Publications

Found 25 results
Filters: Author is Hud, Nicholas V and Keyword is Nucleic Acid Conformation  [Clear All Filters]
2014
G. Portella, Germann, M. W., Hud, N. V., and Orozco, M., “MD and NMR analyses of choline and TMA binding to duplex DNA: on the origins of aberrant sequence-dependent stability by alkyl cations in aqueous and water-free solvents.”, J Am Chem Soc, vol. 136, no. 8, pp. 3075-86, 2014.
A. S. Petrov, Bernier, C. R., Gulen, B., Waterbury, C. C., Hershkovits, E., Hsiao, C., Harvey, S. C., Hud, N. V., Fox, G. E., Wartell, R. M., and Williams, L. Dean, “Secondary structures of rRNAs from all three domains of life.”, PLoS One, vol. 9, no. 2, p. e88222, 2014.
2013
S. S. Athavale, J Gossett, J., Bowman, J. C., Hud, N. V., Williams, L. Dean, and Harvey, S. C., “In vitro secondary structure of the genomic RNA of satellite tobacco mosaic virus.”, PLoS One, vol. 8, no. 1, p. e54384, 2013.
C. Hsiao, 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., J Gossett, J., Trippe, C., Murray, J., Petrov, A. S., Wartell, R. M., Harvey, S. C., Hud, N. V., and Williams, L. Dean, “Molecular paleontology: a biochemical model of the ancestral ribosome.”, Nucleic Acids Res, vol. 41, no. 5, pp. 3373-85, 2013.
A. S. Petrov, Bernier, C. R., Hershkovits, E., Xue, Y., Waterbury, C. C., Hsiao, C., Stepanov, V. G., Gaucher, E. A., Grover, M. A., Harvey, S. C., Hud, N. V., Wartell, R. M., Fox, G. E., and Williams, L. Dean, “Secondary structure and domain architecture of the 23S and 5S rRNAs.”, Nucleic Acids Res, vol. 41, no. 15, pp. 7522-35, 2013.
2012
T. Maehigashi, Hsiao, C., Woods, K. Kruger, Moulaei, T., Hud, N. V., and Williams, L. Dean, “B-DNA structure is intrinsically polymorphic: even at the level of base pair positions.”, Nucleic Acids Res, vol. 40, no. 8, pp. 3714-22, 2012.
S. S. Athavale, J Gossett, 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. Dean, “Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state.”, RNA, vol. 18, no. 4, pp. 752-8, 2012.
S. S. Athavale, Petrov, A. S., Hsiao, C., Watkins, D., Prickett, C. D., J Gossett, J., Lie, L., Bowman, J. C., O'Neill, E., Bernier, C. R., Hud, N. V., Wartell, R. M., Harvey, S. C., and Williams, L. Dean, “RNA folding and catalysis mediated by iron (II).”, PLoS One, vol. 7, no. 5, p. e38024, 2012.
2010
I. Mamajanov, Engelhart, A. E., Bean, H. D., and Hud, N. V., “DNA and RNA in anhydrous media: duplex, triplex, and G-quadruplex secondary structures in a deep eutectic solvent.”, Angew Chem Int Ed Engl, vol. 49, no. 36, pp. 6310-4, 2010.
E. D. Horowitz, Engelhart, A. E., Chen, M. C., Quarles, K. A., Smith, M. W., Lynn, D. G., and Hud, N. V., “Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world.”, Proc Natl Acad Sci U S A, vol. 107, no. 12, pp. 5288-93, 2010.
2009
A. G. Tsai, Engelhart, A. E., Hatmal, M. 'monM., Houston, S. I., Hud, N. V., Haworth, I. S., and Lieber, M. R., “Conformational variants of duplex DNA correlated with cytosine-rich chromosomal fragile sites.”, J Biol Chem, vol. 284, no. 11, pp. 7157-64, 2009.
E. D. Horowitz, Lilavivat, S., Holladay, B. W., Germann, M. W., and Hud, N. V., “Solution structure and thermodynamics of 2',5' RNA intercalation.”, J Am Chem Soc, vol. 131, no. 16, pp. 5831-8, 2009.
2007
N. V. Hud, Jain, S. S., Li, X., and Lynn, D. G., “Addressing the problems of base pairing and strand cyclization in template-directed synthesis: a case for the utility and necessity of 'molecular midwives' and reversible backbone linkages for the origin of proto-RNA.”, Chem Biodivers, vol. 4, no. 4, pp. 768-83, 2007.
P. Podbevsek, Hud, N. V., and Plavec, J., “NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution.”, Nucleic Acids Res, vol. 35, no. 8, pp. 2554-63, 2007.
2006
E. D. Horowitz and Hud, N. V., “Ethidium and proflavine binding to a 2',5'-linked RNA duplex.”, J Am Chem Soc, vol. 128, no. 48, pp. 15380-1, 2006.
I. D. Vilfan, Conwell, C. C., Sarkar, T., and Hud, N. V., “Time study of DNA condensate morphology: implications regarding the nucleation, growth, and equilibrium populations of toroids and rods.”, Biochemistry, vol. 45, no. 26, pp. 8174-83, 2006.
2005
N. V. Hud and Vilfan, I. D., “Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size.”, Annu Rev Biophys Biomol Struct, vol. 34, pp. 295-318, 2005.
2004
O. Persil, Santai, C. T., Jain, S. S., and Hud, N. V., “Assembly of an antiparallel homo-adenine DNA duplex by small-molecule binding.”, J Am Chem Soc, vol. 126, no. 28, pp. 8644-5, 2004.
J. T. Petty, Zheng, J., Hud, N. V., and Dickson, R. M., “DNA-templated Ag nanocluster formation.”, J Am Chem Soc, vol. 126, no. 16, pp. 5207-12, 2004.
2003
S. S. Jain, Polak, M., and Hud, N. V., “Controlling nucleic acid secondary structure by intercalation: effects of DNA strand length on coralyne-driven duplex disproportionation.”, Nucleic Acids Res, vol. 31, no. 15, pp. 4608-15, 2003.
C. C. Conwell, Vilfan, I. D., and Hud, N. V., “Controlling the size of nanoscale toroidal DNA condensates with static curvature and ionic strength.”, Proc Natl Acad Sci U S A, vol. 100, no. 16, pp. 9296-301, 2003.
N. V. Hud and Plavec, J., “A unified model for the origin of DNA sequence-directed curvature.”, Biopolymers, vol. 69, no. 1, pp. 144-58, 2003.
2002
M. Polak and Hud, N. V., “Complete disproportionation of duplex poly(dT)*poly(dA) into triplex poly(dT)*poly(dA)*poly(dT) and poly(dA) by coralyne.”, Nucleic Acids Res, vol. 30, no. 4, pp. 983-92, 2002.
M. Crnugelj, Hud, N. V., and Plavec, J., “The solution structure of d(G(4)T(4)G(3))(2): a bimolecular G-quadruplex with a novel fold.”, J Mol Biol, vol. 320, no. 5, pp. 911-24, 2002.
2001
N. V. Hud and Downing, K. H., “Cryoelectron microscopy of lambda phage DNA condensates in vitreous ice: The fine structure of DNA toroids.”, Proc Natl Acad Sci U S A, vol. 98, no. 26, pp. 14925-30, 2001.