Substrate 2′-Hydroxyl Groups Required for Ribozyme-Catalyzed Polymerization
Open accessAbstract
A polymerase ribozyme has been generated that uses nucleoside triphosphates to elongate an RNA primer by the successive addition of nucleotides complementary to an RNA template. Its polymerization is accurate, with an average error rate less than 3%, and it is general in terms of the sequence and the length of the primer and template RNAs. To begin to understand how the substrate contacts contribute to this accurate and general activity, we investigated which primer and template 2'-hydroxyl groups are involved in substrate recognition. We identified eight positions where 2'-deoxy substitutions can influence polymerization kinetics. All eight are within five nucleotides of the primer 3' terminus. Some, but not all, of the 2'-deoxy effects appear to be sequence dependent. These results begin to build a picture of how the polymerase ribozyme recognizes its substrates.
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The crystal structure of the Class I RNA ligase suggests that this linker sequence is positioned to interact with the downstream RNA template and could strengthen the ribozyme's sequence-general contacts with the upstream duplex, enhancing primer/template binding.
“Examination of the crystal structure of the Class I RNA ligase29,30, from which the catalytic core of the ribozyme polymerase is derived, suggests this sequence is well-positioned to interact with the downstream RNA template (Fig. 3a), and could augment the sequence-general contacts the ribozyme makes with the upstream duplex16,29,31 to enhance primer/template binding.”
From In-ice evolution of RNA polymerase ribozyme activity (2013) · cites this paper as [31]
Cites
Principles of Nucleic Acid Structure
Neidle, S., & Sanderson, M. (2008) · Elsevier eBooks · doi:10.1016/b978-0-12-369507-9.x5001-8 · Cited by 4,519 · see citing works
Kruger, K., Grabowski, P. J., Zaug, A. J., Sands, J., Gottschling, D. E., & Cech, T. R. (1982) · Cell · doi:10.1016/0092-8674(82)90414-7 · Cited by 2,331 · see citing works
The origin of the genetic code
Crick, F. H. C. (1968) · Journal of Molecular Biology · doi:10.1016/0022-2836(68)90392-6 · Cited by 2,320 · see citing works
Gilbert, W. (1986) · Nature · Cited by 1,941 · see citing works
Szostak, J. W., Bartel, D. P., & Luisi, P. L. (2001) · Nature · doi:10.1038/35053176 · Cited by 1,681 · see citing works
Self-citationPrinciples of Nucleic Acid Structure
Parish, J. (1985) · Biochemical Education · doi:10.1016/0307-4412(85)90046-9 · Cited by 1,496 · see citing works
Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing
Cate, J. H. D., Gooding, A. R., Podell, E. R., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R., & Doudna, J. A. (1996) · Science · doi:10.1126/science.273.5282.1678 · Cited by 1,249 · see citing works
Evolution of the genetic apparatus
Orgel, L. E. (1968) · Journal of Molecular Biology · doi:10.1016/0022-2836(68)90393-8 · Cited by 996 · see citing works
Isolation of New Ribozymes from a Large Pool of Random Sequences
Bartel, D. P., & Szostak, J. W. (1993) · Science · doi:10.1126/science.7690155 · Cited by 900 · see citing works
Self-citationRNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension.
Johnston, W. K., Unrau, P. J., Lawrence, M. S., Glasner, M. E., & Bartel, D. P. (2001) · Science · doi:10.1126/science.1060786 · Cited by 768 · see citing works
Self-citationRNA tertiary interactions in the large ribosomal subunit: The A-minor motif
Nissen, P., Ippolito, J. A., Ban, N., Moore, P. B., & Steitz, T. A. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.081082398 · Cited by 659 · see citing works
A conserved double-stranded RNA-binding domain.
Johnston, D. S., Brown, N. H., Gall, J. G., & Jantsch, M. F. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.22.10979 · Cited by 537 · see citing works
RIBONUCLEASE P: Unity and Diversity in a tRNA Processing Ribozyme
Frank, D. N., & Pace, N. R. (1998) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.67.1.153 · Cited by 465 · see citing works
RNA-catalysed RNA polymerization using nucleoside triphosphates
Ekland, E. H., & Bartel, D. P. (1996) · Nature · doi:10.1038/382373a0 · Cited by 250 · see citing works
Self-citationProteins binding to duplexed RNA: one motif, multiple functions
Fierro-Monti, I., & Mathews, M. B. (2000) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)01580-2 · Cited by 243 · see citing works
Bevilacqua, P. C., & Cech, T. R. (1996) · Biochemistry · doi:10.1021/bi9607259 · Cited by 227 · see citing works
1 Prospects for Understanding the Origin of the RNA World
Joyce, G. F., & Orgel, L. E. (1993) · doi:10.1101/087969380.24.1 · Cited by 214 · see citing works
The Proton: Applications to Organic Chemistry
(1985) · Organic chemistry · doi:10.1016/b978-0-12-670370-2.x5001-4 · Cited by 195 · see citing works
Three metal ions at the active site of the Tetrahymena group I ribozyme
Shan, S., Yoshida, A., Sun, S., Piccirilli, J. A., & Herschlag, D. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.22.12299 · Cited by 170 · see citing works
Ribozyme recognition of RNA by tertiary interactions with specific ribose 2′-OH groups
Pyle, A. M., & Cech, T. R. (1991) · Nature · doi:10.1038/350628a0 · Cited by 166 · see citing works
Multiple RNA binding domains (RBDs) just don't add up
Shamoo, Y. E., Abdul-Manan, N., & Williams, K. R. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.5.725 · Cited by 141 · see citing works
The topology of the transcription regulatory network in the yeast, Saccharomyces cerevisiae
Farkas, I. J., Jeong, H., Vicsek, T., Barabási, A.-Ĺ., & Oltvai, Z. N. (2003) · Physica A Statistical Mechanics and its Applications · doi:10.1016/s0378-4371(02)01731-4 · Cited by 133 · see citing works
Poliovirus RNA-dependent RNA Polymerase (3Dpol)
Arnold, J. J., Ghosh, S. K. B., & Cameron, C. E. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.52.37060 · Cited by 125 · see citing works
Izatt, R. M., Rytting, J. H., Hansen, L. D., & Christensen, J. J. (1966) · Journal of the American Chemical Society · doi:10.1021/ja00964a003 · Cited by 121 · see citing works
Woese, C. R. (1968) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.59.1.110 · Cited by 115 · see citing works
RNA structure, not sequence, determines the 5' splice-site specificity of a group I intron.
Doudna, J. A., Cormack, B. P., & Szostak, J. W. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.19.7402 · Cited by 113 · see citing works
Sequence and Structural Conservation in RNA Ribose Zippers
Tamura, M., & Holbrook, S. R. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00515-6 · Cited by 109 · see citing works
Bevilacqua, P. C., & Turner, D. H. (1991) · Biochemistry · doi:10.1021/bi00108a005 · Cited by 107 · see citing works
Energetics and Cooperativity of Tertiary Hydrogen Bonds in RNA Structure
Silverman, S. K., & Cech, T. R. (1999) · Biochemistry · doi:10.1021/bi9906118 · Cited by 102 · see citing works
Strobel, S. A., & Cech, T. R. (1993) · Biochemistry · doi:10.1021/bi00212a027 · Cited by 100 · see citing works
Herschlag, D., Eckstein, F., & Cech, T. R. (1993) · Biochemistry · doi:10.1021/bi00083a034 · Cited by 96 · see citing works
A minor groove RNA triple helix within the catalytic core of a group I intron
Szewczak, A. A., Ortoleva-Donnelly, L., Ryder, S., Moncoeur, E., & Strobel, S. A. (1998) · Nature Structural Biology · doi:10.1038/4146 · Cited by 93 · see citing works
Kirsebom, L. A., & Svärd, S. G. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.3.425 · Cited by 84 · see citing works
DeRose, V. J. (2002) · Chemistry & Biology · doi:10.1016/s1074-5521(02)00217-x · Cited by 72 · see citing works
Artificial ribozymes and deoxyribozymes
Jäschke, A. (2001) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00208-6 · Cited by 69 · see citing works
Processivity of Ribozyme-Catalyzed RNA Polymerization
Lawrence, M. S., & Bartel, D. P. (2003) · Biochemistry · doi:10.1021/bi034228l · Cited by 62 · see citing works
Self-citationMellema, J. ‐., HAASNOOT, C. A. G., van der Marel, G. A., Wille, G., van Boeckel, C. A. A., BOOM, J. H. V., & ALTONA, C. (1983) · Nucleic Acids Research · doi:10.1093/nar/11.16.5717 · Cited by 50 · see citing works
Narlikar, G. J., Khosla, M., Usman, N., & Herschlag, D. (1997) · Biochemistry · doi:10.1021/bi9610820 · Cited by 46 · see citing works
Kim, M.-J., Zhong, W., Hong, Z., & Kao, C. C. (2000) · Journal of Virology · doi:10.1128/jvi.74.22.10312-10322.2000 · Cited by 38 · see citing works
Siegel, R. W., Bellon, L., Beigelman, L. N., & Kao, C. C. (1999) · Journal of Virology · doi:10.1128/jvi.73.8.6424-6429.1999 · Cited by 33 · see citing works
Thermodynamics of 2′-ribose substitutions in UUCG tetraloops
Williams, D. J., Boots, J. L., & Hall, K. B. (2001) · RNA · doi:10.1017/s1355838201001558 · Cited by 32 · see citing works
Lindqvist, M., Sarkar, M., Winqvist, A., Rozners, E., Strömberg, R., & Gräslund, A. (2000) · Biochemistry · doi:10.1021/bi992055n · Cited by 26 · see citing works
Abelson, J. N. (1982) · Nature · doi:10.1038/300400a0 · Cited by 22 · see citing works
Completion of RNA synthesis by viral RNA replicases
Tayon, R. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.17.3576 · Cited by 19 · see citing works
The contribution of 2'-hydroxyls to the cleavage activity of the Neurospora VS ribozyme
Sood, V. D. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.5.1132 · Cited by 18 · see citing works
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In-ice evolution of RNA polymerase ribozyme activity
Attwater, J., Wochner, A., & Holliger, P. (2013) · Nature Chemistry · doi:10.1038/nchem.1781 · Cited by 279 · see citing works
“The G93A and C97A mutations that provide the main cold-specific activity boost are located in the single-stranded linker region of the ribozyme between the catalytic core (1-90) and the processivity domain (105-187).”
BackgroundWolf, Y. I., & Koonin, E. V. (2007) · Biology Direct · doi:10.1186/1745-6150-2-14 · Cited by 235 · see citing works
The origin of replicators and reproducers
Szathmáry, E. (2006) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2006.1912 · Cited by 197 · see citing works
Real ribozymes suggest a relaxed error threshold
Kun, Á., Santos, M., & Szathmáry, E. (2005) · Nature Genetics · doi:10.1038/ng1621 · Cited by 151 · see citing works
Crystal Structure of the Catalytic Core of an RNA-Polymerase Ribozyme
Shechner, D. M., Grant, R. A., Bagby, S. C., Koldobskaya, Y., Piccirilli, J. A., & Bartel, D. P. (2009) · Science · doi:10.1126/science.1174676 · Cited by 136 · see citing works
Self-citationMüller, U. F. (2006) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-006-6047-1 · Cited by 79 · see citing works
Self-citationNew ligase-derived RNA polymerase ribozymes
LAWRENCE, M. S., & BARTEL, D. P. (2005) · RNA · doi:10.1261/rna.2110905 · Cited by 68 · see citing works
Self-citationRNA Synthesis by in Vitro Selected Ribozymes for Recreating an RNA World
Martin, L. L., Unrau, P. J., & Müller, U. (2015) · Life · doi:10.3390/life5010247 · Cited by 47 · see citing works
Self-citationImproved polymerase ribozyme efficiency on hydrophobic assemblies
Müller, U. F., & Bartel, D. P. (2008) · RNA · doi:10.1261/rna.494508 · Cited by 46 · see citing works
Self-citationA small polymerase ribozyme that can synthesize itself and its complementary strand
Gianni, E., Kwok, S., Wan, C. J. K., Goeij, K., Clifton, B. E., Colizzi, E. S., Attwater, J., & Holliger, P. (2026) · Science · doi:10.1126/science.adt2760 · Cited by 36 · see citing works
Chemical fidelity of an RNA polymerase ribozyme
Attwater, J., Tagami, S., Kimoto, M., Butler, K., Kool, E. T., Wengel, J., Herdewijn, P., Hirao, I., & Holliger, P. (2013) · Chemical Science · doi:10.1039/c3sc50574j · Cited by 33 · see citing works
Darwinian chemistry: towards the synthesis of a simple cell
Loakes, D., & Holliger, P. (2009) · Molecular BioSystems · doi:10.1039/b904024b · Cited by 31 · see citing works
3′-End labeling of nucleic acids by a polymerase ribozyme
Samanta, B., Horning, D. P., & Joyce, G. F. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky513 · Cited by 29 · see citing works
Abiogenesis through gradual evolution of autocatalysis into template‐based replication
Pavlinova, P., Lambert, C. N., Malaterre, C., & Nghe, P. (2022) · FEBS Letters · doi:10.1002/1873-3468.14507 · Cited by 26 · see citing works
RNA-Catalyzed Polymerization of Deoxyribose, Threose, and Arabinose Nucleic Acids
Horning, D. P., Bala, S., Chaput, J. C., & Joyce, G. F. (2019) · ACS Synthetic Biology · doi:10.1021/acssynbio.9b00044 · Cited by 25 · see citing works
Bagby, S. C., Bergman, N. H., Shechner, D. M., Yen, C. C., & Bartel, D. P. (2009) · RNA · doi:10.1261/rna.1912509 · Cited by 19 · see citing works
Self-citationRibose 2′-Hydroxyl Groups Stabilize RNA Hairpin Structures Containing GCUAA Pentaloop
Paladino, A., & Zangi, R. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct3006216 · Cited by 12 · see citing works
Polymerase ribozyme efficiency increased by G/T-rich DNA oligonucleotides
Yao, C., & Müller, U. F. (2011) · RNA · doi:10.1261/rna.2726811 · Cited by 8 · see citing works
Self-citationRNA Polymerase Ribozyme That Recognizes the Template–Primer Complex through Tertiary Interactions
Kakoti, A., & Joyce, G. F. (2023) · Biochemistry · doi:10.1021/acs.biochem.3c00091 · Cited by 7 · see citing works
Propensities for loop structures of RNA & DNA backbones
Paladino, A., & Zangi, R. (2013) · Biophysical Chemistry · doi:10.1016/j.bpc.2013.07.003 · Cited by 7 · see citing works
RNA Replication and the RNA Polymerase Ribozyme
Wachowius, F., & Holliger, P. (2021) · Wiley eBooks · doi:10.1002/9783527814527.ch13 · Cited by 7 · see citing works
The NTP binding site of the polymerase ribozyme
Akoopie, A., & Müller, U. F. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky898 · Cited by 6 · see citing works
Self-citationEmergent and Convergent Features in the Laboratory Evolution of Polymerase Ribozymes
Horning, D. P. (2025) · Biochemistry · doi:10.1021/acs.biochem.5c00160 · Cited by 5 · see citing works
Dhar, N., Weinberg, M. S., Michod, R. E., & Durand, P. M. (2017) · Royal Society Open Science · doi:10.1098/rsos.170376 · Cited by 2 · see citing works
Arginine Cofactors on the Polymerase Ribozyme
Yao, C., Moretti, J. E., Struss, P. E., Spall, J. A., & Müller, U. F. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025030 · Cited by 2 · see citing works
Self-citationCopolymersequenzen, Selbstreproduktion und genetischer Code
Kricheldorf, H. R. (2019) · Springer eBooks · doi:10.1007/978-3-662-57978-7_8
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Kricheldorf, H. R. (2025) · Springer eBooks · doi:10.1007/978-3-662-70752-4_8
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Pavlinova, P. (2024) · theses.fr (ABES) · doi:10.70675/d7ccf328zdd57z4a26za426z2d0498b9b3b5
- Authors
- Müller, U. F., & Bartel, D. P.
- Affiliations
- Whitehead Institute for Biomedical Research (US)
- Corresponding author
- Bartel, David P.
- Venue
- Chemistry & Biology
- Publisher
- Elsevier BV
- Published
- 2003-09
- Volume
- 10
- Issue
- 9
- Pages
- 799-806
- ISSN
- 1074-5521 (ISSN-L)
- OpenAlex
- W2078089564
- Cited by
- 30
- References
- 48
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 2 · 2023: 1 · 2022: 1 · 2021: 1 · 2019: 2 · 2018: 3 · 2017: 1 · 2015: 1 · 2013: 4
- FWCI
- 0.46
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 3607 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Chemistry & Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (R01-GM61835, R01GM061835)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Keywords
- RNA polymerization, 2'-hydroxyl group, substrate recognition, nucleoside triphosphates, polymerization kinetics, sequence dependence, RNA template, RNA primers
- MeSH terms
- Catalysis, Kinetics, RNA, RNA Nucleotidyltransferases, RNA, Double-Stranded, Structure-Activity Relationship, Substrate Specificity, Templates, Genetic, RNA, Catalytic, Hydroxyl Radical
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