References
- K. Chin, K. Sharp, B. Honig and A.M. Pyle, Calculating the electrostatic properties of RNA provides
new insights into molecular interactions and function, Nat. Struct. Biol., 1999, 6 , 1055–1061. - M. Egli, S. Portmann and N. Usman, RNA hydration: a detailed look, Biochemistry, 1996, 35 ,
8489–8494. - N.B. Leontis, J. Stombaugh and E. Westhof, The non-Watson–Crick pairs and their isostericity matri-
ces, Nucleic Acids Res., 2002, 30 , 3497–3531. - V. Biou, A. Yaremchuck, M. Tukalo and S. Cusack, The 2.9 Å crystal structure of T. thermophilus
seryl-tRNA synthetase complexed with tRNA(Ser), Science, 1994, 263 , 1404–1410. - N. Ban, P. Nissen, J. Hansen, P.B. Moore and T.A. Steitz, The complete atomic structure of the large
ribosomal subunit at 2.4 Å resolution, Science, 2000, 289 , 905–920. - L. Su, L. Chen, M. Egli, J.M. Berger and A. Rich, RNA triplex in the structure of ribosomal
frameshifting viral pseudoknot, Nat. Struct. Biol., 1999, 3 , 285–292. - C. Baugh, D. Grate and C. Wilson, 2.8 Å crystal structure of the malachite green aptamer, J. Mol.
Biol., 2000, 301 , 117–128. - L. Gold, B. Polisky, O.C. Uhlenbeck and M. Yarus, Diversity of oligonucleotide functions, Ann. Rev.
Biochem., 1995, 64 , 763–797. - J.H. Cate, A.R. Gooding, E. Podell, K. Zhou, B.L. Golden, C.E. Kundrot, T.R. Cech and J.A. Doudna,
Crystal structure of a group I ribozyme domain reveals principles of higher order RNA folding,
Science, 1996, 273 , 1678–1685. - P. Nissen, J.A. Ippolito, N. Ban, P.B. Moore and T.A. Steitz, RNA tertiary interactions in the large
ribosomal subunit: the A-minor motif, Proc. Natl. Acad. Sci. USA, 2001, 98 , 4899–4903. - F.L. Murphy, Y.-H. Wang, J.D. Griffith and T.R. Cech, Coaxially stacked RNA helices in the
catalytic center of the Tetrahymenaribozyme, Science, 1994, 265 , 1709–1712. - E.A. Doherty, R.T. Batey, B. Masquida and J.A. Doudna, A universal mode of helix packing in RNA,
Nat. Struct. Biol., 2001, 8 , 339–343. - A.R. Ferre-D’amare, K. Zhou and J.A. Doudna, Crystal structure of a hepatitis delta virus ribozyme,
Nature, 1998, 395 , 567–574. - V.K. Misra and D.E. Draper, On the role of magnesium ions in RNA stability, Biopolymers, 1998, 48 ,
113–135. - A.M. Pyle, The role of metal ions in ribozymes. In Metal Ions in Biological Systems, H. Sigel and
A. Sigel (eds). Marcel Dekker, Inc., New York, 1996, 479–519. - R. Shiman and D. Draper, Stabilization of RNA tertiary structure by monovalent cations, J. Mol. Biol.,
2000, 302 , 79–91. - R.K.O. Sigel, A. Vaidya and A.M. Pyle, Metal ion binding sites in a group II intron core, Nat. Struct.
Biol., 2000, 7 , 1111–1116. - S. Basu, R.P. Rambo, J. Strauss-Soukup, J.H. Cate, A. Ferre-D’Amare, S.A. Strobel and J.A. Doudna,
A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor, Nat.
Struct. Biol., 1998, 5 , 986–992. - J.H. Cate, A.R. Gooding, E. Podell, K. Zhou, B.L. Golden, A.A. Szewczak, C.E. Kundrot, T.R. Cech
and J.A. Doudna, RNA tertiary structure mediation by adenosine platforms, Science, 1996, 273 ,
1696–1699. - T.R. Sosnick and T. Pan, RNA folding: models and perspectives, Curr. Opin. Struct. Biol., 2003,
13 , 309–316. - R. Schroeder, R. Grossberger, A. Pichler and C. Waldsich, RNA folding in vivo, Curr. Opin. Struct.
Biol., 2002, 12 , 296–300. - S.H. Kim, G. Quigley, F.L. Suddath, A. McPherson, D. Sneden, J.J. Kim, J. Weinzierl, P. Blattman and
A. Rich, The three-dimensional structure of yeast transfer RNA: shape of the molecule at 5.5Å reso-
lution, Proc. Natl. Acad. Sci. USA, 1972, 69 , 3746–3750.
290 Chapter 7