biochemistry, 30, 11388-11402 (1991) (pdf)
  • 14) Feuerstein, BG, Williams, LD, Basu, HS and Marton, LJ "Implications and Concepts of Polyamine-Nucleic Acid Interactions" J Cell Biochemistry, 46, 37-47 (1991) (pdf)
  • 13) Frederick, CA, Williams, LD, Ughetto, G, van der Marel, GA, van Boom, JH, Rich, A and Wang, AH-J "Structural Comparison of Anticancer Drug-DNA Complexes: Adriamycin and Daunomycin" Biochemistry, 29, 2538-2549 (1990) (pdf)
  • 12) Egli, M, Gessner, RV, Williams, LD, Quigley, GJ, van der Marel, GA, van Boom, JH, Rich, A and Frederick, CA "Atomic-Resolution Structure of the Cellulose Synthase Regulator Cyclic Diguanylic Acid" Proceedings of the National Academy of Sciences, USA, 87, 3235-3239 (1990) (pdf)
  • 11) Williams, LD, Egli, M, Ughetto, G, van der Marel, GA, van Boom, JH, Quigley, GJ, Wang, AH-J, Rich, A and Frederick, CA "Structure of 11-Deoxydaunomycin Bound to DNA Containing a Phosphorothioate" J Mol Biol, 215, 313-320 (1990)
  • 10) Williams, LD, Frederick, CA, Ughetto, G and Rich, A "Ternary Interactions of Spermine with DNA:4'-Epiadriamycin and other DNA:Anthracycline Complexes" Nucleic Acids Res, 18, 5533-5541 (1990) (pdf)
  • 9) Williams, LD, Williams, N G and Shaw, BR "In a Model C:G Base Pair, One Amino Group Rotates and the Other Does Not" J Am Chem Soc, 112, 829-833 (1990) (pdf)
  • 8) McCarthy, JG, Williams, LD and Rich, A "Chemical Reactivity of Potassium Permangenate and Diethyl Pyrocarbonate with B DNA: Specific Reactivity with Short A-Tracts" Biochemistry, 29, 6071-6081 (1990) (pdf)
  • 7) Williams, LD, Egli, M, Gao, Q, Bash, P, van der Marel, G A, van Boom, J H, Rich, A and Frederick, CA "Structure of Nogalamycin Bound to a DNA Hexamer" Proc Nat Acad Sci, USA, 87, 2225-2229 (1990) (pdf)
  • 6) Williams, NG, Williams, LD and Shaw, BR "Dimers, Trimers and Tetramers of Cytosine with Guanine" J Am Chem Soc, 111, 7205-7209 (1989) (pdf)
  • 5) Williams, LD and Goldberg, IH "Selective Strand Scission by Intercalating Drugs at DNA Bulges" Biochemistry, 27, 3004-3011 (1988) (pdf)
  • 4) Williams, LD, Thivierge, J and Goldberg, IH "Specific Binding of o-Phenanthroline at a DNA Structural Lesion" Nucleic Acids Research, 16, 11607-11615 (1988) (pdf)
  • 3) Williams, LD, Chawla, B and Shaw, BR "The Hydrogen Bonding of Cytosine with Guanine: Calorimetric and 1H-NMR Analysis of the Molecular Interactions of Nucleic Acid Bases" Biopolymers, 26, 591-603 (1987) (pdf)
  • 2) Williams, LD and Shaw, BR "Protonated Base Pairs Explain the Ambiguous Pairing Properties of O6-Methylguanine" Proceedings of the National Academy of Sciences, USA, 84, 1779-1783 (1987) (pdf)
  • 1) Aartsma, T, Gouterman, M, Jochum, C, Kwiram, A L, Pepich, B V and Williams, LD "Porphyrins 43 Triplet Sublevel Emission of Platinum Tetrabenzoporphyrin by Spectrothermal Principal Component Decomposition" J Am Chem Soc, 104, 6278-6283 (1982) (pdf)