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Publications of Loren Williams
  • 150. Müller, U.F., Elsila, J., Trail, D., DasGupta, S., Giese, C.-C., Walton, C.R., Cohen, Z.R., Stolar, T., Krishnamurthy, R., Lyons, T.W., Rogers, K.L., and Williams, L.D. "Frontiers in Prebiotic Chemistry and Early Earth Environments", Orig. Life Evol. Biosph. pp 1-17 (2022) (pdf)
  • 149. Martin, C., 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., and Liotta, C.L. "Water-Based Dynamic Depsipeptide Chemistry: Building Block Recycling and Oligomer Distribution Control Using Hydration–Dehydration Cycles", JACS Au 2, pp 1395 (2022) (pdf)
  • 148. Frenkel-Pinter, M., Bouza, M., Fernández, F.M., Leman, L.J., Williams, L.D., Hud, N.V., and Guzman-Martinez, A. "Thioesters Provide a Plausible Prebiotic Path to Proto-Peptides", Nature Communications 13, pp 1-8 (2022) (pdf).
  • 147. Frenkel-Pinter, M., Jacobson., K.C., Eskew-Martin, J., Forsythe, J.G., Grover, M.A., Williams, L.D., and Hud, N.V. "Differential Oligomerization of Alpha Versus Beta Amino Acids and Hydroxy Acids in Abiotic Proto-Peptide Synthesis Reactions", Life 12, pp 265-280 (2022) (pdf).
  • 146. Frenkel-Pinter, M, Petrov, A.S., Matange, K, Travisano, M., Glass, J.B., and Williams, L.D. "Adaptation and Exaptation: From Small Molecules to Feathers", J. Mol. Evol. pp 1-10 (2022) (pdf).
  • 145. Penev, P. I., Alvarez-Carreño, C., Smith, E., Petrov, A. S., and Williams, L. D. "TwinCons: Conservation Score for Uncovering Deep Sequence Similarity and Divergence", PLoS Computational Biology 17, e1009541 (2021) (pdf).
  • 144. Alvarez-Carreño, C., Penev, P. I., Petrov, A. S., and Williams, L. D. "Fold Evolution Before LUCA: Common Ancestry of SH3 Domains and OB Domains", Molecular Biology and Evolution 38, pp 5134-5143 (2021) (pdf).
  • 143. Sweeney, B.A., Hoksza, D., Nawrocki, E.P., Ribas, C.E., Madeira, F., Cannone, J.J., Gutell, R., Maddala, A., Meade, C.D., Williams, L.D., Petrov, A.S., Chan, P.P., Lowe, T.M., Finn, R.D., and Petrov, A.I. "R2DT Is a Framework for Predicting and Visualising RNA Secondary Structure Using Templates", Nature Communications 12, pp 1-12 (2021) (pdf).
  • 142. Goldman, A., Fournier, G., Gogarten, J.P., Petrov, A.S., Rothschild, L., Segrè, D., Smith, E., and Williams, L.D. "Understanding the Early Major Transitions in Evolutionary History Part 1: Stages in the Emergence of Complex Life", Bulletin of the American Astronomical Society 53, pp 247 (2021) (pdf).
  • 141. Fournier, G., Gogarten, J.P., Goldman, A.D., Petrov, A.S., Rothschild, L., Segrè, D., Smith, E., and Williams, L.D., "Understanding the Early Major Transitions in Evolutionary History Part 2: Ancient Evolution of Biological Systems and the Biosphere", Bulletin of the American Astronomical Society 53, pp 253 (2021) (pdf).
  • 140. Penev, P.I., McCann, H.M., Meade, C.D., Maddala, A., Bernier, C.R., Chivukula, V.L., Ahmad, M., Gulen, B., Sharma, A., Alvarez-Carreño, C., Williams, L.D., Petrov A.S. “ProteoVision: Web Server for Advanced Visualization of Ribosomal Proteins”, Nucleic Acids Research (2021) (pdf).
  • 139. Frenkel-Pinter, M., Sargon, A.B., Glass, J.B., Hud, N.V., and Williams, L.D. "Transition Metals Enhance Prebiotic Depsipeptide Oligomerization Reactions Involving Histidine", Royal Society of Chemistry Advances 11, pp 3534-3538 (2021) (pdf).
  • 138. Frenkel-Pinter, M., Rajaei, V., Glass, J.B., Hud, N.V., and Williams, L.D. "Water and Life: the Medium Is the Message", Journal of Molecular Evolution 89, pp 2–11 (2021) (pdf).
  • 137. Mestre-Fos, S., Moore, C.M., Reddi, A.R., and Williams, L.D. "Human Ribosomal G-quadruplexes Regulate Heme Bioavailability", Journal of Biological Chemistry 295, pp 14855–14865 (2020) (pdf).
  • 136. Penev, P.I., Fakhretaha-Aval, S., Patel, V.J., Cannone, J.J., Petrov, A.S., Williams, L.D., and Glass, J.B. "Supersized Ribosomal RNA Expansion Segments in Asgard Archaea", Genome Biology and Evolution 12, pp 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, L.D., and Lieberman, R. "A Blueprint for Academic Labs to Produce SARS-CoV-2 RT-qPCR Test Kits", Journal of Biological Chemistry 295, pp 15438-15453 (2020) (pdf).
  • 134. Guth-Metzler, R., Bray, M.S., Suttapitugsakul, S., Montllor-Albalate, C., Bowman, J.C., Wu, R., Reddi, A.R., Okafor, C.D., Glass, J.B., and Williams, L.D. "Cutting in-Line with Iron: Ribosomal Function and Non-Oxidative RNA Cleavage", Nucleic Acids Research 48, pp 8663–8674 (2020) (pdf).
  • 133. Frenkel-Pinter, M., Haynes, J.W., Mohyeldin, A.M., Martin, C., Sargon, A.B., Petrov, A.S., Krishnamurthy, R., Hud, N.V., Williams, L.D., and Leman, L.J. "Mutually Stabilizing Interactions between Proto-Peptides and RNA", Nature Communications 11, pp 1-14 (2020) (pdf).
  • 132. Bowman, J.C., Petrov, A.S., Frenkel-Pinter, M., Penev, P.I., and Williams, L.D. "Root of the Tree: The Significance, Evolution, and Origins of the Ribosome", Chemical Reviews 120, pp 4848-4878 (2020) (pdf).
  • 131. Ghosh, A., Williams, L.D., Pestov, D.G., and Shcherbik, N. "Proteotoxic Stress Promotes Entrapment of Ribosomes and Misfolded Proteins in a Shared Cytosolic Compartment", Nucleic Acids Research 48, pp 3888-3905 (2020) (pdf).
  • 130. Mestre-Fos S., Penev P.I., Richards J.C., Dean W.L., Gray R.D., Chaires J.B., and Williams, L.D. "Profusion of G-quadruplexes on both subunits of metazoan ribosomes", PLoS One 14, e0226177 (2019) (pdf).
  • 129. Frenkel-Pinter, M., Haynes, J.W., C, M., Petrov, A.S., Burcar, B.T., Krishnamurthy, R., Hud, N.V., Leman, L.J. and Williams, L.D. "Selective Incorporation of Proteinaceous over Nonproteinaceous Cationic Amino Acids in Model Prebiotic Oligomerization Reactions." Proceedings of the National Academy of Sciences, USA 116, pp 16338-16346 (2019) (pdf).
  • 128. Mestre-Fos, S., Penev, P.I., Suttapitugsakul, S., Ito, C., Petrov, A.S., Wartell, R.M., Wu, R., and Williams, L.D. "G-quadruplexes in Human Ribosomal RNA", Journal of Molecular Biology. 431, pp 1940-1955 (2019) (pdf).
  • 127. Bowman, J.C., Petrov, A.S., and Williams, L.D. "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, K.A., WIlliams, J.K., Bowman, J.C., Petrov, A.S., Hud, N.V., and Williams, L.D. "Folding, Assembly, and Persistence: The Essential Nature and Origins of Biopolymers", Journal of Molecular Evolution 86, pp 598–610 (2018) doi.org/10.1007/s00239-018-9876-2 (pdf).
  • 125. Bray, M.S., Lenz, T.K., Haynes, J.W., Bowman, J.C., Petrov, A.S., Reddi, A.R., Hud, N.V., Williams, L.D., and Glass, J.B. "Multiple Prebiotic Metals Mediate Translation", Proceedings of the National Academy of Sciences, USA 115, pp 12164-12169 (2018) doi.org/10.1073/pnas.1803636115 (pdf).
  • 124. Kovacs, N.A., Penev, P.I., Venapally, A., Petrov, A.S., and Williams, L.D. "Circular Permutation Obscures Universality of a Ribosomal Protein", Journal of Molecular Evolution pp 1-12 (2018) doi.org/10.1007/s00239-018-9869-1 (pdf).
  • 123. Okafor, C.D., Bowman, J.C., Hud, N.V., Glass, J.B., and Williams, L.D. "Folding and Catalysis near Life’s Origin: Support for Fe2+ as a Dominant Divalent Cation, in Prebiotic Chemistry and Chemical Evolution of Nucleic Acids" (Cesar Menor-Salván, ed.), [Review] pp 227-243, (2018) Springer International Publishing AG (pdf).
  • 122. Fang, P.-Y., Bowman, J.C., Gómez Ramos, L., Hsiao, C., and Williams, L.D. "RNA: Packaged and Protected by VLPs", Royal Society of Chemistry Advances 8, pp 21399-21406 (2018) doi.org/10.1039/c8ra02084a (pdf).
  • 121. Bernier, C.R., Petrov, A.S., Kovacs, N.A., Penev, P.I., and Williams, L.D. "Translation: The Universal Structural Core of Life", Mol. Biol. Evol. 34, pp 2065–2076 (2018) doi.org/10.1093/molbev/msy101 (pdf).
  • 120. Lenz, T.K., Norris, A.M., Hud, N.V., and Williams, L.D. "Protein-Free Ribosomal RNA Folds to a near-Native State in the Presence of Mg2+", Royal Society of Chemistry Advances 7, pp 54674-54681, (2017) doi.org/10.1039/c1037ra08696b (pdf).
  • 119. Gomez Ramos, L.M., Degtyareva, N.N., Kovacs, N.A., Holguin, S.Y., Jiang, L., Petrov, A.S., Biesiada, M., Hu, M.Y., Purzycka, K.J., Arya, D.P., and Williams, L.D. "Eukaryotic Ribosomal Expansion Segments as Antimicrobial Targets", Biochemistry 56, pp 5288-5299 (2017) 10.1021/acs.biochem.7b00703 (pdf).
  • 118. Lanier, K.A., Petrov, A.S., and Williams, L.D. "The Central Symbiosis of Molecular Biology", J. Mol. Evol. 85, pp 8-13 (2017) doi.org/10.1007/s00239-017-9804-x (pdf).
  • 117. Lanier, K.A., Roy, P., Schneider, D.M., and Williams, L.D. "Ancestral Interactions of Ribosomal RNA and Ribosomal Proteins", Biophys. J. 13, pp 268-276 (2017) (pdf).
  • 116. Okafor, C.D., Lanier, K.A., Petrov, A.S., Athavale, S.S., Bowman, J.C., Hud, N.V., and Williams, L.D. "Iron Mediates Catalysis of Nucleic Acid Processing Enzymes: Support for Fe(II) as a Cofactor before the Great Oxidation Event", Nucleic Acids Research 45, pp 3634-3642 (2017) (pdf).
  • 115. Kovacs, N.A., Petrov, A.S., Lanier, K.A., and Williams, L.D. "Frozen in Time: The History of Proteins", Mol. Biol. Evol. 34, pp 1252-1260 (2017) (pdf).
  • 114. Lanier, K.A., and Williams, L.D. "The Origin of Life: Models and Data", J. Mol. Evol. 84, pp 85-92 (2017) (pdf).
  • 113. Jones, B.L., Walker, C.L., Azizi, B., Tolbert, L., Williams, L.D., and Snell, T.W. "Conservation of Estrogen Receptor Function in Invertebrate Reproduction", BMC Evolutionary Biology 17, pp 65-75 (2017) (pdf).
  • 112. Fang, P.-Y., Gomez Ramos, L.M., Holguin, Y.S., Hsiao, C., Bowman, J.C., Yang, H.-W., and Williams, L.D. "Functional RNAs: Combined Assembly and Packaging in VLPs", Nucleic Acids Research, (2016) 10.1093/nar/gkw1154 (pdf).
  • 111. Gomez Ramos, L.M., Smeekens, J.M., Kovacs, N.A., Bowman, J.C., Wartell, R.M., Wu, R., and Williams, L.D. "Yeast rRNA Expansion Segments: Folding and Function", J. Mol. Biol. 428, pp 4048-4059 (2016) (pdf).
  • 110. Lanier, K.A., Athavale, S.S., Petrov, A.S., Wartell, R., and Williams, L.D. "Imprint of Ancient Evolution on rRNA Folding", Biochemistry 55, pp 4603-4613 (2016) (pdf).
  • 109. Komeda, S., Qu, Y., Mangrum, J.B., Hegmans, A., Williams, L.D., and Farrell, N.P. "The Phosphate Clamp as Recognition Motif in Platinum-DNA Interactions", Inorg. Chim. Acta 452, pp 25-33 (2016) (pdf).
  • 108. Gulen, B., Petrov, A.S., Okafor, C.D., Vander Wood, D., O'Neill, E.B., Hud, N.V., and Williams, L.D. "Ribosomal Small Subunit Domains Radiate from a Central Core", Scientific Reports 6, pp 20885 (2016) (pdf).
  • 107. Petrov, A.S., Gulen, B., Norris, A.M., Kovacs, N.A., Bernier, C.R., Lanier, K.A., Fox, G.E., Harvey, S.C., Wartell, R.M., Hud, N.V., and Williams, L.D. "History of the Ribosome and the Origin of Translation", Proceedings of the National Academy of Sciences, USA 112, pp 15396-15401 (2015) (pdf).
  • 106. Petrov, A.S., and Williams, L.D. "The Ancient Heart of the Ribosomal Large Subunit: A Response to Caetano-Anolles", J. Mol. Evol. 80 pp 166-170 (2015) (pdf).
  • 105. Bowman, J.C., Hud, N.V., and Williams, L.D. "The Ribosome Challenge to the RNA World", J. Mol. Evol. 80, pp 143-161 (2015) (pdf).
  • 104. Ma, Z., Chen, W., Johnson, M., Schmidt-Krey, I., Williams, L.D., and Schuster, G.B. "Modular-DNA Programmed Molecular Construction of "Fixed" 2D and 3D-Au Nanoparticle Arrays", Chem. Mater. 26, pp 5499-5505 (2015) (pdf).
  • 103. Petrov, A.S., Bernier, C.R., Gulen, B., Waterbury, C.C., Hershkovitz, E., Hsiao, C., Harvey, S.C., Hud, N.V., Fox, G.E., Wartell, R.M., and Williams, L.D. "Secondary Structures of rRNAs from All Three Domains of Life", PLoS One 9, pp e88222 (2014) (pdf).
  • 102. Petrov, A.S., Bernier, C.R., Hsiao, C., Norris, A.M., Kovacs, N.A., Waterbury, C.C., Stepanov, V.G., Harvey, S.C., Fox, G.E., Wartell, R.M., Hud, N.V., and Williams, L.D. "Evolution of the Ribosome at Atomic Resolution", Proceedings of the National Academy of Sciences, USA 111, pp 10251-10256 (2014) (pdf).
  • 101. Harris, L.A., Williams, L.D., and Koudelka, G.B. "Specific Minor Groove Solvation Is a Crucial Determinant of DNA Binding Site Recognition", Nucleic Acids Research 42, pp 14053-14059 (2014) (pdf)
  • 100. Bernier, C., Petrov, A.S., Waterbury, C., Jett, J., Li, F., Freil, L.E., Xiong, b., Wang, L., Le, A., Milhouse, B.L., Hershkovitz, E., Grover, M., Xue, Y., Hsiao, C., Bowman, J.C., Harvey, S.C., Wartel, J.Z., and Williams, L.D. "Ribovision: Visualization and Analysis of Ribosomes", Faraday Discuss. 169, pp 1-12 (2014) (pdf).
  • 99. Jones, B.L., VanLoozen, J., Kim, M.H., Miles, S.J., Dunham, C.M., Williams, L.D., and Snell, T.W. "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, pp 375-384 (2013) (pdf).
  • 98. Petrov, A.S., Bernier, C.R., Hershkovitz, E., Xue, Y., Waterbury, C.C., Grover, M.A., C., H.S., Hud, N.V., Wartell, R.M., and Williams, L.D. "Secondary Structure and Domain Architecture of the 23S rRNA", Nucleic Acids Research 41, pp 7522-7535 (2013) (pdf).
  • 97. Hsiao, C., Chou, I.-C., Okafor, C.D., Bowman, J.C., O'Neill, E.B., Athavale, S.S., Petrov, A.S., Hud, N.V., Wartell, R.M., Harvey, S.C., and Williams, L.D. "Iron(II) Plus RNA Can Catalyze Electron Transfer", Nature Chemistry 5, pp 525-528 (2013) (pdf).
  • 96. Hud, N.V., Cafferty, B.J., Krishnamurthy, R., and Williams, L.D. "The Origin of RNA and "My Grandfather's Axe"", Chem. Biol. 20, pp 466-474 (2013) (pdf).
  • 95. Hsiao, C., Lenz, T.K., Peters, J.K., Fang, P.Y., Schneider, D.M., Anderson, E.J., Preeprem, T., Bowman, J.C., O'Neill, E.B., Lie, L., Athavale, S.S., Gossett, J.J., Trippe, C., Murray, J., Petrov, A.S., Wartell, R.M., Harvey, S.C., Hud, N.V., and Williams, L.D. "Molecular Paleontology: A Biochemical Model of the Ancestral Ribosome", Nucleic Acids Research 41, pp 3373-3385 (2013) (pdf).
  • 94. Athavale, S.S., Gossett, J.J., Bowman, J.C., Hud, N.V., Williams, L.D., and Harvey, S.C. "In Vitro Secondary Structure of the Genomic RNA of Satellite Tobacco Mosaic Virus", PLoS One 8, pp e54384 (2013) (pdf).
  • 93. Harris, L.A., Watkins, D., Williams, L.D., and Koudelka, G.B. "Indirect Readout of DNA Sequence by P22 Repressor: Roles of DNA and Protein Functional Groups in Modulating DNA Conformation", J. Mol. Biol. 425, pp 133-143 (2013) (pdf).
  • 92. Williams, L.D. "Yin and Yang: Polypeptide and Polynucleotide", Origins of LIfe Community Page (2012) (pdf).
  • 91. Peters, J.W., and Williams, L.D. "The Origin of Life: Look up and Look Down", Astrobiology 12, pp 1087-1092 (2012) (pdf).
  • 90. Bowman, J.C., Azizi, B., Lenz, T.K., Roy, P., and Williams, L.D. 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.), pp 19-41, Springer Science, LLC (2012) (pdf).
  • 89. Petrov, A.S., Bernier, C.R., Hsiao, C.L., Okafor, C.D., Tannenbaum, E., Stern, J., Gaucher, E., Schneider, D., Hud, N.V., Harvey, S.C., and Williams, L.D. "RNA-Magnesium-Protein Interactions in Large Ribosomal Subunit", J. Phys. Chem. B 116, pp 8113-8120 (2012) (pdf).
  • 88. Bowman, J.C., Lenz, T.K., Hud, N.V., and Williams, L.D. "Cations in Charge: Magnesium Ions in RNA Folding and Catalysis ", Current Opinion in Structural Biology 22, pp 262-272 (2012) (pdf).
  • 87. Engelhart, A.E., Cafferty, B.J., Okafor, C.D., Chen, M.C., Williams, L.D., Lynn, D.G., and Hud, N.V. "Nonenzymatic Ligation of DNA with a Reversible Step and a Final Linkage That Can Be Used in PCR", ChemBioChem 13, pp 1121-1124 (2012) (pdf).
  • 86. Athavale, S.S., Petrov, A.S., Hsiao, C., Watkins, D., Prickett, C.D., Gossett, J.J., Lie, L., Bowman, J.C., O'Neill, E., Bernier, C.R., Hud, N.V., Wartell, R.M., Harvey, S.C., and Williams, L.D. "RNA Folding and Catalysis Mediated by Iron (II)", PLoS ONE 7, pp e38024 (2012) (pdf).
  • 85. Athavale, S.S., Gossett, J.J., Hsiao, C., Bowman, J.C., O'Neill, E., Hershkovitz, E., Preeprem, T., Hud, N.V., Wartell, R.M., Harvey, S.C., and Williams, L.D. "Domain III of the T. thermophilus 23S rRNA Folds Independently to a near-Native State", RNA 18, pp 752-758 (2012) (pdf).
  • 84. Maehigashi, T., Hsiao, C., Kruger Woods, K., Moulaei, T., Hud, N.V., and Williams, L.D. "B-DNA Structure Is Intrinsically Polymorphic: Even at the Level of Base Pair Positions", Nucleic Acids Research 8, pp 3714-3722. (2012) (pdf).
  • 83. Bowman, J.C., and Williams, L.D. 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, L.D. "Protein: Feeling the Groove of DNA", in Frontiers in Nucleic Acids (Sheardy, R. D., and Winkle, S. A., Eds.), pp 133-145, American Chemical Society (2011) (pdf).
  • 81. Buckley, R., Enekwa, C.D., Williams, L.D., and Hud, N.V. "Molecular Recognition of Watson-Crick-Like Purine-Purine Base Pairs", ChemBioChem 12, pp 2155-2158 (2011) (pdf).
  • 80. Petrov, A.S., Bowman, J.C., Harvey, S.C., and Williams, L.D. "Bidentate RNA-Magnesium Clamps: On the Origin of the Special Role of Magnesium in RNA Folding", RNA, 17, pp 291-297 (2011) (pdf).
  • 79. Schneider, D.M., and Williams, L.D. "You Can't Change That: Arsenic, Phosphorus and Life", J. Cosmology 13, pp 3627-3630 (2010) (commentary).
  • 78. Komeda, S., Moulaei, T., Chikuma, M., Odani, A., Kipping, R., Farrell, N.P., and Williams, L.D. "The Phosphate Clamp: A Small and Independent Motif for Nucleic Acid Backbone Recognition" Nucleic Acids Research, 24, pp 1-12 (2010) (pdf).
  • 77. Mohan, S., Hsiao, C., Bowman, J.C., Wartell, R., and Williams, L.D. "RNA Tetraloop Folding Reveals Tension between Backbone Restraints and Molecular Interactions. J. Am. Chem. Soc., 132, pp 12679-12689 (2010) (pdf).
  • 76. Watkins, D., Mohan, S., Koudelka, G. B. and Williams, L. D. "Sequence Recognition of DNA by Protein-Induced Conformational Transitions", J. Mol. Biol., 396, pp 1145-1164 (2010) (pdf).
  • 75. Watkins, D., Moulaei, T., Komeda, S., and Williams, L. D. "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, B. K., and Williams, L. D. "Peeling the Onion: Ribosomes are Ancient Molecular Fossils", Mol. Bio. Evol., 26, pp 2415-2425 (2009) (pdf).
  • 73. Hsiao, C. and Williams, L.D. "A Recurrent Magnesium-Binding Motif Provides a Framework for the Ribosomal Peptidyl Transferase Center", Nucleic Acids Research, 37, pp 3134-3142 (2009) (pdf).
  • 72. Apostolico, A., Ciriello, G., Guerra, C., Heitsch, C. E., Hsiao, C., and Williams, L. D. "Finding 3D Motifs in Ribosomal RNA Structures", Nucleic Acids Research, 37, pp e29 (2009) (pdf).
  • 71. Mohan, S., Hsiao, C., VanDeusen, H., Gallagher, R., Krohn, E., Kalahar, B., Wartell, R. M., and Williams, L. D. "Mechanism of RNA Double Helix-Propagation at Atomic-Resolution", J. Phys. Chem. B, 113, pp 2614-2623 (2009) (pdf).
  • 70. Hsiao, C., Tannenbaum, M., VanDeusen, H., Hershkovitz, E., Perng, G., Tannenbaum, A., and Williams, L. D. "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, pp 1-35 (2008) (pdf).
  • 69. Richardson, J. S., Schneider, B., Murray, L. W., Kapral, G. J., Immormino, R. M., Headd, J. J., Richardson, D. C., Ham, D., Hershkovits, E., Williams, L. D., Keating, K. S., Pyle, A. M., Micallef, D., Westbrook, J., and Berman, H. M. "RNA Backbone: Consensus All-angle Conformers and Modular String Nomenclature", RNA, 14, 1-17 (2008) (pdf).
  • 68. Watkins, D., Hsiao, C., Woods, K. K., Koudelka, G. B., and Williams, L. D. "P22 c2 Repressor-Operator Complex: Mechanisms of Direct and Indirect Readout", Biochemistry, 47, 2325-2338 (2008) (pdf).
  • 67. Gold, B., Marky, L. M., Stone, M. P. and Williams, L. D. "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, K. K., Chikuma, M., Farrell, N. P., and Williams, L. D. "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, L. D. "Single Nucleotide RNA Choreography", Nucleic Acids Research 34, 1481-1491 (2006) (pdf).
  • 64. Hershkovitz, E., Sapiro, G., Tannenbaum, A. and Williams, L. D. "Statistical Analysis of RNA Backbone", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3, 33-46 (2006) (pdf).
  • 63. Williams, L. D. "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, L. A., Li, J.-S., Gold, B. and Williams, L. D. "Structure of B-DNA with Cations Tethered in the Major Groove", Biochemistry, 44, 7458-7468, (2005) (pdf).
  • 61. Williams, L. D. "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, K. K., Maehigashi, T., Howerton, S. B., Sines, C. C., Tannenbaum, S. and Williams, L. D. "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, S. B., Sheth, A., Tannenbaum, A., and Williams, L. D. "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, S. B., Williams, L. D. and Bernhard, W. A. "Strand Breaks in X-Irradiated Crystalline DNA: Alternating CG Oligomers", Radiation Research, 160, 334-339 (2003) (pdf).
  • 57. Howerton, S. B., Nagpal, A., and Williams, L. D. "Surprising Roles of Electrostatic Interactions in DNA-Ligand Complexes", Biopolymers, 69, 87-99 (2003) (pdf).
  • 56. Reynisson, J., Schuster, G. B., Howerton, S.B., Williams, L. D., Barnett, R. N., Cleveland, C. L., Landman, U., Harrit, N. and Chaires, J. B. "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, K. K., Lan, T., McLaughlin, L. W. and Williams, L. D. "The Role of Minor Groove Functional Groups in DNA Hydration", Nucleic Acids Research, 31, 1536-1540 (2003) (pdf).
  • 54. Hamelberg, D., Williams, L. D. and Wilson, W. D. "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, L. D. and Wilson, W. D. "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, S. B., Sines, C. C., VanDerveer, D. and Williams, L. D. "Locating Monovalent Cations in the Grooves of B-DNA", Biochemistry, 40, 10023-10031 (2001) (pdf).
  • 51. Peek, M. E. and Williams, L. D. "X-Ray Crystallography of DNA-Drug Complexes", Methods in Enzymology, 340, 282-290 (2001) (pdf).
  • 50. Sines, C. C., McFail-Isom, L., Howerton, S. B., VanDerveer, D. and Williams, L. D. "Cations Mediate B-DNA Conformational Heterogeneity", J. Am. Chem. Soc., 122, 11048-11056 (2000) (pdf).
  • 49. Hamelberg, D., McFail-Isom, L., Williams, L. D. and Wilson, W. D. "Flexible Structure of DNA: Ion Dependence of Minor-Groove Structure and Dynamics", J. Am. Chem. Soc., 122, 10513-10520 (2000) (pdf).
  • 48. Williams, L. D. and Maher, L. J. "Electrostatic Mechanisms of DNA Deformation", Annual Review of Biophysics and Biomolecular Structure, 29, 497-521 (2000) (pdf).
  • 47. Woods, K. K., McFail-Isom, L., Sines, C. C., Howerton, S. B., Stephens, R. K. and Williams, L. D. "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, M. E., Lipscomb, L. A., Gao, Q., Ogata, C., Roquest, B. P., Garbay-Jaureguiberry, C., Wilkinson, A. P. and Williams, L. D. " 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, C. C. and Williams, L. D. "DNA Structure: Cations in Control?", Current Opinion in Structural Biology, 9, 298-304 (1999) (pdf).
  • 44. Zhang, Y., Ghasemzadeh, S., Kotliar, A. M., Kumar, S. Presnell, S. and Williams, L. D. "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, G. G., Yu, C., Schuster, G. B. and Williams, L. D. "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, L. D. "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, L. D. "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, G. G. and Williams, L. D. "The B-DNA Dodecamer at High Resolution Reveals a Spine of Water on Sodium", Biochemistry, 37, 8541-8555 (1998) (pdf).
  • 39. Presnell, S. R., Patil, G. S., Mura, C., Jude, K. M., Conley, J. M., Bertrand, J. A., Kam, C.-M., Powers, J. C. and Williams, L. D. "Oxyanion-Mediated Inhibition of Serine Proteases", Biochemistry, 37, 17068-17081 (1998) (pdf).
  • 38. Milano, M. T., Hu, G. G., Williams, L. D. and Bernhard, W. A. "Migration of Electrons and Holes in Crystalline d(CGATCG)-anthracycline Complexes X-Irradiated at 4K", Radiation Research, 150, 101-114 (1998) (abstract).
  • 37. Davis, T. M., McFail-Isom, L., Keane, E. and Williams, L. D. "Melting of a DNA Hairpin without Hyperchromism", Biochemistry, 37, 6975-6978 (1998) (pdf).
  • 36. Breslin, D. T., Coury, J. E., Anderson, J. R., McFail-Isom, L., Kan, Y., Williams, L. D., Bottomley, L. A. and Schuster, G. B. "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, G. G., Shui, X., Leng, F., Preibe, W., Chaires, J. B. and Williams, L. D. "Structure of a DNA-Bisdaunmycin Complex", Biochemistry, accelerated publication, 36, 5940-5946 (1997) (pdf).
  • 34. Coury, J. E., Anderson, J. R., McFail-Isom, L., Williams, L. D. and Bottomley, L. A. "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, J. E., McFail-Isom, L., Williams, L. D. and Bottomley, L. A. "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, B. R. and Williams, L. D. "2'-Deoxycytidine-N3-cyanoborane", Acta Cryst., C52, 1823-1825 (1996) (pdf).
  • 31. Lipscomb, L. A., Zhou, F. X., Presnell, S. R., Woo, R. J., Peek, M. E., Plaskon, R. R. and Williams, L. D. "Structure of a DNA-Porphyrin Complex", Biochemistry, accelerated publication, 35, 2818-2823 (1996) (pdf).
  • 30. Lipscomb, L. A., Zhou, F. X. and Williams, L. D. "Clathrate Hydrates are Poor Models for Biomolecule Hydration", Bioploymers, 38, 177-181 (1996) (pdf).
  • 29. Bertrand, J. A., Oleksyszyn, J., Kam, C.-M., Boduszek, B., Presnell, S., Plaskon, R. R., Suddath, F. L., Powers, J. C. and Williams, L. D. "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, J. E., McFail-Isom, L., Presnell, S., Williams, L. D. and Bottomley, L. A. "Scanning Probe Visualization of Electrostatically Immobilized Intercalating Drug-Nucleic Acid Complexes", J. Vac. Sci. and Technol., 13, 1746-1751 (1995) (pdf).
  • 27. Lipscomb, L. A., Peek, M. E., Morningstar, M. L., Verghis, S. M., Miller, E. M., Rich, A., Essigmann, J. M. and Williams, L. D. "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, M. E., Lipscomb, L. A., Haseltine, J., Gao, Q., Roques, B. P., Garbay-Jaureguiberry, C. and Williams, L. D. "Asymmetry and Dynamics in Bis-Intercalated DNA", J. Bioorg. and Med. Chem., 3, 693-699 (1995) (pdf).
  • 25. Lipscomb, L. A., Peek, M. E., Zhou, F. X., Bertrand, J. A., VanDerveer, D. and Williams, L. D. "Water Ring Structure at DNA Interfaces: Hydration and Dynamics of DNA-Anthracycline Complexes", Biochemistry, 33, 3649-3659 (1994) (pdf).
  • 24. Peek, M. E., Lipscomb, L. A., Bertrand, J. A., Gao, Q., Roques, B. P., Garbay-Jaureguiberry, C. and Williams, L. D. "DNA Distortion in bis-Intercalated Complexes", Biochemistry, accelerated publication, 33, 3794-3800 (1994) (pdf).
  • 23. Bancroft, D., Williams, L. D., 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, R. A., Williams, L. D., Jones, D. A. and Shaw, B. R. "Variable Temperature Infrared Spectroscopy of Cytosine-Guanine Base Pairs: Tautomerism versus Polarization", J. Biomol. Struct. Dynam., 9, 881-898 (1992).
  • 21. Williams, L. D. and Gao, Q. "DNA-Ditercalinium Interactions: Implications for Recognition of Damaged DNA", Biochemistry, 31, 4315-4324 (1992) (pdf).
  • 20. Williams, L. D. 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, L. D., 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, L. D., Frederick, C. A., Gessner, R. V. and Rich, A. "Molecular Structures of Spermine: Nucleic Acid Complexes", in Molecular Conformation and Biological Interactions, (Balaram, P. andamp; Ramaseshan, S., eds.) 295-309 (1991).
  • 17. Gao, Q., Williams, L. D., Egli, M., Rabinovich, D., Chen, S.-H., Quigley, G. J. and Rich, A. "Drug-Induced DNA Repair: X-Ray Structure of a DNA-Ditercalinium Complex", Proceedings of the National Academy of Sciences, USA, 88, 2422-2426 (1991) (pdf).
  • 16. Egli, M., Williams, L. D., Frederick, C. A. and Rich, A. "DNA-Nogalamycin Interactions", Biochemistry, 30, 1364-1372 (1991) (pdf).
  • 15. Egli, M., Williams, L. D., 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, B. G., Williams, L. D., Basu, H. S. and Marton, L. J. "Implications and Concepts of Polyamine-Nucleic Acid Interactions", J. Cell. Biochemistry, 46, 37-47 (1991) (pdf).
  • 13. Frederick, C. A., Williams, L. D., Ughetto, G., van der Marel, G. A., van Boom, J. H., Rich, A. and Wang, A. H.-J. "Structural Comparison of Anticancer Drug-DNA Complexes: Adriamycin and Daunomycin", Biochemistry, 29, 2538-2549 (1990) (pdf).
  • 12. Egli, M., Gessner, R. V., Williams, L. D., Quigley, G. J., van der Marel, G. A., van Boom, J. H., Rich, A. and Frederick, C. A. "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, L. D., Egli, M., Ughetto, G., van der Marel, G. A., van Boom, J. H., Quigley, G. J., Wang, A. H.-J., Rich, A. and Frederick, C. A. "Structure of 11-Deoxydaunomycin Bound to DNA Containing a Phosphorothioate", J. Mol. Biol., 215, 313-320 (1990).
  • 10. Williams, L. D., Frederick, C. A., Ughetto, G. and Rich, A. "Ternary Interactions of Spermine with DNA:4'-Epiadriamycin and other DNA:Anthracycline Complexes", Nucleic Acids Research, 18, 5533-5541 (1990) (pdf).
  • 9. Williams, L. D., Williams, N. G. and Shaw, B. R. "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, J. G., Williams, L. D. 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, L. D., Egli, M., Gao, Q., Bash, P., van der Marel, G. A., van Boom, J. H., Rich, A. and Frederick, C. A. "Structure of Nogalamycin Bound to a DNA Hexamer", Proceedings of the National Academy of Sciences, USA, 87, 2225-2229 (1990) (pdf).
  • 6. Williams, N. G., Williams, L. D. and Shaw, B. R. "Dimers, Trimers and Tetramers of Cytosine with Guanine", J. Am. Chem. Soc., 111, 7205-7209 (1989) (pdf).
  • 5. Williams, L. D. and Goldberg, I. H. "Selective Strand Scission by Intercalating Drugs at DNA Bulges", Biochemistry, 27, 3004-3011 (1988) (pdf).
  • 4. Williams, L. D., Thivierge, J. and Goldberg, I. H. "Specific Binding of o-Phenanthroline at a DNA Structural Lesion", Nucleic Acids Research, 16, 11607-11615 (1988) (pdf).
  • 3. Williams, L. D., Chawla, B. and Shaw, B. R. "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, L. D. and Shaw, B. R. "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, L. D. "Porphyrins 43. Triplet Sublevel Emission of Platinum Tetrabenzoporphyrin by Spectrothermal Principal Component Decomposition", J. Am. Chem. Soc., 104, 6278-6283 (1982) (pdf).