2454 Nucleic Acids Research, 2006, Vol. 34, No. 8 37. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406–3415. 38. Ordoukhanian,P. and Joyce,G.F. (2002) RNA-cleaving DNA enzymes with altered regio- or enantioselectivity. J. Am. Chem. Soc., 124, 12499–12506. 39. Esteban,J.A., Banerjee,A.R. and Burke,J.M. (1997) Kinetic mechanism of the hairpin ribozyme. Identification and characterization of two nonexchangeable conformations. J. Biol. Chem., 272, 13629–13639. 40. Esteban,J.A., Walter,N.G., Kotzorek,G., Heckman,J.E. and Burke,J.M. (1998) Structural basis for heterogeneous kinetics: reengineering the hairpin ribozyme. Proc. Natl Acad. Sci. USA, 95, 6091–6096. 41. Schlosser,K. and Li,Y. (2005) Diverse evolutionary trajectories characterize a community of RNA-cleaving deoxyribozymes: a case study into the population dynamics of in vitro selection. J. Mol. Evol., 61, 192–206. 42. Legiewicz,M., Lozupone,C., Knight,R. and Yarus,M. (2005) Size, constant sequences, and optimal selection. RNA, 11, 1701–1709. 43. Lozupone,C., Changayil,S., Majerfeld,I. and Yarus,M. (2003) Selection of the simplest RNA that binds isoleucine. RNA, 9, 1315–1322. 44. Nutiu,R. and Li,Y. (2005) In vitro selection of structure-switching signaling aptamers. Angew Chem. Int. Ed. Engl., 44, 1061–1065. 45. Salehi-Ashtiani,K. and Szostak,J.W. (2001) In vitro evolution suggests multiple origins for the hammerhead ribozyme. Nature, 414, 82–84. 46. Tang,J. and Breaker,R.R. (2000) Structural diversity of self-cleaving ribozymes. Proc. Natl Acad. Sci. USA, 97, 5784–5789. 47. Lehman,N. (2004) Assessing the likelihood of recurrence during RNA evolution in vitro. Artif Life, 10, 1–22. 48. Breaker,R.R. and Joyce,G.F. (1994) A DNA enzyme that cleaves RNA. Chem. Biol., 1, 223–229. 49. Breaker,R.R. and Joyce,G.F. (1995) A DNA enzyme with Mg(2+)- dependent RNA phosphoesterase activity. Chem. Biol., 2, 655–660. 50. Carrigan,M.A., Ricardo,A., Ang,D.N. and Benner,S.A. (2004) Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection. Biochemistry, 43, 11446–11459. 51. Feldman,A.R. and Sen,D. (2001) A new and efficient DNA enzyme for the sequence-specific cleavage of RNA. J. Mol. Biol., 313, 283–294. 52. Geyer,C.R. and Sen,D. (1997) Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme. Chem. Biol., 4, 579–593. 53. Santoro,S.W., Joyce,G.F., Sakthivel,K., Gramatikova,S. and Barbas,C.F.,IIIrd. (2000) RNA cleavage by a DNA enzyme with extended chemical functionality. J. Am. Chem. Soc., 122, 2433–2439. 54. Roth,A. and Breaker,R.R. (1998) An amino acid as a cofactor for a catalytic polynucleotide. Proc. Natl Acad. Sci. USA, 95, 6027–6031. 55. Nelson,K.E., Bruesehoff,P.J. and Lu,Y. (2005) In vitro selection of high temperature Zn(2+)-dependent DNAzymes. J. Mol. Evol., 61, 216–225. 56. Sidorov,A.V., Grasby,J.A. and Williams,D.M. (2004) Sequence-specific cleavage of RNA in the absence of divalent metal ions by a DNAzyme incorporating imidazolyl and amino functionalities. Nucleic Acids Res., 32, 1591–1601. 57. Perrin,D.M., Garestier,T. and Helene,C. (2001) Bridging the gap between proteins and nucleic acids: a metal-independent RNAseA mimic with two protein-like functionalities. J. Am. Chem. Soc., 123, 1556–1563. 58. Bruesehoff,P.J., Li,J., Augustine,A.J. 3rd and Lu,Y. (2002) Improving metal ion specificity during in vitro selection of catalytic DNA. Comb Chem High Throughput Screen, 5, 327–335. 59. Gevertz,J., Gan,H.H. and Schlick,T. (2005) In vitro RNA random pools are not structurally diverse: a computational analysis. RNA, 11, 853–863. 60. Cox,J.C., Rudolph,P. and Ellington,A.D. (1998) Automated RNA selection. Biotechnol. Prog., 14, 845–850. 61. Cox,J.C., Rajendran,M., Riedel,T., Davidson,E.A., Sooter,L.J., Bayer,T.S., Schmitz-Brown,M. and Ellington,A.D. (2002) Automated acquisition of aptamer sequences. Comb Chem. High Throughput Screen, 5, 289–299. 62. Drolet,D.W., Jenison,R.D., Smith,D.E., Pratt,D. and Hicke,B.J. (1999) A high throughput platform for systematic evolution of ligands by exponential enrichment (SELEX). Comb Chem. High Throughput Screen, 2, 271–278. 63. Eulberg,D., Buchner,K., Maasch,C. and Klussmann,S. (2005) Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonist. Nucleic Acids Res., 33, e45. 64. Johns,G.C. and Joyce,G.F. (2005) The promise and peril of continuous in vitro evolution. J. Mol. Evol., 61, 253–263.