Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 85

35. Chen S-J. RNA folding: conformational statistics, folding kinetics, and ion electrostat-
ics. Annu Rev Biophys. 2008;37:197-214.
36. Hashem Y, Auffinger P. A short guide for molecular dynamics simulations of RNA
systems. Methods . 2009;47:187-197.
37. Forster AC, Symons RH. Self-cleavage of plus and minus RNAs of a virusoid and a
structural model for the active sites. Cell . 1987;49:211-220.
38. Scott WG. Biophysical and biochemical investigations of RNA catalysis in the ham-
merhead ribozyme. Q Rev Biophys. 1999;32:241-294.
39. Blount KF, Uhlenbeck OC. The hammerhead ribozyme. Biochem Soc Trans.
2002;30:1119-1122.
40. Scott WG. RNA catalysis. Curr Opin Struct Biol. 1998;8:720-726.
41. Scott WG. Ribozymes. Curr Opin Struct Biol. 2007;17:280-286.
42. Doherty EA, Doudna JA. Ribozyme structures and mechanisms. Annu Rev Biophys
Biomol Struct. 2001;30:457-475.
43. Rios AC, Tor Y. Model systems: how chemical biologists study RNA. Curr Opin Chem
Biol. 2009;13:660-668.
44. Cochrane JC, Strobel SA. Catalytic strategies of self-cleaving ribozymes. Acc Chem Res.
2008;41:1027-1035.
45. Bevilacqua PC, Yajima R. Nucleobase catalysis in ribozyme mechanism. Curr Opin
Chem Biol. 2006;10:455-464.
46. Sarver N, Cantin EM, Chang PS, et al. Ribozymes as potential anti-HIV-1 therapeutic
agents. Science . 1990;247:1222-1225.
47. Michienzi A, Cagnon L, Bahner I, Rossi JJ. Ribozyme-mediated inhibition of HIV 1
suggests nucleolar trafficking of HIV-1 RNA. Proc Natl Acad Sci USA.

2000;97:8955-8960.
48. Nazari R, Ma XZ, Joshi S. Inhibition of human immunodeficiency virus-1 entry using
vectors expressing a multimeric hammerhead ribozyme targeting the CCR5 mRNA.
J Gen Virol. 2008;89:2252-2261.
49. Unwalla HJ, Li H, Li S-Y, Abad D, Rossi JJ. Use of a U16 snoRNA-containing ribo-
zyme library to identify ribozyme targets in HIV-1. Mol Ther. 2008;16:1113-1119.
50. Snyder DS, Wu Y, Wang JL, et al. Ribozyme-mediated inhibition of bcr-abl gene
expression in a Philadelphia chromosome-positive cell line. Blood . 1993;82:600-605.
51. Feng Y, Kong YY, Wang Y, Qi GR. Intracellular inhibition of the replication of hep-
atitis B virus by hammerhead ribozymes. J Gastroenterol Hepatol. 2001;16:1125-1130.
52. Weinberg M, Passman M, Kew M, Arbuthnot P. Hammerhead ribozyme-mediated
inhibition of hepatitis B virus X gene expression in cultured cells. J Hepatol.

2000;33:142-151.
53. Sano M, Taira K. Hammerhead ribozyme-based target discovery. Methods Mol Biol.
2007;360:143-153.
54. Weinberg MS, Ely A, Passman M, Mufamadi SM, Arbuthnot P. Effective anti-hepatitis
B virus hammerhead ribozymes derived from multimeric precursors. Oligonucleotides .
2007;17:104-112.
55. Ferbeyre G, Bourdeau V, Pageau M, Miramontes P, Cedergren R. Distribution of
hammerhead and hammerhead-like RNA motifs through the GenBank. Genome
Res. 2000;10:1011-1019.
56. Martick M, Horan LH, Noller HF, Scott WG. A discontinuous hammerhead ribozyme
embedded in a mammalian messenger RNA. Nature . 2008;454:899-902.
57. Takagi Y, Ikeda Y, Taira K. Ribozyme mechanisms. Top Curr Chem. 2004;232:213-251.
58. Shepotinovskaya IV, Uhlenbeck OC. Catalytic diversity of extended hammerhead
ribozymes. Biochemistry . 2008;47:7034-7042.
59. Thomas JM, Perrin DM. Probing general base catalysis in the hammerhead ribozyme.
J Am Chem Soc. 2008;130:15467-15475.