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Chapter 28: Protein-dependent Ribozymes as Reporters of Protein–Protein Interactions—References

Beaucage S.L., Bergstrom D.E., Glick G.D., and Jones R.A., eds. 2003a. Synthesis of unmodified oligonucleotides. In Current protocols in nucleic acid chemistry, vol. 1, pp. 3.0.1–3.10.15. Wiley, New York.

Beaucage S.L., Bergstrom D.E., Glick G.D., and Jones R.A. 2003b. Synthesis of modified oligonucleotides and conjugates. In Current protocols in nucleic acid chemistry, vol. 1, pp. 4.0.1–4.24.26. Wiley, New York.

Breaker R.R. 2002. Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol. 13: 31–39.

Cox J.C. and Ellington A.D. 2001. Automated selection of anti-protein aptamers. Bioorg. Med. Chem. 9: 2525–2531.

Cox J.C., Hayhurst A., Hesselberth J., Bayer T.S., Georgiou G., and Ellington A.D. 2002. Automated selection of aptamers against protein targets translated in vitro: From gene to aptamer. Nucleic Acids Res. 30: e108.

Hartig J.S. and Famulok M. 2002. Reporter ribozymes for real-time analysis of domain-specific interactions in biomolecules: HIV-1 reverse transcriptase and the primer-template complex. Angew. Chem. Int. Ed. 41: 4263–4266.

Hartig J.S., Grune I., Najafi-Shoushtari S.H., and Famulok M. 2004. Sequence-specific detection of MicroRNAs by signal-amplifying ribozymes. J. Am. Chem. Soc. 126: 722–723.

Hartig J.S., Najafi-Shoushtari S.H., Grune I., Yan A., Ellington A.D., and Famulok M. 2002. Protein-dependent ribozymes report molecular interactions in real time. Nat. Biotechnol. 20: 717–722.

Hertel K.J., Herschlag D., and Uhlenbeck O.C. 1994. A kinetic and thermodynamic framework for the hammerhead ribozyme reaction. Biochemistry 33: 3374–3385.

Hertel K.J., Stage-Zimmermann T.K., Ammons G., and Uhlenbeck O.C. 1998. Thermodynamic dissection of the substrate-ribozyme interaction in the hammerhead ribozyme. Biochemistry 37: 16983–16988.

Jaeger J., Restle T., and Steitz T.A. 1998. The structure of HIV-1 reverse transcriptase complexed with an RNA pseudoknot inhibitor. EMBO J. 17: 4535–4542.

Jenne A., Gmelin W., Raffler N., and Famulok M. 1999. Real-time characterization of ribozymes by fluorescence resonance energy transfer (FRET). Angew. Chem. Int. Ed. 38: 1300–1303.

Jenne A., Hartig J.S., Piganeau N., Tauer A., Samarsky D.A., Green M.R., Davies J., and Famulok M. 2001. Rapid identification and characterization of hammerhead-ribozyme inhibitors using fluorescence-based technology. Nat. Biotechnol. 19: 56–61.

Joyce G.F. 1994. In vitro evolution of nucleic acids. Curr. Opin. Struct. Biol. 4: 331–336.

Kawasaki H. and Taira K. 2001. Discovery of functional genes in the post-genome era by novel RNA-protein hybrid ribozymes. Nucleic Acids Res. Suppl. 2001: 133–134.

Kensch O., Connolly B.A., Steinhoff H.J., McGregor A., Goody R.S., and Restle T. 2000. HIV-1 reverse transcriptase-pseudoknot RNA aptamer interaction has a binding affinity in the low picomolar range coupled with high specificity. J. Biol. Chem. 275: 18271–18278.

Kertsburg A. and Soukup G.A. 2002. A versatile communication module for controlling RNA folding and catalysis. Nucleic Acids Res. 30: 4599–4606.

Klug S.J. and Famulok M. 1994. All you wanted to know about SELEX. Mol. Biol. Rep. 20: 97–107.

Koizumi M., Soukup G.A., Kerr J.N., and Breaker R.R. 1999. Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nat. Struct. Biol. 6: 1062–1071.

Najafi-Shoushtari S.H., Mayer G., and Famulok M. 2004. Sensing complex regulatory networks by conformationally controlled hairpin ribozymes. Nucleic Acids Res. 32: 3212–3219.

Piganeau N., Thuillier V., and Famulok M. 2001a. In vitro selection of allosteric ribozymes: Theory and experimental validation. J. Mol. Biol. 312: 1177–1190.

Piganeau N., Jenne A., Thuillier V., and Famulok M. 2001b. An allosteric ribozyme regulated by doxycycline. Angew. Chem. Int. Ed. 40: 3503.

Sambrook J. and Russell D.W. 2001. Molecular cloning: A laboratory manual, 3rd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

Seetharaman S., Zivarts M., Sudarsan N., and Breaker R.R. 2001. Immobilized RNA switches for the analysis of complex chemical and biological mixtures. Nat. Biotechnol. 19: 336–341.

Soukup G.A. and Breaker R.R. 1999. Engineering precision RNA molecular switches. Proc. Natl. Acad. Sci. 96: 3584–3589.

Soukup G.A., Emilsson G.A., and Breaker R.R. 2000. Altering molecular recognition of RNA aptamers by allosteric selection. J. Mol. Biol. 298: 623–632.

Stage-Zimmermann T.K. and Uhlenbeck O.C. 1998. Hammerhead ribozyme kinetics. RNA 4: 875–889.

Stojanovic M.N. and Stefanovic D. 2003. A deoxyribozyme-based molecular automaton. Nat. Biotechnol. 21: 1069–1074.

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Takagi Y., Suyama E., Kawasaki H., Miyagishi M., and Taira K. 2002. Mechanism of action of hammerhead ribozymes and their applications in vivo: Rapid identification of functional genes in the post-genome era by novel hybrid ribozyme libraries. Biochem. Soc. Trans. 30: 1145–1149.

Tang J. and Breaker R.R. 2000. Structural diversity of self-cleaving ribozymes. Proc. Natl. Acad. Sci. 97: 5784–5789.

Tuerk C., MacDougal S., and Gold L. 1992. RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc. Natl. Acad. Sci. 89: 6988–6992.

Vaish N.K., Kore A.R., and Eckstein F. 1998. Recent developments in the hammerhead ribozyme field. Nucleic Acids Res. 26: 5237–5242.

Vaish N.K., Dong F., Andrews L., Schweppe R.E., Ahn N.G., Blatt L., and Seiwert S.D. 2002. Monitoring post-translational modification of proteins with allosteric ribozymes. Nat. Biotechnol. 20: 810–815.

Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31: 3406–3415.

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