Basics of nucleic acid structure. 1) Saenger, W. (1984) Principles of Nucleic Acid Structure. Springer-Verlag, New York.

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1 Biophysics 204 Alan Frankel David Weinberg Helices Basics of nucleic acid structure 1) Saenger, W. (1984) Principles of Nucleic Acid Structure. Springer-Verlag, New York. 2) Egli, M., Portmann, S., and Usman, N. (1996) RNA hydration: A detailed look. Biochemistry 35, ) Neidle, S. (1998) New insights into sequence-dependent DNA structure. Nat. Struct. Biol. 5, ) Shui, X., McFail-Isom, L., Hu, G.G., and Williams, L.D. (1998) The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry 37, ) Rasmussen, H., Kastrup, J.S., Nielsen, J.N., Nielsen, J.M., and Nielsen, P.E. (1997) Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7Å resolution. Nat. Struct. Biol. 4, ) Liu, H., Gao, J., Lynch, S.R., Saito, Y.D., Maynard, L., and Kool, E.T. (2003) A fourbase paired genetic helix with expanded size. Science 302, ) Richmond, T.J. and Davey, C.A. (2003) The structure of DNA in the nucleosome core. Nature 423, Multi-stranded helices 8) Radhakrishnan, I. and Patel, D.J. (1994) DNA triplexes: solution structures, hydration sites, energetics, interactions, and function. Biochemistry 33, ) Mitton-Fry, R.M., DeGregorio, S.J., Wang, J., Steitz, T.A., and Steitz, J.A. (2010) Poly(A) tail recognition by a viral RNA element through assembly of a triple helix. Science 330, ) Parkinson, G.N. (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature. 417, ) Berger, I., Egli, M., and Rich, A. (1996) Inter-strand C-H-O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4' in cytosine-rich DNA. Proc. Natl. Acad. Sci. USA 93,

2 Small structural motifs Nucleic acid tertiary structure and RNA folding 1) Heus, H.A. and Pardi, A. (1991) Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science 253, ) Klein, D.J., Scheming, T.M., Moore, P.B., and Steitz, T.A. (2001) The kink-turn: a new RNA secondary structure motif. EMBO J. 20, ) ten Dam, E., Pleij, K., and Draper, D. (1992) Structural and functional aspects of RNA pseudoknots. Biochemistry 31, ) Doherty, E.A., Batey, R.T., Masquida, B., and Doudna, J.A. (2001) A universal mode of helix packing in RNA. Nat. Struct. Biol. 8, ) Ennifar, E., Walter, P., Ehresmann, B., Ehresmann, C., and Dumas, P. (2001) Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site. Nat. Struct. Biol. 8, Principles of RNA architecture 6) Cruz, J.A. and Westhof, E. (2009) The dynamic landscapes of RNA architecture. Cell 136, ) Butcher, S.E. and Pyle, A.M. (2011) The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. Acc. Chem. Res. 44, ) Quigley, G. J. and Rich, A. (1976) Structural domains of transfer RNA molecules. Science 194, ) Draper, D.E. (2004) A guide to ions and RNA structure. RNA 10, ) Watts, J.M, Dang, K.K., Gorelick, R.J., Leonard, C.W., Bess Jr., J.W., Swanstrom, R., Burch, C.L., and Weeks, K.M. (2009) Architecture and secondary structure of an entire HIV-1 RNA genome. Nature 460, ) Das, R., Karanicolas, J., and Baker, D. (2010) Atomic accuracy in predicting and designing noncanonical RNA structure. Nat. Meth. 7, Some examples of RNA structure 12) Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R., and Doudna, J. A. (1996) Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273, ) Cate, J.H., Hanna, R.L., and Doudna, J.A. (1997) A magnesium ion core at the heart of a ribozyme domain. Nat. Struct. Biol. 4,

3 14) Ke, A., Zhou, K., Ding, F., Cate, J.H.D., and Doudna, J.A.. (2004) A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature 429, Riboswitches and RNA sensors 15) Mandal, M. and Breaker, R.R. (2004) Gene regulation by riboswitches. Nat. Rev. Mol. Cell Biol. 5, ) Klein, D. J. and Ferre-Amare, A.R. (2006) Structural basis of glms ribozyme activation by glucosamine-6-phosphate. Science 313, ) Mandal, M., Lee, M., Barrick, J.E., Weinberg, Z., Emilsson, G.M., Ruzzo, W.L., and Breaker, R.R. (2004) A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306, ) Winkler, W.C., Nahvi, A., Roth, A., Collins, J.A., and Breaker, R.R. (2004) Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428, The RNA folding problem 19) Tinoco Jr., I. and Bustamante, C. (1999) How RNA folds. J. Mol. Biol. 293, ) Schroeder, R., Barta, A., and Semrad, K. (2004) Strategies for RNA folding and assembly. Nat. Rev. Molec. Cell Biol. 5, ) Treiber, D.K., Rook, M.S., Zarrinker, P.P., and Williamson, J.R. (1994) Kinetic intermediates trapped by native interactions in RNA folding. Science 279, ) Sclavi, B., Sullivan, M., Chance, M.R., Brenowitz, M., and Woodson, S.A. (1998) RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 279, ) Russell, R., Millett, I. S., Doniach, S., and Herschlag, D. (2000) Small angle x-ray scattering reveals a compact intermediate in RNA folding. Nat. Struct. Biol. 7, ) Chen, S.-J. and Dill, K.A. (2000) RNA folding energy landscapes. Proc. Natl. Acad. Sci. USA 97, ) Schultes, E.A,, Spasic, A., Mohanty, U., and Bartel,D.P. (2005) Compact and ordered collapse of randomly generated RNA sequences. Nat. Struct. Mol. Biol. 12, ) Greenleaf, W.J., Frieda, K.L., Foster, D.A.N., Woodside, M.T., and Block, S.M. (2008) Direct observation of hierarchical folding in single riboswitch aptamers. Science 319, ) Lee, M.-K., Gal, M., Frydman, L., and Varani, G. (2010) Real-rime multidimensional NMR follows RNA folding with second resolution. Proc. Natl. Acad. Sci. USA 107,

4 RNA chaperones 28) Herschlag, D. (1995) RNA chaperones and the RNA folding problem. J. Biol. Chem. 270, ) Weeks, K.M. and Cech, T.R. (1996) Assembly of a ribonucleoprotein catalyst by tertiary structure capture. Science 271, ) Clodi, E., Semrad, K., and Schroeder, R. (1999) Assaying RNA chaperone activity in vivo using a novel RNA folding trap. EMBO J. 18, ) Webb, A.E. and Weeks, K.M. (2001) A collapsed state functions to self-chaperone RNA folding into a native ribonucleoprotein complex. Nat. Struct. Biol. 8,

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