Abstract
RNA and DNA molecules can form complex, three-dimensional folded structures that have surprisingly sophisticated functions, including catalysing chemical reactions and controlling gene expression. Although natural nucleic acids make occasional use of these advanced functions, the true potential for sophisticated function by these biological polymers is far greater. An important challenge for biochemists is to take RNA and DNA beyond their proven use as polymers that form double-helical structures. Molecular engineers are beginning to harness the power of nucleic acids that form more complex three-dimensional structures, and apply them as tools for exploring biological systems and as therapeutics.
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References
Kolkman, J. A. & Stemmer, P. C. Directed evolution of proteins by exon shuffling. Nature Biotechnol. 19, 423–428 (2001).
Zhao, H., Chockalingam, K. & Chen, Z. Directed evolution of enzymes and pathways for industrial biocatalysis. Curr. Opin. Biotechnol. 13, 104–110 (2002).
Joyce, G. F. Directed evolution of nucleic acid enzymes. Annu. Rev. Biochem. 73, 791–836 (2004).
Wilson, D. S. & Szostak, J. W. In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68, 611–647 (1999).
McPherson, M. J. & Møller, S. G. PCR (Springer, New York, 2000).
Dykxhoorn, D. M., Novina, C. D. & Sharp, P. A. Killing the messenger: short RNAs that silence gene expression. Nature Rev. Mol. Cell Biol. 23, 1961–1967 (2003).
Novina, C. D. & Sharp, P. A. The RNAi revolution. Nature 430, 161–164 (2004).
Khudyakov, Y. E. & Fields, H. A. Artificial DNA: methods and applications (CRC, Boca Raton, Florida, 2002).
Muller, S., Wolf, J. & Ivanov, S. A. Current strategies for the synthesis of RNA. Curr. Org. Syn. 1, 293–307 (2004).
Milligan, J. F. & Uhlenbeck, O. C. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180, 51–62 (1989).
Watson, J. D. & Crick, F. H. C. Molecular structure of nucleic acids. Nature 171, 737–738 (1953).
Uhlenbeck, O. C. A small catalytic oligoribonucleotide. Nature 328, 596–600 (1989).
Nissen, P., Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920–930 (2000).
Steitz, T. A. & Moore, P. B. RNA, the first macromolecular catalyst: the ribosome is a ribozyme. Trends Biochem. Sci. 28, 411–418 (2003).
Stein, C. A. & Krieg, A. M. Applied Antisense Oligonucleotide Technology. (eds Stein, C. A. & Krieg, A. M.) (Wiley, New York, 1998).
Crooke, S. T. Progress in antisense technology. Annu. Rev. Med. 55, 61–95 (2004).
Reese, C. B. & Yan, H. B. Solution phase synthesis of ISIS 2922 (Vitravene) by the modified H-phosphonate approach. J. Chem. Soc. Perkins Trans. 1, 2619–2633 (2002).
Holmlund, J. T. Applying antisense technology. Ann. NY Acad. Sci. 1002, 244–251 (2003).
Meister, G. & Tuschl, T. Mechanisms of gene silencing by double-stranded RNA. Nature 431, 343–349 (2004).
Eaton, B. E. & Pieken, W. A. Ribonucleosides and RNA. Annu. Rev. Biochem. 64, 837–863 (1995).
Sarafianos, S. G., Hughes, S. H. & Arnold, E. Designing anti-AIDS drugs targeting the major mechanism of HIV-1 RT resistance to nucleoside analog drugs. Int. J. Biochem. Cell Biol. 36, 1706–1715 (2004).
Gold, L., Polisky, B., Uhlenbeck, O. & Yarus, M. Diversity of oligonucleotide functions. Annu. Rev. Biochem. 64, 763–797 (1995).
Osborne, S. E. & Ellington, A. D. Nucleic acid selection and the challenge of combinatorial chemistry. Chem. Rev. 97, 349–370 (1997).
Koizumi, M., Soukup, G. A., Kerr, J. N. Q. & Breaker, R. R. Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nature Struct. Biol. 6, 1062–1071 (1999).
Soukup, G. A., DeRose, E. C., Koizumi, M. & Breaker, R. R. Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes. RNA 7, 524–536 (2001).
Jayasena, S. D. Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin. Chem. 9, 1628–1650 (1999).
Brockstedt, U., Uzarowska, A., Montpetit, A., Pfau, W. & Labuda, D. In vitro evolution of RNA aptamers recognizing carcinogenic aromatic amines. Biochem. Biophys. Res. Commun. 313, 1004–1008 (2004).
Sayer, N. M. et al. Structural determinants of conformationally selective, prion-binding aptamers. J. Biol. Chem. 279, 13102–13109 (2004).
Romig, T. S., Bell, C. & Drolet, D. W. Aptamer affinity chromatography: combinatorial chemistry applied to protein purification. J. Chromatogr. B. Biomed. Sci. Appl. 731, 275–284 (1999).
Deng, Q., German, I., Buchanan, D. & Kennedy, R. T. Retention and separation of adenosine and analogues by affinity chromatography with an aptamer stationary phase. Anal. Chem. 73, 5415–5421 (2001).
Hermann, T. & Patel, D. J. Adaptive recognition by nucleic acid aptamers. Science 287, 820–825 (2000).
Hamaguchi, N., Ellington, A. & Stanton, M. Aptamer beacons for the direct detection of proteins. Anal. Biochem. 294, 126–131 (2001).
McCauley, T. G., Hamaguchi, N. & Stanton, M. Aptamer-based biosensor arrays for detection and quantification of biological macromolecules. Anal. Biochem. 319, 244–250 (2003).
Jhaveri, S., Rajendran, M. & Ellington, A. D. In vitro selection of signaling aptamers. Nature Biotechnol. 18, 1293–1297 (2000).
Peracchi, A. Prospects for antiviral ribozymes and deoxyribozymes. Rev. Med. Virol. 14, 47–64 (2004).
Opalinska, J. B. & Gewirtz, A. M. Nucleic acid therapeutics: basic principles and recent applications. Nature Rev. Drug Disc. 1, 503–514 (2002).
Lin, Y., Qiu, Q., Gill, C. & Jayasena, S. D. Modified RNA sequence pools for in vitro selection. Nucleic Acids Res. 22, 5229–5234 (1994).
Beaudry, A., DeFoe, J., Zinnen, S., Burgin, A. & Beigelman, L. In vitro selection of a novel nuclease-resistant RNA phosphodiesterase. Chem. Biol. 7, 323–334 (2000).
Famulok, M. & Verma, S. In vivo-applied functional RNAs as tools in proteomics and genomics research. Trends Biotechnol. 20, 462–466 (2002).
Toulmé, J. -J., Di Primo, C. & Boucard, D. Regulating eukaryotic gene expression with aptamers. FEBS Lett. 567, 55–62 (2004).
Homann, M. & Göringer, H. U. Uptake and intracellular transport of RNA aptamers in African trypanosomes suggests therapeutic ‘piggy-back’ approach. Bioorg. Med. Chem. 9, 2571–2580 (2001).
Vater, A. & Klussmann, S. Towards third-generation aptamers: spiegelmers and their therapeutic prospects. Curr. Opin. Drug Disc. Devel. 6, 253–261 (2003).
Eulberg, D. & Klussmann, S. Spiegelmeers: biostable aptamers. Chembiochem. 4, 979–983 (2003).
Nolte, A., Klussmann, S., Bald, R., Erdmann, V. A. & Furste, J. P. Mirror-design of L-oligonucleotide ligands binding to L-arginine. Nature Biotechnol. 14, 1112–1115 (1996).
Cox, J. C. & Ellington, A. D. Automated selection of anti-protein aptamers. Bioorg. Med. Chem. 9, 2525–2531 (2001).
Sooter, L. J. et al. Towards automated nucleic acid enzyme selection. Biol. Chem. 9, 1327–1334 (2001).
Cox, J. C. et al. Automated acquisition of aptamer sequences. Comb. Chem. High Throughput Screen. 4, 289–299 (2002).
Cox, J. C. et al. Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. Nucleic Acids Res. 30, e108 (2002).
Csaky, K. Anti-vascular endothelial growth factor therapy for neovascular age-related macular degeneration: promises and pitfalls. Ophthalmology 110, 879–881 (2003).
Boncler, M. A., Koziolkiewicz, M. & Watala, C. Aptamer inhibits degradation of platelet proteolytically activatable receptor, PAR-1, by thrombin. Thromb. Res. 104, 215–222 (2002).
Rusconi, C. P. et al. RNA aptamers as reversible antagonists of coagulation factor IXa. Nature 419, 90–94 (2002).
Nissen, P., Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. The structural basis of ribosomal activity in peptide bond synthesis. Science 289, 920–930 (2000).
Hansen, J. L. et al. The structures of four macrolide antibiotics bound to the large ribosomal subunit. Mol. Cell 10, 117–128 (2002).
Hansen, J. L., Moore, P. B. & Steitz, T. A. Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit. J. Mol. Biol. 330, 1061–1075 (2003).
Schlünzen, F. et al. Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 413, 814–821 (2001).
Bagheri, S. & Kashani-Sabet, M. Ribozymes in the age of molecular therapeutics. Curr. Mol. Med. 4, 489–506 (2004).
Kawa, D., Wang, J., Yuan, Y. & Liu, F. Inhibition of viral gene expression by human ribonuclease P. RNA 4, 1397–1406 (1998).
Plehn-Dujowich, D. & Altman, S. Effective inhibition of influenza production in cultured cells by external guide sequences and ribonuclease P. Proc. Natl Acad. Sci. USA 95, 7327–7331 (1998).
Rangarajan, S., Raj, M. L. S., Hernandez, J. M., Grotewold, E. & Gopalan, V. RNase P as a tool for disruption of gene expression in maize cells. Biomed. J. 380, 611–616 (2004).
Byun, J., Lan, N., Long, M. & Sullenger, B. A. Efficient and specific repair of sickle beta-globin RNA by trans-splicing ribozymes. RNA 9, 1254–1263 (2003).
Sullenger, B. A. & Gilboa, E. Emerging clinical applications of RNA. Nature 418, 252–258 (2002).
Perutka, J., Wang, W. J., Goerlitz, D. & Lambowitz, A. M. Use of computer-designed group II introns to disrupt Escherichia coli DExH/D-box protein and DNA helicase genes. J. Mol. Biol. 336, 421–439 (2004).
Jarvis, T. C. et al. Ribozymes as tools for therapeutic target validation in arthritis. J. Immunol. 165, 493–498 (2000).
Wilson, C. & Szostak, J. W. In vitro evolution of a self-alkylating ribozyme. Nature 374, 777–782 (1995).
Unrau, P. J. & Bartel, D. P. RNA-catalysed nucleotide synthesis. Nature 395, 260–263 (1998).
Baskerville, S. & Bartel, D. P. A ribozyme that ligates RNA to protein. Proc. Natl Acad. Sci. USA 99, 9154–9159 (2002).
Tang, J. & Breaker, R. R. Structural diversity of self-cleaving ribozymes. Proc. Natl Acad. Sci. USA 97, 5784–5789 (2000).
Lazarev, D., Puskarz, I. & Breaker, R. R. Substrate specificity and reaction kinetics of an X-motif ribozyme. RNA 9, 688–697 (2003).
Emilsson, G. M. & Breaker, R. R. Deoxyribozymes: new activities and new applications. Cell. Mol. Life Sci. 59, 596–607 (2002).
Santoro, S. W. & Joyce, G. F. A general purpose RNA-cleaving DNA enzyme. Proc. Natl Acad. Sci. USA 94, 4262–4266 (1997).
Santoro, S. W. & Joyce, G. F. Mechanism and utility of an RNA-cleaving DNA enzyme. Biochemistry 37, 13330–13342 (1998).
Santiago, F. S. et al. New DNA enzyme targeting Erg-1 mRNA inhibits vascular smooth muscle proliferation and regrowth after injury. Nature Med. 5, 1264–1269 (1999).
Santiago, F. S. & Khachigian, L. M. Nucleic acid based strategies as potential therapeutic tools: mechanistic considerations and implications to restenosis. J. Mol. Med. 79, 695–706 (2001).
Li, Y. & Breaker, R. R. Phosphorylating DNA with DNA. Proc. Natl Acad. Sci. USA 96, 2746–2751 (1999).
Wang, W., Billen, L. P. & Li, Y. Sequence diversity, metal specificity, and catalytic proficiency of metal-dependent phosphorylating DNA enzymes. Chem. Biol. 9, 507–517 (2002).
Sreedhara, A., Li, Y. F. & Breaker, R. R. Ligating DNA with DNA. J. Am. Chem. Soc. 126, 3454–3460 (2004).
Uhlenbeck, O. C. Keeping RNA happy. RNA 1, 4–6 (1995).
Jiang, F., Kumar, R. A., Jones, R. A. & Patel, D. J. Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature 382, 183–186 (1996).
Soukup, G. A. & Breaker, R. R. Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5, 1308–1325 (1999).
Tang, J. & Breaker, R. R. Rational design of allosteric ribozymes. Chem. Biol. 4, 453–459 (1997).
Breaker, R. R. Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol. 13, 31–39 (2002).
Silverman, S. K. Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA. RNA 9, 377–383 (2003).
Seetharaman, S., Zivarts, M., Sudarsan, N. & Breaker, R. R. Immobilized switches for the analysis of complex chemical and biological mixtures. Nature Biotechnol. 19, 336–341 (2001).
Hesselberth, J. R., Robertson, M. P., Knudsen, S. M. & Ellington, A. D. Simultaneous detection of diverse analytes with an aptazyme ligase array. Anal. Biochem. 312, 106–112 (2003).
Vaish, N. K. et al. Zeptomole detection of a viral nucleic acid using a target-activated ribozymes. RNA 9, 1058–1072 (2003).
Kossen, K. et al. High-throughput ribozyme-based assays for detection of viral nucleic acids. Chem. Biol. 11, 807–815 (2004).
Srinivasan, J. et al. ADP-specific sensors enable universal assay of protein kinase assay. Chem. Biol. 11, 499–508 (2004).
Ferguson, A. et al. A novel strategy for selection of allosteric ribozymes yields RiboReporter™ sensors for caffeine and aspartame. Nucleic Acids Res. 32, 1756–1766 (2004).
Najafi-Shoushtari, S. H., Mayer, G. & Famulok, M. Sensing complex regulatory networks by conformationally controlled hairpin ribozymes. Nucleic Acids Res. 32, 3212–3219 (2004).
Hartig, J. S. et al. Protein-dependent ribozymes report molecular interactions in real time. Nature Biotechnol. 20, 717–722 (2002).
Mandal, M. & Breaker, R. R. Gene regulation by riboswitches. Nature Rev. Mol. Cell Biol. 5, 451–463 (2004).
Barrick, J. E. et al. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl Acad. Sci. USA 101, 6421–6426 (2004).
Nahvi, A. et al. Genetic control by a metabolite binding mRNA. Chem. Biol. 9, 1043–1049 (2002).
Winkler, W., Nahvi, A. & Breaker, R. R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419, 952–956 (2002).
Mandal, M., Boese, B., Barrick, J. E., Winkler, W. C. & Breaker, R. R. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113, 577–586 (2003).
Mandal, M. & Breaker, R. R. Adenine riboswitches and gene activation by disruption of a transcription terminator. Nature Struct. Mol. Biol. 11, 29–35 (2004).
Johansen, L. E., Nygaard, P., Lassen, C., Agerso, Y. & Saxild, H. H. Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA) and pbuE (ydhL). J. Bacteriol. 185, 5200–5209 (2003).
Werstuck, G. & Green, M. R. Controlling gene expression in living cells through small molecule-RNA interactions. Science 282, 296–298 (1998).
Grate, D. & Wilson, C. Inducible regulation of the S. cerevisiae cell cycle mediated by an RNA aptamer-ligand complex. Bioorg. Med. Chem. 9, 2565–2570 (2001).
Harvey, I., Garneau, P. & Pelletier, J. Inhibition of translation by RNA-small molecule interactions. RNA 8, 452–463 (2002).
Suess, B. et al. Conditional gene expression by controlling translation with tetracycline-binding aptamers. Nucleic Acids Res. 31, 1853–1858 (2003).
Hanson, S., Berthelot, K., Fink, B., McCarthy, J. E. G. & Suess, B. Tetracycline-aptamer-mediated translational regulation in yeast. Mol. Microbiol. 49, 1627–1637 (2003).
Suess, B., Fink, B., Berens, C., Stenz, R. & Hillen, W. A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Res. 32, 1610–1614 (2004).
Sudarsan, N., Barrick, J. E. & Breaker, R. R. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9, 644–647 (2003).
Sudarsan, N., Wickiser, J. K., Nakamura, S., Ebert, M. S. & Breaker, R. R. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev. 17, 2688–2697 (2003).
Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A. & Breaker, R. R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428, 281–286 (2004).
Kawasaki, H. & Taira, K. Identification of genes by hybrid ribozymes that couple cleavage activity with the unwinding activity of an endogenous RNA helicase. EMBO Rep. 3, 443–450 (2002).
Rhoades, K. & Wong-Staal, F. Inverse Genomics™ as a powerful tool to identify novel targets for the treatment of neurodegenerative diseases. Mech. Age. Dev. 124, 125–132 (2003).
Gruenert, D. C. et al. Sequence-specific modification of genomic DNA by small DNA fragments. J. Clin. Invest. 112, 637–641 (2003).
Walther, W. & Stein, U. Viral vectors for gene transfer: a review of their use in the treatment of human diseases. Drugs 60, 249–271 (2000).
Kuan, J. Y. & Glazer, P. M. Targeted gene modification using triplex-forming oligonucleotides. Methods Mol. Biol. 262, 173–194 (2004).
Long, M. B., Jones, J. P., Sullenger, B. A. & Byun, J. Ribozyme-mediated revision of RNA and DNA. J. Clin. Invest. 112, 312–318 (2003).
Garcia-Blanco, M. A., Baraniak, A. P. & Lasda, E. L. Alternative splicing in disease and therapy. Nature Biotechnol. 22, 535–546 (2004).
Gusarov, I. & Nudler, E. The mechanism of intrinsic transcription termination. Mol. Cell 3, 495–504 (1999).
Yarnell, W. S. & Roberts, J. W. Mechanism of intrinsic transcription termination and antitermination. Science 284, 611–615 (1999).
Acknowledgements
Nucleic acids research in the Breaker laboratory is supported by the David and Lucile Packard Foundation, NIH and NSF.
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R. Breaker is a cofounder of Archemix, which holds intellectual property in RiboReporter and aptamer technologies.
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Breaker, R. Natural and engineered nucleic acids as tools to explore biology. Nature 432, 838–845 (2004). https://doi.org/10.1038/nature03195
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DOI: https://doi.org/10.1038/nature03195
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