Publications

2011-present 

86. Portella, G., Germann, M.W., Hud, N.V.,* Orozco, M.* (2014) 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. 136, 3075-3086. doi: 10.1021/ja410698u

85. Mamajanov, I. et al., (2014) Ester formation and hydrolysis during wet-dry cycles: Generation of far-from-equilibrium polymers in a model prebiotic reaction, Macromolecules 47, 1334-1343. doi: 10.1021/ma402256d

84. Petrov, A.S., et al. (2014) Secondary Structures of rRNAs from All Three Domains of Life, PLoS ONE 9, e88222. doi: 10.1371/journal.pone.0088222

83. Chen, M.C., Cafferty, B.J., Mamajanov, I., Gállego, I., Khanam, J., Krishnamurthy, R., Hud, N.V. (2014) Spontaneous prebiotic formation of -ribofuranoside that self-assembles with a complementary heterocycle, J. Am. Chem. Soc., in press. doi: 10.1021/ja410124v

82. Petrov, A.S., et al. (2013) Secondary structure and domain architecture of the 23S and 5S rRNAs, Nucleic Acids Res. 41, 7522-7535.
doi: 10.1093/nar/gkt513

81. 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., Williams, L.D. (2013) RNA with iron(II) as a cofactor catalyses electron transfer, Nat. Chem. 5, 525-528. doi: 10.1038/nchem.1649

80. Hud, N.V., Cafferty, B.J., Krishnamurthy, R., Williams, L.D. (2013) The origin of RNA and “My Grandfather’s Axe”, Chem. Biol. 20, 466-474. doi: 10.1016/j.chembiol.2013.03.012

79. Hsiao, CL et al. (2013) Molecular paleontology: a biochemical model of the ancestral ribosome, Nucleic Acids Res. 41, 3373-3385. doi: 10.1093/nar/gkt023

78. Cafferty, B.J., Gállego, I., Chen, M.C., Farley, K.I., Eritja, R. and Hud, N.V. (2013) Efficient self-assembly in water of long noncovalent polymers by nucleobase analogs, J. Am. Chem. Soc. 135, 2447-2450. doi:10.1021/ja3121555v

77. Hsiao, C., H., Lenz, T., Peters, J., Fang, P.-Y., Schneider, D., Anderson, E., Preeprem, T., Bowman, J., O'Neill, E., Athavale, S., Gossett, J., Lie, L., Trippe, C., Murray, J., Petrov, A.S., Wartell, R., Harvey, S.C., Hud, N.V., Williams, L.D., (2013) Molecular paleontology: A biochemical model of the ancestral ribosome, Nucleic Acids Res. 41, 3373-3385. doi:10.1093/nar/gkt023

76. Parker, T.M., Hohenstein, E.G., Parrish, R.M., Hud, N.V., and Sherrill, C.D. (2013) Quantum mechanical analysis of the energetic contributions to π stacking in nucleic acids versus rise, twist, and slide, J. Am. Chem. Soc. 135, 1306-1316. doi:10.1021/ja3063309

75. Athavale, S.S., Gossett, J.J., Bowman, J.C., Hud, N.V., Williams, L.D. and Harvey, S.C. (2013) Secondary structure of the free RNA of satellite tobacco mosaic virus, PLoS ONE 8, e54384. doi:10.1371/journal.pone.0054384

74. Kuruvilla, E., Schuster, G.B., and Hud, N.V. (2013) Enhanced non-enzymatic ligation of homo-purine miniduplexes: Support for greater base stacking in a pre-RNA world, ChemBioChem 14, 45-48. doi:10.1002/cbic.201200601

73. Athavale, S.S.,,Petrov, A.S., Hsiao, C., Watkins, D., Pricket, 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. (2012) RNA folding and catalysis mediated by iron (II), PLoS ONE 7, e38024. doi: 10.1371/pone.0038024

72. Lannan, F., Mamajanov, I. and Hud, N.V. (2012) Human telomere sequence DNA in water-free and high-viscosity solvents: G-quadruplex folding governed by Kramers rate theory, J. Am. Chem. Soc. 134, 15324-15330. doi:10.1021/ja303499m

71. Petrov, A.S., Bernier, C.R., Hsiao, C., Okafor, C.D., Tannenbaum, E., Stern, J., Gaucher, E., Schneider, D., Hud, N.V., Harvey, S.C. and Williams, L.D. (2012) RNA–magnesium–protein interactions in large ribosomal subunit, J. Phys. Chem. B 116, 8113–8120. doi: 10.1021/jp304723w

70. Bowan, J.C., Lenz, T.D, Hud, N.V. and Williams, L.D. (2012) Cations in charge: Magnesium ions in RNA folding and catalysis, Curr. Opin. Struc. Biol. 22, 262–272. doi: 10.1016/j.sbi.2012.04.006
 
69. Engelhart, A.E., Cafferty, B.J., Okafor, C.D., Chen, M.C., Williams, L.D., Lynn, D.G. and Hud, N.V. (2012) Nonenzymatic ligation of DNA with a reversible step and a final linkage that can be used in PCR, ChemBioChem 13, 1121–1124. doi: 10.1002/cbic.201200167
 
68. Walker, S.I., Grover, M.A. and Hud, N.V. (2012) Universal sequence replication, reversible polymerization and early functional biopolymers: A model for the initiation of prebiotic sequence evolution, PLoS ONE 7, e34166. doi: 10.1371/pone.0034166
 
67. Athavale, S.S., Gossett, J.J., Hsiao, C., Bowman, J.C., O'Neill, E. H., Preeprema, T., Hud, N.V., Wartell, R. and Williams, L.D. (2012) Domain III of the T. Thermophilus 23S rRNA folds independently to a near-native State, RNA 18, 752-758. doi:10.1261/rna.030692.111
 
66. Maehigashi, T., Hsiao, C., Woods, K.K., Moulaei, T., Hud, N.V. and Williams, L.D. (2012) B-DNA structure is intrinsically polymorphic: even at the level of base pair positions. Nucleic Acids Res. 40, 3714-3722. doi: 10.1093/nar/gkr1168
 
65. Anumukonda, L.N., Young, A., Lynn, D.G., Buckley, R., Warrayat, A., Graves, C.L., Bean, H.D. and Hud, N.V. (2011) Adenine synthesis in a model prebiotic reaction: connecting origin of life chemistry with biology. J. Chem. Ed. 88, 1698-1701. Free Download
 
64. Buckley, R., Enekwa, C.D., Williams, L. D. and Hud, N.V. (2011) Molecular recognition of Watson-Crick-like purine-purine base pairs. ChemBioChem 12, 2155-2158. doi: 10.1002/cbic.201100375
 
63. Li, X. Y., Hernandez, A. F., Grover, M. A., Hud, N. V. and Lynn, D. G. (2011) Step-growth control in template-directed polymerization. Heterocycles 82, 1477-1488. doi: 10.3987/COM-10-S(E)99
 
62. Mamajanov, I. and Hud, N. V. (2011) DNA, 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, 443-447.

2006-2010

61. Engelhart, A. E.; Hud, N. V. (2010) Primitive Genetic Polymers. Cold Spring Harbor Perspectives in Biology 2. doi: 10.1101/cshperspect.a002196v1
 
60. Barks, H. L., Buckley, R., Grieves, G. A., Di Mauro, E.; Hud, N. V.; Orlando, T. M. (2010) Guanine, adenine, and hypoxanthine production in UV-irradiated formamide solutions: Relaxation of the requirements for prebiotic purine nucleobase formation. ChemBioChem 11, 1240-1243. doi: 10.1002/cbic.201090037
 
59. Horowitz, E. D.; Engelhart, A. E.; Chen, M. C.; Quarles, K. A.; Smith, M. W.; Lynn, D. G.; Hud, N. V. (2010) Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world. Proc. Natl. Acad. Sci. USA 107, 5288-5293. doi: 10.1073/pnas.0914172107
 
58. Mamajanov, I., Engelhart, A. E., Bean, H. D. and Hud, N. V. (2010) DNA and RNA in anhydrous media: duplex, triplex, and G-Quadruplex secondary structures in a deep eutectic solvent. Angew. Chem. Int. Ed. 49, 6310-6314. doi: 10.1002/ange.201001561
 
57. Bean, H. D., Lynn, D. G. and Hud, N. V. (2010) Self-Assembly and the Origin of the First RNA-Like Polymers,
Chemical Evolution II: From the Origins of Life to Modern Society, ACS Symposium Series 1025, 109-132. doi: 10.1021/bk-2009-1025.ch006
 
56. Joung I. S., Çetinkol Ö. P., Hud*, N. V.,  and Cheatham III*, T. E. (2009) Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of A center dot A base pairing and a putative structure of the coralyne-induced homo-adenine duplex. Nucleic Acids Res. 37, 7715-7727. doi: 10.1093/nar/gkp730
 
55. Sheng, Y., Bean, H. D., Mamajanova, I., Hud, N. V. and Leszczynski, J. (2009) A comprehensive investigation of the energetics of pyrimidine nucleoside formation in a model prebiotic reaction, J. Am. Chem. Soc. 131, 16088-16095. doi: 10.1021/ja900807m
 
54. Hud N. V. (2009) Nucleotide Adsorption on Mineral Surfaces — A mixed blessing for the RNA World?, Astrobiology 9, 253-255. doi:10.1089/ast.2008.0928
 
53. Tsai, A. G., Engelhart, A. E., Hatmal, M. M., Houston, S. I., Hud, N. V., Haworth, I. S. and Lieber M. R. (2009) Conformational variants of duplex DNA correlated with cytosine-rich chromosomal fragile sites, J. Biol. Chem. 284, 7157-7164. doi: 10.1074/jbc.M806866200
 
52. Horowitz, E. D., Lilavivat, S., Holladay, B. W., Germann M. W., and Hud, N. V. (2009) Solution structure and thermodynamics of 2',5' RNA intercalation, J. Am. Chem. Soc. 131, 5716-6036. doi: 10.1021/ja810068e
 
51. Sarkar, T., Petrov, A. S., Vitko, J. R., Santai, C.T., Harvey, S. C., Mukerji, I. and Hud, N. V. (2009) Integration host factor (IHF) dictates the structure of polyamine-DNA condensates: Implications for the role of IHF in the compaction of bacterial chromatin, Biochemistry 48, 667-675. doi: 10.1021/bi8019965
 
50. Engelhart, A. E., Morton, T.H. and Hud, N. V. (2009) Evidence of strong hydrogen bonding by 8-amino-guanine, Chem. Comm., 647-649. doi: 10.1039/B818409G
 
49. Çetinkol, Ö. P. and Hud, N. V. (2009) Molecular recognition of poly(A) by small ligands: An alternative method of analysis reveals nanomolar, cooperative and shape-selective binding, Nucleic Acids Res. 37, 611-621. doi: 10.1093/nar/gkn977
 
48. Nucleic Acid-Metal Ion Interactions, Nicholas V. Hud, Ed., Royal Society of Chemistry, 2009, 448 pp., ISBN 978-0854041954
 
47. Çetinkol, Ö. P., Engelhart, A.E., Nanjunda, R. K, Wilson, W. D. and Hud, N. V. (2008) Submicromolar, selective G-quadruplex ligands from one pot: Thermodynamic and structural studies of human telomeric DNA binding by azacyanines, ChemBioChem 9, 1889-1892. doi: 10.1002/cbic.200800234
 
46. Persil, Ö. and Hud, N.V. (2007) Harnessing DNA intercalation, Trends Biotech. 25, 433-436. doi: 10.1016/j.tibtech.2007.08.003
 
45. Bean, H.D., Sheng, Y., Collins, J.P., Anet, F. A. L., Leszczynski, J. and Hud, N. V. (2007) Formation of a β-pyrimidine nucleoside by a free pyrimidine base and ribose in a plausible prebiotic reaction, J. Am. Chem. Soc. 129, 9556-9557. doi: 10.1021/ja072781a
 
44. Podbevsek, P., Hud, N.V. and Plavec, J. (2007) NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution, Nucleic Acids Res. 35, 2554-2563. doi: 10.1093/nar/gkm138
 
43. Hud, N.V., Jain, S.S., Li, X. and Lynn, D.G. (2007) Addressing the problems of base pairing and strand cyclization in template-directed synthesis, Chem. Biodiv. 4, 768-783. doi: 10.1002/cbdv.200790063
 
42. Hud, N.V. and Morton, T.H. (2007) DFT energy surfaces for aminopurine homodimers and their conjugate acid ions, J. Phys. Chem. A. 111, 3369-3377. doi: 10.1021/jp065786n
 
41. Sarkar, T., Vitoc, I., Mukerji, I. and Hud, N.V. (2007) Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines, Nucleic Acids Res. 35, 951-961. doi: 10.1093/nar/gkl1093
 
40. Plavec, J. and Hud, N.V., The Role of Ions in Governing the structure and properties of quadruplexes, In Quadruplex Nucleic Acids, Royal Society of Chemistry, London, 2006, S. Balsubramanian and S. Neidle, Eds., 100-130 pp. Link
 
39. Horowitz, E.D. and Hud, N.V. (2006) Ethidium and proflavine binding to a 2',5'-linked RNA duplex, J. Am. Chem. Soc. 128, 15380-15381. doi: 10.1021/ja065339l
 
38. Vilfan, I. D., Conwell, C.C., Sarkar, T. and Hud, N.V. (2006) A time study of DNA condensate morphology: Implications regarding the nucleation, crowth and equilibrium populations of toroids and rods, Biochemistry 45, 8174-8183. doi: 10.1021/bi060396c
 
37. Bean, H. B., Anet, F. A. L., Gould, I. R. and Hud, N. V. (2006) Glyoxylate as a linkage for an ancestor of RNA, Origins Life Evol. B. 36, 39-63. doi: 10.1007/s11084-005-2082-4
 

2001-2005

36. Hud, N. V. and Vilfan, I. D. (2005) Toroidal DNA condensates: Unraveling the rine structure and the role of nucleation in determining size in vitro, Ann. Rev. Biophys. Biomol. Struc. 34, 295-318. doi: 10.1146/annurev.biophys.34.040204.144500
 
35. Sarkar, T., Conwell, C. C., Harvey, L. C. and Hud, N. V. (2005) Condensation of oligonucleotides assembled into nicked and gapped duplexes: Potential structures for oligonucleotide delivery, Nucleic Acids Res. 33, 143-151. doi: 10.1093/nar/gki156
 
34. Hud, N. V. and Lynn, D. G. (2004) Model systems: From life's origins to a synthetic biology (Editorial overview) Curr. Opin. Chem. Biol. 8, 627-628. doi: 10.1016/j.cbpa.2004.10.008
 
33. Persil, Ö., Santai, C., Jain, S. S. and Hud, N. V. (2004) Assembly of an antiparallel duplex from homo-adenine sequences by small molecule binding, J. Am. Chem. Soc. 126, 8644-8645. doi: 10.1021/ja0492891
 
32. Petty, J. T., Zheng, J., Hud, N. V. and Dickson, R. M. (2004) DNA Templated Ag nanocluster formation, J. Am. Chem. Soc. 126, 5207-5212. doi: 10.1021/ja031931o
 
31. Conwell, C. C. and Hud, N. V. (2004) Evidence that both kinetic and thermodynamic factors govern DNA toroid dimensions: Effects of magnesium(II) on DNA condensation by hexammine cobalt(III), Biochemistry 43, 538-5387. doi: 10.1021/bi049872u
 
30. Vilfan, I.D., Conwell, C.C. and Hud, N.V. (2004) Formation of native-like mammalian sperm cell chromatin with folded bull protamine, J. Biol. Chem. 279, 20088-20095. doi: 10.1074/jbc.M312777200
 
29. Jain, S.S., Anet, F.A.L., Stahle, C.J. and Hud, N.V. (2004) Enzymatic behavior by intercalating molecules in a template-directed ligation reaction, Angew. Chem. Int. Ed. Eng. 43, 2004-2008. doi: 10.1002/anie.200353155
 
28. Jain, S.S., Polak, M., Hud, N.V. (2003) Controlling nucleic acid secondary structure by intercalation: Effects of strand length on coralyne-driven disproportionation, Nucleic Acids Res. 31, 4608-4615. doi: 10.1093/nar/gkg648
 
27. Conwell, C.C. and Hud, N.V. (2003) MgCl2 enhances cluster formation by nanoscale toroidal DNA condensates, J. Clust. Sci. 14, 115-122. doi: 10.1023/A:1024837520146
 
26. Conwell, C.C., Vilfan, I. D. and Hud, N.V. (2003) Controlling the size of nanoscale toroidal DNA condensates with wtatic curvature and ionic strength, Proc. Natl. Acad. Sci. USA 100, 9296-9301. doi: 10.1073/pnas.1533135100
 
25. Hud, N.V. and Plavec, J. (2003) A unified model for the origin of sequence-directed curvature, Biopolymers 69, 144-158. doi: 10.1002/bip.10364
 
24. Coulberson, A. L., Hud, N.V., LeDoux, J. M. and Prausnitz, M. R. (2003) Gene packaging with lipids, peptides and viruses inhibits transfection by electroporation, J. Controlled Release 86, 361-370. doi: 10.1016/S0168-3659(02)00417-0
 
23. Črnugelj, M., Hud, N. V. and Plavec, J. (2002) The solution structure of d(G4T4G3)2: A bimolecular G-quadruplex with a novel fold, J. Mol. Biol. 320, 911-924. doi: 10.1016/S0022-2836(02)00569-7
 
22. Hud, N. V. and Feigon, J. (2002) Characterization of divalent cation localization in the minor groove of the AnTn and TnAn DNA sequence elements by 1H NMR spectroscopy and manganese(II), Biochemistry 41, 9900-9910. doi: 10.1021/bi020159j
 
21. Polak, M. and Hud, N.V. (2002) Complete disproportionation of the duplex poly(dT):poly(dA) into the triplex poly(dT):poly(dA):poly(dT) and single stranded poly(dA) by Coralyne. Nucleic Acids Res. 30, 983-992. doi: 10.1093/nar/30.4.983
 
20. Hud, N.V. and Downing, K.H. (2001) Cryoelectron microscopy of lambda phage DNA condensates in vitreous ice: The fine structure of DNA toroids. Proc. Natl. Acad. Sci. USA 98, 14925-14930. doi: 10.1073/pnas.261560398
 
19. Hud, N.V. and Polak, M. (2001) DNA-cation interactions: the major and minor grooves are flexible ionophores. Curr. Opin. Struct. Biol. 11, 293-301. doi: 10.1016/S0959-440X(00)00205-0
 
18. Feigon, J., Butcher, S.E., Finger, L.D. and Hud, N.V. (2001) Nuclear Magnetic Resonance of Biological Macromolecules, Pt A, Methods Enzymol. 338, pp. 400-420. Link
 

1996-2000

17. Shen, M.R., Downing, K.H., Balhorn, R. and Hud, N.V. (2000) Nucleation of DNA condensation by static loops: Formation of DNA toroids with reduced dimensions. J. Am. Chem. Soc. 122, 4833-4834. doi: 10.1021/ja000200a
 
16. Rovnyak, D., Baldus, M., Wu, G., Hud, N.V., Feigon, J. and Griffin, R.G. (2000) Localization of 23Na+ in a DNA quadruplex by high-field solid-state NMR. J. Am. Chem. Soc. 122, 11423-11429. doi: 10.1021/ja001022o
 
15. Hud, N.V. and Anet, F.A.L. (2000) Intercalation-mediated synthesis and replication: A new approach to the origin of life. J. theor. Biol. 205, 543-562. doi: 10.1006/jtbi.2000.2084
 
14. Schultze, P., Hud, N.V., Smith, F.W. and Feigon, J. (1999) The effect of sodium, potassium and ammonium ions on the conformation of the dimeric quadruplex formed by the Oxytricha nova telomere repeat oligonucleotide d(G4T4G4). Nucleic Acids Res. 27, 3018-3028. doi: 10.1093/nar/27.15.3018
 
13. Hud, N.V., Sklenar, V. and Feigon, J. (1999) Localization of ammonium lon in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending. J. Mol. Biol. 286, 651-660. doi: 10.1006/jmbi.1998.2513
 
12. Hud, N.V., Schultze, P., Sklenar, V. and Feigon, J. (1999) Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex. J. Mol. Biol. 285, 233-243. doi: 10.1006/jmbi.1998.2327. doi: 10.1021/ja9811039
 
11. Hud, N.V., Schultze, P. and Feigon, J. (1998) Ammonium ion as an NMR probe for monovalent cation coordination sites of DNA quadruplexes. J. Am. Chem. Soc. 120, 6403-6404. doi: 10.1021/ja9811039
 
10. Altschuler, E.L., Hud, N.V., Mazrimas, J.A. and Rupp, B. (1997) Random coil conformation for extended polyglutamine stretches in aqueous soluble monomeric peptides. J. Pept. Res. 50, 73-75. doi: 10.1111/j.1399-3011.1997.tb00622.x
 
9. Hud, N.V. and Feigon, J. (1997) Localization of divalent metal ions in the minor groove of DNA A-tracts. J. Am. Chem. Soc. 119, 5756-5757. doi: 10.1021/ja9704085
 
8. Shonnard, G.C., Hud, N.V. and Mohrenweiser, H.W. (1996) Arginine to tryptophan substitution in the active site of a human lactate dehydrogenase variant - LDHB (*) GUA1: Postulated effects on subunit structure and catalysis. Biochim. Biophys. Acta-Mol. Basis Dis. 1315, 9-14. doi: 10.1016/0925-4439(95)00089-5
 
7. Hud, N.V., Smith, F.W., Anet, F.A.L. and Feigon, J. (1996) The selectivity for K+ versus Na+ in DNA quadruplexes is dominated by relative free energies of hydration: A thermodynamic analysis by 1H NMR. Biochemistry 35, 15383-15390. doi: 10.1021/bi9620565
 

1991-1995

6. Hud, N.V. (1995) Double-stranded DNA organization in bacteriophage heads - an alternative toroid-based model. Biophys. J. 69, 1355-1362. doi: 10.1016/S0006-3495(95)80002-0

5. Hud, N.V., Downing, K.H. and Balhorn, R. (1995) A constant radius of curvature model for the organization of DNA in toroidal condensates. Proc. Natl. Acad. Sci. USA 92, 3581-3585. Article Link

4. Hud, N.V., Milanovich, F.P. and Balhorn, R. (1994) Evidence of novel secondary structure in DNA-bound protamine is revealed by Raman-spectroscopy. Biochemistry 33, 7528-7535. doi: 10.1021/bi00190a005

3. Hud, N.V., Allen, M.J., Downing, K.H., Lee, J. and Balhorn, R. (1993) Identification of the elemental packing unit of DNA in mammalian sperm cells by atomic-force microscopy. Biochem. Biophys. Res. Commun. 193, 1347-1354. doi: 10.1006/bbrc.1993.1773

2. Allen, M.J., Hud, N.V., Balooch, M., Tench, R.J., Siekhaus, W.J. and Balhorn, R. (1992) Tip-radius-induced artifacts in AFM images of protamine-complexed DNA fibers. Ultramicroscopy 42, 1095-1100. doi: 10.1016/0304-3991(92)90408-C

1. Myrick, M.L., Hud, N.V., Angel, S.M. and Garvis, D.G. (1991) Tunneling spectroscopy on graphite defects - implications for biological STM. Chem. Phys. Lett. 180, 156-160. doi: 10.1016/0009-2614(91)87133-V