Salk Institute

Joyce Lab
Joyce Lab

Joyce Lab - Publications

Olea, C, Joyce GF (2016) Real-time detection of a self-replicating RNA enzyme, Molecules, Sep 30;21(10). pii: E1310. (Link)

Horning, DP, Joyce GF (2016) Amplification of RNA by an RNA polymerase ribozyme, PNAS, 113: 9786-9791 (Link)

Sczepanski JT, Joyce GF (2015) Specific inhibition of MicroRNA processing using L-RNA aptamers.  JACS 137:16032-16037 (Link)

Joyce GF  (2015) Reflections of a Darwinian engineer.  J. Mol. Evol. 81:145-149 (Link)

Olea C. Jr., Weidmann J, Dawson PE, Joyce GF (2015) An L-RNA aptamer that binds and inhibits ribonuclease. Chem Biol. 22:1437-1441 (Link)

Olea C. Jr., Joyce GF (2015) Ligand-dependent exponential amplification of self-replicating RNA enzymes. Methods Enzymol. 550:23-29. (Link)

Sczepanski JT, Joyce GF (2014) A cross-chiral RNA polymerase ribozyme. Nature 515:440-442 (Link)

Breaker RR, Joyce GF (2014) The expanding view of RNA and DNA function. Chem Biol. 21:1059-1065. (Link)

Petrie KL, Joyce GF (2014) Limits of neutral drift: lessons from the in vitro evolution of two ribozymes. J. Mol Evol. 79:75-90. (Link)

Robertson MP, Joyce GF (2014) Highly efficient self-replicating RNA enzymes.  Chem Biol. 21:238-245. (Link)

Sczepanski JT, Joyce GF (2013) Binding of a structured D-RNA molecule by an L-RNA aptamer.  J AM Chem Soc. 135:13290-13293. (Link)

Ferretti AC, Joyce GF (2013) Kinetic properties of an RNA enzyme that undergoes self-sustained exponential amplification.  Biochemistry. 52:1227-1235. (Link)

Sczepanski JT, Joyce GF (2012) Synthetic evolving systems that implement a user-specified genetic code of arbitrary design. Chem Biol. 19:1324-1332. (Link)

Joyce GF (2012) Bit by bit: the Darwinian basis of life. PLoS Biol. 10(5)e1001323.  Epub 2012 May 8. (Link)

Olea C, Horning DP, Joyce GF (2012) Ligand-dependent Exponential Amplification of a Self-replicating L-RNA Enzyme. J Am Chem Soc. 134:8050-8053. (Link)

Joyce GF. Evolution. (2012) Toward an alternative biology. Science. 336(6079):307-308. (Link)

Lam BJ, Joyce GF (2011) An isothermal system that couples ligand-dependent catalysis to ligand-independent exponential amplification. J Am Chem Soc. 133:3191-3197. (Link)

Robertson MP, Joyce GF (2012) The origins of the RNA world. Cold Spring Harb Perspect Biol. 4(5). pii: a003608. doi: 10.1101/cshperspect.a003608. (Link)

Petrie, KL and Joyce, GF (2010) Deep sequencing analysis of mutations resulting from the incorporation of dNTP analogs. Nucleic Acids Res. 38:2095-2104. (Link)

Paegel, BM and Joyce, GF (2010) Microfluidic compartmentalized directed evolution. Chem. Biol. 17:717-724. (Link)

Joyce, GF (2009) Evolution in an RNA world. Cold Spring Harbor Symp. Quant. Biol. 74:17-23. (Link)

Voytek, SB & Joyce, GF (2009) Niche partitioning in the coevolution of 2 distinct RNA enzymes. Proc. Natl. Acad. Sci. USA, 106:7780-7785. (Link)

Lam, BJ & Joyce, GF (2009) Autocatalytic aptazymes: ligand-dependent exponential amplification of RNA. Nature Biotechnol. 27:288-292. (Link)

Lincoln, TA & Joyce, GF (2009) Self-sustained replication of an RNA enzyme. Science. 323:1229-1232. (Link)

Paegel, BM & Joyce, GF (2008) Darwinian evolution on a chip. PLoS Biol. 6, 900–906. (Link)

Joyce, GF (2007) Leslie Orgel (1927–2007; obituary). Nature 450:627. (Link)

Voytek, SB & Joyce, GF (2007) Emergence of a fast-reacting ribozyme that is capable of undergoing continuous evolution. Proc. Natl. Acad. Sci. USA 104:15288–15293. (Link)

Joyce, GF (2007) Forty years of in vitro evolution. Angew. Chemie 46:6420–6436. (Link)

Joyce, GF (2007) A glimpse of biology’s first enzyme (commentary). Science 315:1507–1508. (Link)

Paegel, BM, Grover, WH, Skelley, AM, Mathies, RA & Joyce, GF (2006) Microfluidic serial dilution circuit. Anal. Chem., 78:7522–7527. (Link)

Paul, N, Springsteen, G & Joyce, GF (2006) Conversion of a ribozyme to a deoxyribozyme through in vitro evolution. Chem. & Biol. 13:329-338. (Link)

Joyce, GF (2006) “Foreward.” In The Aptamer Handbook, Klussman, S. (ed.), Wiley-VCH Verlag, Weinheim, Germany, pp. xix–xxi.

Joyce, GF & Orgel, LE (2006) “Progress toward understanding the origin of the RNA world.” In The RNA World, Third Edition, Gesteland, R.F., Cech, T.R. & Atkins, J.F. (eds.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 23–56.

Paegel, BM & Joyce, GF (2005) “Microfluidic serial transfer circuit: automated evolution of RNA catalysts.” In Ninth International Conference on Miniaturized Systems for Chemistry and Life Sciences, Jensen, K.F., Han, J., Harrison, D.J. & Voldman J. (eds), Transducer Research Foundation, Boston, MA, pp. 28–30.

Oberhuber, M & Joyce, GF (2005) A DNA-templated aldol reaction as a model for the formation of pentose sugars in the RNA world. Angew. Chem. Int. Ed. 44:7580-7583. (Link)

Johns, GC & Joyce, GF (2005) The promise and peril of continuous in vitro evolution. J. Mol. Evol. 61:253-263. (Link)

Kim, D-E. & Joyce, GF (2004) Cross-catalytic replication of an RNA ligase ribozyme. Chem. & Biol. 11:1505-1512. (Link)

Paul, N & Joyce, GF (2004) Minimal self-replicating system. Curr. Opin. Chem. Biol. 8:634-639. (Link)

Springsteen, G & Joyce, GF (2004) Selective derivatization and sequestration of ribose from a prebiotic mix. J. Am. Chem. Soc. 12:9578-9583. (Link)

Joyce, GF (2004) Directed evolution of nucleic acid enzymes. AR Reviews In Advance 73:791–836. (Link)

Shih, WM, Quispe, JD & Joyce, GF (2004) A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427:618–621. (Link)

Kuhne, H & Joyce, GF (2003) Continuous in vitro evolution of ribozymes that operate under conditions of extreme pH. J. Mol. Evol. 57:292–298. (Link)

Kumar, RM & Joyce, GF (2003) A modular, bifunctional RNA that integrates itself into a target RNA. Proc. Natl. Acad. Sci. USA 100:9738–9743. (Link)

Kuhns, S & Joyce, GF (2003) Perfectly complementary nucleic acid enzymes. J. of Mol. Evol. 56:711–717. (Link)

Paul, N & Joyce, GF (2003) Self-replication. Curr. Biol. 13, R46. (Link)

McGinness, KE & Joyce, GF (2003) In search of an RNA replicase ribozyme. Chem. & Bio. 10:5–14. (Link)

Reader, JS & Joyce, GF (2002) A ribozyme composed of only two different nucleotides. Nature 420:841–844. (Link)

Joyce, GF (2002) Booting up life. Nature 420:278–279. (Link)

Ordoukhanian, P & Joyce, GF (2002) RNA-cleaving DNA enzymes with altered regio- or enantio-selectivity. J. Am. Chem. Soc. 124:12499–12506. (Link)

Paul, N & Joyce, GF (2002) A self-replicating ligase ribozyme. Proc. Natl. Acad. Sci. USA 99:12733–12740. (Link)

Joyce, GF (2002) The antiquity of RNA based evolution. Nature Insight 418:214–221. (Link)

McGinness, KE, Wright, MC & Joyce, GF (2002) Continuous in vitro evolution of a ribozyme that catalyzes three successive nucleotidyl addition reactions. Chem. & Biol. 9:585–596. (Link)

McGinness, KE & Joyce, GF (2002) RNA-catalyzed RNA ligation on an external RNA template. Chem. & Biol. 9:297–307. (Link)

McGinness, KE & Joyce, GF (2002) Substitution of ribonucleotides in the T7 RNA polymerase promoter element. J. Biol. Chem. 7:2987–2991. (Link)

Rogers, J & Joyce, GF (2001) The effect of cytidine on the structure and function of an RNA ligase ribozyme. RNA 7:395–404. (Link)

Joyce, GF (2001) RNA cleavage by 10-23 DNA Enzyme. Methods in Enzymology 341:503–517. (Link)

Sheppard, TL, Wong, C & Joyce, GF (2000) Nucleoglycoconjugates: design and synthesis of a new class of DNA-carbohydrate conjugates. Angew. Chem. Int. Ed. 39:3660–3663. (Link)

Joyce, GF (2000) RNA structure: ribozyme evolution at the crossroads. Science 289:401–402. (Link)

Sheppard, TL, Ordoukhanian, P & Joyce, GF (2000) A DNA enzyme with N-glycosylase activity. Proc. Natl. Acad. Sci. USA 97:7802–7807. (Link)

Nowakowski, J, Shim, PJ, Stout, CD & Joyce, GF (2000) Alternative conformations of a nucleic acid four-way junction. J. Mol. Biol. 300:93–102. (Link)

Joyce, GF (2000) Employing DNAzymes to target bcr-abl mRNA in chronic myelogenous leukemia. Blood Cells, Molecules, and Diseases 26:60–61. (Link)

Santoro, SW, Joyce, GF, Sakthivel, K., Gramatikova, S. & Barbas, CF (2000) RNA cleavage by a DNA enzyme with protein-like functionality. J. Am. Chem. Soc. 122:2433–2439. (Link)

Ordoukhanian, P & Joyce, GF (1999) A molecular description of the evolution of resistance. Chem. Biol. 6:881–889. (Link)

Rogers, J & Joyce, GF (1999) A ribozyme that lacks cytidine. Nature 402:323–325. (Link)

Nowakowski, J, Shim, PJ, Joyce, GF & Stout, CD (1999) Crystallization of the 10-23 DNA enzyme using a combinatorial screen of paired oligonucleotides. Acta. Cryst. 55:1885–1892. (Link)

Joyce, GF (1999) The Counterforce. Curr. Biol. 9, R500–501. (Link)

Kumar, RM & Joyce, GF (1999) “Developing ribozymes for therapeutic application through in vitro evolution." In Intracellular Ribozyme Technology: Protocols and Applications, Horizon Scientific Press, Norfolk, England, 21–35.

Arrhenius, G, Bada, JL, Joyce, GF, Lazcano, A, Miller, S & Orgel, LE (1999) Origin and ancestor: separate environments (letter). Science 283: 792. (Link)

Nowakowski, J, Shim, PJ, Prasad, GS, Stout, CD & Joyce, GF (1999) Crystal structure of an 82-nucleotide RNA-DNA complex formed by the 10-23 DNA enzyme. Nature Struct. Biol. 6:151–156.(Link)

Joyce, GF & Orgel, LE (1999) “Prospects for Understanding the Origin of the RNA World." In The RNA World, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 49–77.

Joyce, GF (1999) “Appendix 3: Reactions Catalyzed by RNA and DNA Enzymes.” In The RNA World, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 687–689.

Santoro, SW & Joyce, GF (1998) Mechanisms and utility of an RNA-cleaving DNA enzyme. Biochemistry 37:13330–13342. (Link)

Joyce, GF (1998) Nucleic acid enzymes: Playing with a fuller deck. Proc. Natl. Acad. Sci. USA 95:5845–5847. (Link)

Joyce, GF & Orgel, LE (1998) The origins of life - a status report. Am. Biol. Teacher 60:No. 1, 10–12. (Link)

Bruick, RK, Koppitz, M, Joyce, GF & Orgel, LE (1997) A simple procedure for constructing 5'-amino-terminated oligodeoxynucleotides in aqueous solution. Nucleic Acids Res. 25:1309–1310. (Link)

Hendrix, M, Priestley, ES, Joyce, GF, & Wong, C (1997) Direct observation of aminoglycoside-RNA interactions by surface plasmon resonance. J. Am. Chem. Soc. 119:3641–3648. (Link)

Wright, MC & Joyce, GF (1997) Continuous in vitro evolution of catalytic function. Science 276:614–617. (Link)

Santoro, SW & Joyce, GF (1997) A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. USA 94:4262–4266. (Link)

Joyce, GF (1997) Evolutionary Chemistry: getting there from here (commentary). Science  276:1658–1659. (Link)

Bruick, RK, Dawson, PE, Kent, SBH, Usman, N & Joyce, GF (1996) Template-directed ligation of peptides to oligonucleotides. Chem. Biol. 3:49–56. (Link)

Joyce, GF (1996) Building the RNA world (commentary). Curr. Biol. 6:965–967. (Link)

Raillard, S.-A. & Joyce, G.F. (1996) Targeting sites within HIV-1 cDNA with a DNA-cleaving ribozyme. Biochemistry 36:11693–11701. (Link)

Tsang, J & Joyce, GF (1996) “In vitro evolution of randomized ribozymes.” In Methods in Enzymology, vol. 267, J. Abelson (ed.), Academic Press, Orlando, pp. 410–426.

Tsang, J & Joyce, GF (1996) Specialization of the DNA-cleaving activity of a group I ribozyme through in vitro evolution. J. Mol. Biol. 262:31–42. (Link)

Breaker, RR & Joyce, GF (1995) A DNA enzyme with Mg2+-dependent RNA phosphoesterase activity. Chem. Biol. 2:655–660. (Link)

Breaker, RR & Joyce, GF (1995) Self-incorporation of coenzymes by ribozymes. J. Mol. Evol. 40:551–558. (Link)

Dai, X, De Mesmaeker, A & Joyce, GF. (1995) Cleavage of an amide bond by a ribozyme. Science 267:237–240; see also Science 272:18–19, 1996. (Link)

Joyce, GF (1995) “The RNA world: life before DNA and protein” In Extraterrestrials, Where are They? B. Zuckerman & M.H. Hart (eds.), Cambridge University Press, Cambridge, 139–151.

Breaker, RR, Banerji, A & Joyce, GF (1994) Continuous in vitro evolution of bacteriophage RNA polymerase promoter elements. Biochemistry 33:11980–11986.(Link)

Breaker, RR & Joyce, GF (1994) A DNA enzyme that cleaves RNA. Chem. Biol. 1:223–229. (Link)

Breaker, RR & Joyce, GF (1994) Emergence of a replicating species from an in vitro RNA evolution reaction. Proc. Natl. Acad. Sci. USA 91:6093–6097. (Link)

Breaker, RR & Joyce, GF (1994) Inventing and improving ribozyme function: rational design versus iterative selection methods. Trends Biotechnol. 12:268–275.(Link)

Breaker, R.R. & Joyce, G.F. (1994) “Minimonsters: evolutionary byproducts of in vitro RNA amplification.” In Proceedings of the NATO Conference on Self-Reproduction of Supramolecular Structures, Maratea, Italy, September 12-16, 1993, G.R. Fleischaker, S. Colonna & P.L. Luisi (eds.), Kluwer Academic Press, Dordrecht, The Netherlands, pp. 127–135.

Cadwell, RC & Joyce, GF (1994) Mutagenic PCR. PCR Methods Appl. 3:S136–S140. (Link)

Chakrabarti, AC, Breaker, RR, Joyce, GF & Deamer, DW (1994) Production of RNA by a polymerase protein encapsulated within phospholipid vesicles. J. Mol. Evol. 39:555–559. (Link)

Joyce, GF (1994) “Foreward” In Origins of Life: The Central Concepts, D.W. Deamer & G.R. Fleischacker (eds.), Jones and Bartlett Publishers, Boston, pp. xi–xii.

Joyce, GF (1994) In vitro evolution of nucleic acids. Curr. Opin. Struct. Biol. 4:331–336. (Link)

Li, T, Zeng, Z, Estevez, VA, Baldenius, KU, Nicolaou, KC & Joyce, GF (1994) Carbohydrate minor groove interactions in the binding of calicheamicin g1I to duplex DNA. Journal of the American Chemical Society 116:3709–3715. (Link)

Tsang, J & Joyce, GF (1994) Evolutionary optimization of the catalytic properties of a DNA-cleaving ribozyme. Biochemistry 33:5966–5973. (Link)

Joyce, GF (1993) Climbing Darwin’s ladder (commentary). Current Biol. 3:703–704. (Link)

Joyce, GF (1993) Evolution of catalytic function. Pure & Appl. Chem. 65:1205–1212. (Link)

Joyce, GF & Orgel, LE (1993) “Prospects for understanding the origin of the RNA world.” In The RNA World, R.F. Gesteland & J.F. Atkins (eds.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1–25.

Lehman, N & Joyce, GF (1993) Evolution in vitro of an RNA enzyme with altered metal dependence. Nature 361:182–185. (Link)

Lehman, N & Joyce, GF (1993) In vitro evolution: Analysis of a lineage of ribozymes. Curr. Biol. 3:723–734. (Link)

Beaudry, AA & Joyce, GF (1992) Directed evolution of an RNA enzyme. Science 257:635–641. (Link)

Cadwell, RC & Joyce, GF (1992) Randomization of genes by PCR mutagenesis. PCR Methods Appl. 2:28–33. (Link)

Joyce, GF (1992) Directed molecular evolution. Sci. Am. 267:90–97.

Joyce GF (1992) “Selective amplification techniques for optimization of ribozyme function.” In Antisense RNA and DNA, J.A.H. Murray (ed.), Modern Cell Biology Series, Alan R. Liss, New York, 353–372.

Nicolaou, KC, Tsay, S-C, Suzuki, T & Joyce, GF (1992) DNA-carbohydrate interactions. Specific binding of the calicheamicin g1I oligosaccharide with duplex DNA. J. Amer. Chem. Soc. 114:7555–7557. (Link)

Joyce, GF (1991) RNA today (meeting review), New Biologist 3:565–569.

Joyce, GF (1991) The rise and fall of the RNA world, New Biologist 3:399–407.

Robertson, DL & Joyce, GF (1991) “The catalytic potential of RNA.” In Molecular Evolution on Rugged Landscapes: Proteins, RNA and the Immune System, A.S. Perelson & S.A. Kauffman (eds.), Santa Fe Institute Studies in the Sciences of Complexity, vol. 8, Addison-Wesley, Redwood City, 265–277.

Beaudry, AA & Joyce, GF (1990) Minimum secondary structure requirements for catalytic activity of a self-splicing group I intron. Biochemistry 29:6534–6539. (Link)

Joyce, GF (1990) In the beginning (book review). Nature 346:806. (Link)

Robertson, DL & Joyce, GF (1990) Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344:467–468. (Link)

Joyce, GF (1989) Amplification, mutation, and selection of catalytic RNA. Gene 82:83–87. (Link)

Joyce, GF (1989) “Building the RNA world: evolution of catalytic RNA in the laboratory.” In Molecular Biology of RNA, T.R. Cech (ed.), UCLA Symposia on Molecular and Cellular Biology, vol. 94, Alan R. Liss, New York, 361–37.

Joyce, GF (1989) RNA evolution and the origins of life. Nature 33:217–224.

Joyce, GF & Inoue, T (1989) A novel technique for the rapid preparation of mutant RNAs. Nucleic Acids Res. 17, 711–722. (Link)

Joyce, GF, van der Horst, G & Inoue, T (1989) Catalytic activity is retained in the Tetrahymena group I intron despite removal of the large extension of element P5. Nucleic Acids Res. 17:7879–7889. (Link)

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