Nathan A. Siegfried, Ph.D.

Affiliations: 
2009 Pennsylvania State University, State College, PA, United States 
Area:
RNA Folding and Catalysis
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"Nathan Siegfried"
Mean distance: 9.23
 
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Parents

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Philip C. Bevilacqua grad student 2009 Penn State
 (Folding cooperativity and its influence on pKa shifting in nucleic acids.)
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Publications

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Smola MJ, Rice GM, Busan S, et al. (2015) Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis. Nature Protocols. 10: 1643-69
Siegfried NA, Busan S, Rice GM, et al. (2014) RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nature Methods. 11: 959-65
Mauger DM, Siegfried NA, Weeks KM. (2013) The genetic code as expressed through relationships between mRNA structure and protein function. Febs Letters. 587: 1180-8
Chadalavada DM, Cerrone-Szakal AL, Wilcox JL, et al. (2012) Mechanistic analysis of the hepatitis delta virus (HDV) ribozyme: methods for RNA preparation, structure mapping, solvent isotope effects, and co-transcriptional cleavage. Methods in Molecular Biology (Clifton, N.J.). 848: 21-40
Steen KA, Siegfried NA, Weeks KM. (2011) Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) for direct analysis of covalent adducts and of nucleotide flexibility in RNA. Nature Protocols. 6: 1683-94
Siegfried NA, Kierzek R, Bevilacqua PC. (2010) Role of unsatisfied hydrogen bond acceptors in RNA energetics and specificity. Journal of the American Chemical Society. 132: 5342-4
Siegfried NA, O'Hare B, Bevilacqua PC. (2010) Driving forces for nucleic acid pK(a) shifting in an A(+).C wobble: effects of helix position, temperature, and ionic strength. Biochemistry. 49: 3225-36
Siegfried NA, Bevilacqua PC. (2009) Thinking inside the box: designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in RNA and DNA folding. Methods in Enzymology. 455: 365-93
Cerrone-Szakal AL, Siegfried NA, Bevilacqua PC. (2008) Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid. Journal of the American Chemical Society. 130: 14504-20
Bevilacqua PC, Cerrone-Szakal AL, Siegfried NA. (2007) Insight into the functional versatility of RNA through model-making with applications to data fitting. Quarterly Reviews of Biophysics. 40: 55-85
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