Best Georgia Tech Faculty Research Paper of 2001, Awarded by the Georgia Tech chapter of Sigma Xi. Research Innovation Award, The Research Corporation, 2000

Biochemistry/Chemical Biology/Chemical Evolution/Molecular Biophysics

The research in our laboratory is directed towards elucidating the fundamental chemical and physical principles that govern nucleic acid (RNA and DNA) assembly. We are interested in how the physical properties of nucleic acids govern biological functions in contemporary life, and how these same properties provide clues to the origin and early evolution of life. We are also applying our knowledge of nucleic acids to problems that are of current importance in medicine and biotechnology. Specific projects include investigations of: 1) the origin and evolution of RNA; 2) cation, solvent and small molecule binding to nucleic acids; 3) nucleic acid condensation and packaging; and 4) folding and evolution of the ribosome. Our research involves the application of a wide variety of physical and chemical techniques.

Cafferty, B.J., Hud, N.V. (2014) Abiotic synthesis of RNA in water: a common goal of prebiotic chemistry and bottom-up synthetic biology. Curr. Opin. Chem. Biol. 22, 146-157.

Cafferty, B.J. Avirah, R.R., Schuster, G.B., Hud, N.V. (2014) Ultra-sensitive pH Control of Supramolecular Polymers and Hydrogels: pKa Matching of Biomimetic Monomers, Chem. Sci. 5, 4681-4686.

Petrov, A.S., et al., Hud, N.V., Williams, L.D., (2014) Evolution of the Ribosome at Atomic Resolution, Proc. Natl. Acad. Sci. USA. 111, 10251-10256.

Chen, M.C., Cafferty, B.J., Mamajanov, I., Gállego, I., Khanam, J., Krishnamurthy, R., Hud, N.V. (2014) Spontaneous prebiotic formation of a beta-ribofuranoside that self-assembles with a complementary heterocycle, J. Am. Chem. Soc. 136, 5640-5646. doi: 10.1021/ja410124v

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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