The Hammerhead Ribozyme: Structure, Catalysis, and Gene Regulation - Progress in Molecular Biology and Translational Science - page 21

26. Dahm SC, Derrick WB, Uhlenbeck OC. Evidence for the role of solvated metal
hydroxide in the hammerhead cleavage mechanism. Biochemistry . 1993;32:

13040-13045.
27. Bassi GS, Mollegaard NE, Murchie AI, et al. RNA folding and misfolding of the ham-
merhead ribozyme. Biochemistry . 1999;38:3345-3354.
28. Bassi GS, Mollegaard NE, Murchie AI, et al. Ionic interactions and the global confor-
mations of the hammerhead ribozyme. Nat Struct Biol . 1995;2:45-55.
29. Bassi GS, Murchie AI, Lilley DM. The ion-induced folding of the hammerhead ribo-
zyme: core sequence changes that perturb folding into the active conformation.
RNA . 1996;2:756-768.
30. Bassi GS, Murchie AI, Walter F, et al. Ion-induced folding of the hammerhead ribozyme:
a fluorescence resonance energy transfer study. EMBO J . 1997;16:7481-7489.
31. Hammann C, Cooper A, Lilley DM. Thermodynamics of ion-induced RNA folding in
the hammerhead ribozyme: an isothermal titration calorimetric study. Biochemistry .
2001;40:1423-1429.
32. Hammann C, Lilley DM. Folding and activity of the hammerhead ribozyme.

Chembiochem . 2002;3:690-700.
33. Hammann C, Norman DG, Lilley DM. Dissection of the ion-induced folding of the
hammerhead ribozyme using 19F NMR. Proc Natl Acad Sci USA . 2001;98:5503-5508.
34. Penedo JC, Wilson TJ, Jayasena SD, et al. Folding of the natural hammerhead ribozyme
is enhanced by interaction of auxiliary elements. RNA . 2004;10:880-888.
35. Zhou JM, Zhou DM, Takagi Y, et al. Existence of efficient divalent metal ion-catalyzed
and inefficient divalent metal ion-independent channels in reactions catalyzed by a ham-
merhead ribozyme. Nucleic Acids Res . 2002;30:2374-2382.
36. Murray JB, Seyhan AA, Walter NG, et al. The hammerhead, hairpin and VS ribozymes
are catalytically proficient in monovalent cations alone. Chem Biol . 1998;5:587-595.
37. Murray JB, Terwey DP, Maloney L, et al. The structural basis of hammerhead ribozyme
self-cleavage. Cell . 1998;92:665-673.
38. Murray JB, Dunham CM, Scott WG. A pH-dependent conformational change, rather
than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage
reaction. J Mol Biol . 2002;315:121-130.
39. Rupert PB, Massey AP, Sigurdsson ST, et al. Transition state stabilization by a catalytic
RNA. Science . 2002;298:1421-1424.
40. Rupert PB, Ferr´-D'Amar´ AR. Crystal structure of a hairpin ribozyme-inhibitor com-
plex with implications for catalysis. Nature . 2001;410:780-786.
41. Martick M, Scott WG. Tertiary contacts distant from the active site prime a ribozyme for
catalysis. Cell . 2006;126:309-320.
42. Ferre-D'Amare AR, Zhou K, Doudna JA. A general module for RNA crystallization.
J Mol Biol . 1998;279:621-631.
43. Ke A, Zhou K, Ding F, et al. A conformational switch controls hepatitis delta virus ribo-
zyme catalysis. Nature . 2004;429:201-205.
44. Scott WG, Murray JB, Arnold JR, et al. Capturing the structure of a catalytic RNA
intermediate: the hammerhead ribozyme. Science . 1996;274:2065-2069.
45. Han J, Burke JM. Model for general acid-base catalysis by the hammerhead ribozyme:
pH-activity relationships of G8 and G12 variants at the putative active site. Biochemistry .
2005;44:7864-7870.
46. Heckman JE, Lambert D, Burke JM. Photocrosslinking detects a compact, active struc-
ture of the hammerhead ribozyme. Biochemistry . 2005;44:4148-4156.
47. Hertel KJ, Herschlag D, Uhlenbeck OC. A kinetic and thermodynamic framework for
the hammerhead ribozyme reaction. Biochemistry . 1994;33:3374-3385.
48. Stage-Zimmermann TK, Uhlenbeck OC. Hammerhead ribozyme kinetics. RNA .
1998;4:875-889.