1
|
Jia X, Fang Z, Kim SC, Ding D, Zhou L, Szostak JW. Diaminopurine in Nonenzymatic RNA Template Copying. J Am Chem Soc 2024; 146:15897-15907. [PMID: 38818863 PMCID: PMC11177312 DOI: 10.1021/jacs.4c02560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/07/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
In the RNA World before the emergence of an RNA polymerase, nonenzymatic template copying would have been essential for the transmission of genetic information. However, the products of chemical copying with the canonical nucleotides (A, U, C, and G) are heavily biased toward the incorporation of G and C, which form a more stable base pair than A and U. We therefore asked whether replacing adenine (A) with diaminopurine (D) might lead to more efficient and less biased nonenzymatic template copying by making a stronger version of the A:U pair. As expected, primer extension substrates containing D bound to U in the template more tightly than substrates containing A. However, primer extension with D exhibited elevated reaction rates on a C template, leading to concerns about fidelity. Our crystallographic studies revealed the nature of the D:C mismatch by showing that D can form a wobble-type base pair with C. We then asked whether competition with G would decrease the mismatched primer extension. We performed nonenzymatic primer extension with all four activated nucleotides on randomized RNA templates containing all four letters and used deep sequencing to analyze the products. We found that the DUCG genetic system exhibited a more even product distribution and a lower mismatch frequency than the canonical AUCG system. Furthermore, primer extension is greatly reduced following all mismatches, including the D:C mismatch. Our study suggests that D deserves further attention for its possible role in the RNA World and as a potentially useful component of artificial nonenzymatic RNA replication systems.
Collapse
Affiliation(s)
- Xiwen Jia
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Ziyuan Fang
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Seohyun Chris Kim
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Dian Ding
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Lijun Zhou
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn
Institute
for RNA Innovation, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
2
|
Jia X, Zhang SJ, Zhou L, Szostak J. Constraints on the emergence of RNA through non-templated primer extension with mixtures of potentially prebiotic nucleotides. Nucleic Acids Res 2024; 52:5451-5464. [PMID: 38726871 PMCID: PMC11162797 DOI: 10.1093/nar/gkae355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/10/2024] [Accepted: 04/22/2024] [Indexed: 06/11/2024] Open
Abstract
The emergence of RNA on the early Earth is likely to have been influenced by chemical and physical processes that acted to filter out various alternative nucleic acids. For example, UV photostability is thought to have favored the survival of the canonical nucleotides. In a recent proposal for the prebiotic synthesis of the building blocks of RNA, ribonucleotides share a common pathway with arabino- and threo-nucleotides. We have therefore investigated non-templated primer extension with 2-aminoimidazole-activated forms of these alternative nucleotides to see if the synthesis of the first oligonucleotides might have been biased in favor of RNA. We show that non-templated primer extension occurs predominantly through 5'-5' imidazolium-bridged dinucleotides, echoing the mechanism of template-directed primer extension. Ribo- and arabino-nucleotides exhibited comparable rates and yields of non-templated primer extension, whereas threo-nucleotides showed lower reactivity. Competition experiments confirmed the bias against the incorporation of threo-nucleotides. The incorporation of an arabino-nucleotide at the end of the primer acts as a chain terminator and blocks subsequent extension. These biases, coupled with potentially selective prebiotic synthesis, and the templated copying that is known to favour the incorporation of ribonucleotides, provide a plausible model for the effective exclusion of arabino- and threo-nucleotides from primordial oligonucleotides.
Collapse
Affiliation(s)
- Xiwen Jia
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Stephanie J Zhang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Lijun Zhou
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute for RNA Innovation, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
3
|
Callaghan KL, Sherrell PC, Ellis AV. The Impact of Activating Agents on Non-Enzymatic Nucleic Acid Extension Reactions. Chembiochem 2024; 25:e202300859. [PMID: 38282207 DOI: 10.1002/cbic.202300859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/21/2024] [Accepted: 01/28/2024] [Indexed: 01/30/2024]
Abstract
Non-enzymatic template-directed primer extension is increasingly being studied for the production of RNA and DNA. These reactions benefit from producing RNA or DNA in an aqueous, protecting group free system, without the need for expensive enzymes. However, these primer extension reactions suffer from a lack of fidelity, low reaction rates, low overall yields, and short primer extension lengths. This review outlines a detailed mechanistic pathway for non-enzymatic template-directed primer extension and presents a review of the thermodynamic driving forces involved in entropic templating. Through the lens of entropic templating, the rate and fidelity of a reaction are shown to be intrinsically linked to the reactivity of the activating agent used. Thus, a strategy is discussed for the optimization of non-enzymatic template-directed primer extension, providing a path towards cost-effective in vitro synthesis of RNA and DNA.
Collapse
Affiliation(s)
- Kimberley L Callaghan
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Peter C Sherrell
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
- School of Science, RMIT University, Melbourne, Victoria, 3000, Australia
| | - Amanda V Ellis
- Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria, 3010, Australia
| |
Collapse
|
4
|
Todisco M, Ding D, Szostak JW. Transient states during the annealing of mismatched and bulged oligonucleotides. Nucleic Acids Res 2024; 52:2174-2187. [PMID: 38348869 PMCID: PMC10954449 DOI: 10.1093/nar/gkae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/19/2024] [Accepted: 01/29/2024] [Indexed: 03/22/2024] Open
Abstract
Oligonucleotide hybridization is crucial in various biological, prebiotic and nanotechnological processes, including gene regulation, non-enzymatic primer extension and DNA nanodevice assembly. Although extensive research has focused on the thermodynamics and kinetics of nucleic acid hybridization, the behavior of complex mixtures and the outcome of competition for target binding remain less well understood. In this study, we investigate the impact of mismatches and bulges in a 12 bp DNA or RNA duplex on its association (kon) and dissociation (koff) kinetics. We find that such defects have relatively small effects on the association kinetics, while the dissociation kinetics vary in a position-dependent manner by up to 6 orders of magnitude. Building upon this observation, we explored a competition scenario involving multiple oligonucleotides, and observed a transient low specificity of probe hybridization to fully versus partially complementary targets in solution. We characterize these long-lived metastable states and their evolution toward equilibrium, and show that sufficiently long-lived mis-paired duplexes can serve as substrates for prebiotically relevant chemical copying reactions. Our results suggest that transient low accuracy states may spontaneously emerge within all complex nucleic acid systems comprising a large enough number of competing strands, with potential repercussions for gene regulation in the realm of modern biology and the prebiotic preservation of genetic information.
Collapse
Affiliation(s)
- Marco Todisco
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Dian Ding
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
5
|
Saha R, Kao WL, Malady B, Heng X, Chen IA. Effect of montmorillonite K10 clay on RNA structure and function. Biophys J 2024; 123:451-463. [PMID: 37924206 PMCID: PMC10912936 DOI: 10.1016/j.bpj.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 09/29/2023] [Accepted: 11/01/2023] [Indexed: 11/06/2023] Open
Abstract
One of the earliest living systems was likely based on RNA ("the RNA world"). Mineral surfaces have been postulated to be an important environment for the prebiotic chemistry of RNA. In addition to adsorbing RNA and thus potentially reducing the chance of parasitic takeover through limited diffusion, minerals have been shown to promote a range of processes related to the emergence of life, including RNA polymerization, peptide bond formation, and self-assembly of vesicles. In addition, self-cleaving ribozymes have been shown to retain activity when adsorbed to the clay mineral montmorillonite. However, simulation studies suggest that adsorption to minerals is likely to interfere with RNA folding and, thus, function. To further evaluate the plausibility of a mineral-adsorbed RNA world, here we studied the effect of the synthetic clay montmorillonite K10 on the malachite green RNA aptamer, including binding of the clay to malachite green and RNA, as well as on the formation of secondary structures in model RNA and DNA oligonucleotides. We evaluated the fluorescence of the aptamer complex, adsorption to the mineral, melting curves, Förster resonance energy transfer interactions, and 1H-NMR signals to study the folding and functionality of these nucleic acids. Our results indicate that while some base pairings are unperturbed, the overall folding and binding of the malachite green aptamer are substantially disrupted by montmorillonite. These findings suggest that minerals would constrain the structures, and possibly the functions, available to an adsorbed RNA world.
Collapse
Affiliation(s)
- Ranajay Saha
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, California; Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Wei-Ling Kao
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Brandon Malady
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, California; Department of Chemistry and Biochemistry, University of California, Santa Barbara, California.
| |
Collapse
|
6
|
Ding D, Fang Z, Kim SC, O’Flaherty DK, Jia X, Stone TB, Zhou L, Szostak JW. Unusual Base Pair between Two 2-Thiouridines and Its Implication for Nonenzymatic RNA Copying. J Am Chem Soc 2024; 146:3861-3871. [PMID: 38293747 PMCID: PMC10870715 DOI: 10.1021/jacs.3c11158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
2-Thiouridine (s2U) is a nucleobase modification that confers enhanced efficiency and fidelity both on modern tRNA codon translation and on nonenzymatic and ribozyme-catalyzed RNA copying. We have discovered an unusual base pair between two 2-thiouridines that stabilizes an RNA duplex to a degree that is comparable to that of a native A:U base pair. High-resolution crystal structures indicate similar base-pairing geometry and stacking interactions in duplexes containing s2U:s2U compared to those with U:U pairs. Notably, the C═O···H-N hydrogen bond in the U:U pair is replaced with a C═S···H-N hydrogen bond in the s2U:s2U base pair. The thermodynamic stability of the s2U:s2U base pair suggested that this self-pairing might lead to an increased error frequency during nonenzymatic RNA copying. However, competition experiments show that s2U:s2U base-pairing induces only a low level of misincorporation during nonenzymatic RNA template copying because the correct A:s2U base pair outcompetes the slightly weaker s2U:s2U base pair. In addition, even if an s2U is incorrectly incorporated, the addition of the next base is greatly hindered. This strong stalling effect would further increase the effective fidelity of nonenzymatic RNA copying with s2U. Our findings suggest that s2U may enhance the rate and extent of nonenzymatic copying with only a minimal cost in fidelity.
Collapse
Affiliation(s)
- Dian Ding
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Ziyuan Fang
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Seohyun Chris Kim
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Derek K. O’Flaherty
- Department
of Chemistry, College of Engineering and Physical Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Xiwen Jia
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Talbot B. Stone
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn
Institute for RNA Innovation, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Lijun Zhou
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn
Institute for RNA Innovation, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
7
|
Toparlak Ö, Sebastianelli L, Egas Ortuno V, Karki M, Xing Y, Szostak JW, Krishnamurthy R, Mansy SS. Cyclophospholipids Enable a Protocellular Life Cycle. ACS NANO 2023; 17:23772-23783. [PMID: 38038709 PMCID: PMC10722605 DOI: 10.1021/acsnano.3c07706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
There is currently no plausible path for the emergence of a self-replicating protocell, because prevalent formulations of model protocells are built with fatty acid vesicles that cannot withstand the concentrations of Mg2+ needed for the function and replication of nucleic acids. Although prebiotic chelates increase the survivability of fatty acid vesicles, the resulting model protocells are incapable of growth and division. Here, we show that protocells made of mixtures of cyclophospholipids and fatty acids can grow and divide in the presence of Mg2+-citrate. Importantly, these protocells retain encapsulated nucleic acids during growth and division, can acquire nucleotides from their surroundings, and are compatible with the nonenzymatic extension of an RNA oligonucleotide, chemistry needed for the replication of a primitive genome. Our work shows that prebiotically plausible mixtures of lipids form protocells that are active under the conditions necessary for the emergence of Darwinian evolution.
Collapse
Affiliation(s)
- Ö.
Duhan Toparlak
- Department
of Cellular, Computational and Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo, Trentino, Italy
| | - Lorenzo Sebastianelli
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton Alberta T6G 2G2, Canada
| | - Veronica Egas Ortuno
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Megha Karki
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yanfeng Xing
- Department
of Biochemistry and Molecular Biology, University
of Chicago, Chicago, Illinois 60637, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Ramanarayanan Krishnamurthy
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sheref S. Mansy
- Department
of Cellular, Computational and Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo, Trentino, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton Alberta T6G 2G2, Canada
| |
Collapse
|
8
|
Patki GM, Rajamani S. Nonenzymatic RNA replication in a mixture of 'spent' nucleotides. FEBS Lett 2023; 597:3125-3134. [PMID: 38058189 DOI: 10.1002/1873-3468.14785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/23/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023]
Abstract
Nonenzymatic template-directed replication would have been affected by co-solutes in a heterogeneous prebiotic soup due to lack of enzymatic machinery. Unlike in contemporary biology, these reactions use chemically activated nucleotides, which undergo rapid hydrolysis forming nucleoside monophosphates ('spent' monomers). These co-solutes cannot extend the primer but continue to base pair with the template, thereby interfering with replication. We, therefore, aimed to understand how a mixture of 'spent' ribonucleotides would affect nonenzymatic replication. We observed the inhibition of replication in the mixture, wherein the predominant contribution came from the cognate Watson-Crick monomer, showing potential sequence dependence. Our study highlights how nonenzymatic RNA replication would have been directly affected by co-solutes, with ramifications for the emergence of functional polymers in an RNA World.
Collapse
Affiliation(s)
- Gauri M Patki
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| |
Collapse
|
9
|
Núñez-Villanueva D, Hunter CA. Replication of synthetic recognition-encoded oligomers by ligation of trimer building blocks. Org Chem Front 2023; 10:5950-5957. [PMID: 38022796 PMCID: PMC10661083 DOI: 10.1039/d3qo01717f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023]
Abstract
The development of methods for replication of synthetic information oligomers will underpin the use of directed evolution to search new chemical space. Template-directed replication of triazole oligomers has been achieved using a covalent primer in conjunction with non-covalent binding of complementary building blocks. A phenol primer equipped with an alkyne was first attached to a benzoic recognition unit on a mixed sequence template via selective covalent ester base-pair formation. The remaining phenol recognition units on the template were then used for non-covalent binding of phosphine oxide oligomers equipped with an azide. The efficiency of the templated CuAAC reaction between the primer and phosphine oxide building blocks was investigated as a function of the number of H-bonds formed with the template. Increasing the strength of the non-covalent interaction between the template and the azide lead to a significant acceleration of the templated reaction. For shorter phosphine oxide oligomers intermolecular reactions compete with the templated process, but quantitative templated primer elongation was achieved with a phosphine oxide 3-mer building block that was able to form three H-bonds with the template. NMR spectroscopy and molecular models suggest that the template can fold, but addition of the phosphine oxide 3-mer leads to a complex with three H-bonds between phosphine oxide and phenol groups, aligning the azide and alkyne groups in a favourable geometry for the CuAAC reaction. In the product duplex, 1H and 31P NMR data confirm the presence of the three H-bonded base-pairs, demonstrating that the covalent and non-covalent base-pairs are geometrically compatible. A complete replication cycle was carried out starting from the oligotriazole template by covalent attachment of the primer, followed by template-directed elongation, and hydrolysis of the the ester base-pair in the resulting duplex to regenerate the template and liberate the copy strand. We have previously demonstrated sequence-selective oligomer replication using covalent base-pairing, but the trimer building block approach described here is suitable for replication of sequence information using non-covalent binding of the monomer building blocks to a template.
Collapse
Affiliation(s)
- Diego Núñez-Villanueva
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| |
Collapse
|
10
|
Cruz HA, Jiménez EI, Krishnamurthy R. Enhancing Prebiotic Phosphorylation and Modulating the Regioselectivity of Nucleosides with Diamidophosphate†. J Am Chem Soc 2023; 145:23781-23793. [PMID: 37856825 DOI: 10.1021/jacs.3c08539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Among the many prebiotic phosphorylation chemistries investigated, diamidophosphate (DAP) has shown promising potential for nucleoside phosphorylation. Herein, we show that DAP's phosphorylation capability is enhanced significantly (up to 90%) in wet-dry cycles by a range of prebiotically plausible pHs (6-10) and temperatures (up to 80 °C) in the presence of additives such as formamide, cyanamide, urea, guanidine, 2-aminoimidazole, and hydantoin. For ribonucleosides, the main products are the 2',3'-cyclic phosphates along with the corresponding 2'- and 3'-phosphates, while deoxyribonucleosides form 5'- and 3'-phosphates, the ratios of which are affected by cycles and the presence and nature of the additives. A simple change of temperature to 80 °C with additives leads to higher conversion yields (≈80-90%) with an increased level of 5'-phosphorylation (≈40-49%). This demonstration of enhancing and controlling the regioselectivity of DAP-mediated phosphorylation by a range of additives and conditions potentiates transitioning to the search for more efficient catalysts, enabling regiospecific phosphorylations and oligonucleotide formation in the same milieu and setting.
Collapse
Affiliation(s)
- Harold A Cruz
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Eddy I Jiménez
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
11
|
Dantsu Y, Zhang Y, Zhang W. Insight into the structures of unusual base pairs in RNA complexes containing a primer/template/adenosine ligand. RSC Chem Biol 2023; 4:942-951. [PMID: 37920395 PMCID: PMC10619131 DOI: 10.1039/d3cb00137g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/29/2023] [Indexed: 11/04/2023] Open
Abstract
In the prebiotic RNA world, the self-replication of RNA without enzymes can be achieved through the utilization of 2-aminoimidazole activated nucleotides as efficient substrates. The mechanism of RNA nonenzymatic polymerization has been extensively investigated biophysically and structurally by using the model of an RNA primer/template complex which is bound by the imidazolium-bridged or triphosphate-bridged diguanosine intermediate. However, beyond the realm of the guanosine substrate, the structural insight into how alternative activated nucleotides bind and interact with the RNA primer/template complex remains unexplored, which is important for understanding the low reactivity of adenosine and uridine substrates in RNA primer extension, as well as its relationship with the structures. Here we use crystallography as a method and determine a series of high-resolution structures of RNA primer/template complexes bound by ApppG, a close analog of the dinucleotide intermediate containing adenosine and guanosine. The structures show that ApppG ligands bind to the RNA template through both Watson-Crick and noncanonical base pairs, with the primer 3'-OH group far from the adjacent phosphorus atom of the incoming substrate. The structures indicate that when adenosine is included in the imidazolium-bridged intermediate, the complexes are likely preorganized in a suboptimal conformation, making it difficult for the primer to in-line attack the substrate. Moreover, by co-crystallizing the RNA primer/template with chemically activated adenosine and guanosine monomers, we successfully observe the slow formation of the imidazolium-bridged intermediate (Ap-AI-pG) and the preorganized structure for RNA primer extension. Overall, our studies offer a structural explanation for the slow rate of RNA primer extension when using adenosine-5'-phosphoro-2-aminoimidazolide as a substrate during nonenzymatic polymerization.
Collapse
Affiliation(s)
- Yuliya Dantsu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine Indianapolis IN 46202 USA
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine Indianapolis IN 46202 USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine Indianapolis IN 46202 USA
| |
Collapse
|
12
|
Bartolucci G, Calaça Serrão A, Schwintek P, Kühnlein A, Rana Y, Janto P, Hofer D, Mast CB, Braun D, Weber CA. Sequence self-selection by cyclic phase separation. Proc Natl Acad Sci U S A 2023; 120:e2218876120. [PMID: 37847736 PMCID: PMC10614837 DOI: 10.1073/pnas.2218876120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 09/06/2023] [Indexed: 10/19/2023] Open
Abstract
The emergence of functional oligonucleotides on early Earth required a molecular selection mechanism to screen for specific sequences with prebiotic functions. Cyclic processes such as daily temperature oscillations were ubiquitous in this environment and could trigger oligonucleotide phase separation. Here, we propose sequence selection based on phase separation cycles realized through sedimentation in a system subjected to the feeding of oligonucleotides. Using theory and experiments with DNA, we show sequence-specific enrichment in the sedimented dense phase, in particular of short 22-mer DNA sequences. The underlying mechanism selects for complementarity, as it enriches sequences that tightly interact in the dense phase through base-pairing. Our mechanism also enables initially weakly biased pools to enhance their sequence bias or to replace the previously most abundant sequences as the cycles progress. Our findings provide an example of a selection mechanism that may have eased screening for auto-catalytic self-replicating oligonucleotides.
Collapse
Affiliation(s)
- Giacomo Bartolucci
- Division Biological Physics, Max Planck Institute for the Physics of Complex Systems, Dresden01187, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
| | - Adriana Calaça Serrão
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Philipp Schwintek
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Alexandra Kühnlein
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Yash Rana
- Division Biological Physics, Max Planck Institute for the Physics of Complex Systems, Dresden01187, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
| | - Philipp Janto
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Dorothea Hofer
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Christof B. Mast
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Dieter Braun
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Christoph A. Weber
- Faculty of Mathematics, Natural Sciences, and Materials Engineering: Institute of Physics, University of Augsburg, Augsburg86159, Germany
| |
Collapse
|
13
|
Welsch F, Kervio E, Tremmel P, Richert C. Prolinyl Nucleotides Drive Enzyme-Free Genetic Copying of RNA. Angew Chem Int Ed Engl 2023; 62:e202307591. [PMID: 37382466 DOI: 10.1002/anie.202307591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]
Abstract
Proline is one of the proteinogenic amino acids. It is found in all kingdoms of life. It also has remarkable activity as an organocatalyst and is of structural importance in many folded polypeptides. Here, we show that prolinyl nucleotides with a phosphoramidate linkage are active building blocks in enzyme- and ribozyme-free copying of RNA in the presence of monosubstituted imidazoles as organocatalysts. Both dinucleotides and mononucleotides are incorporated at the terminus of RNA primers in aqueous buffer, as instructed by the template sequence, in up to eight consecutive extension steps. Our results show that condensation products of amino acids and ribonucleotides can act like nucleoside triphosphates in media devoid of enzymes or ribozymes. Prolinyl nucleotides are metastable building blocks, readily activated by catalysts, helping to explain why the combination of α-amino acids and nucleic acids was selected in molecular evolution.
Collapse
Affiliation(s)
- Franziska Welsch
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Eric Kervio
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Peter Tremmel
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| |
Collapse
|
14
|
Georgiou CD, McKay C, Reymond JL. Organic Catalytic Activity as a Method for Agnostic Life Detection. ASTROBIOLOGY 2023; 23:1118-1127. [PMID: 37523279 DOI: 10.1089/ast.2023.0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
An ideal life detection instrument would have high sensitivity but be insensitive to abiotic processes and would be capable of detecting life with alternate molecular structures. In this study, we propose that catalytic activity can be the basis of a nearly ideal life detection instrument. There are several advantages to catalysis as an agnostic life detection method. Demonstrating catalysis does not necessarily require culturing/growing the alien life and in fact may persist even in dead biomass for some time, and the amplification by catalysis is large even by minute amounts of catalysts and, hence, can be readily detected against abiotic background rates. In specific, we propose a hydrolytic catalysis detection instrument that could detect activity in samples of extraterrestrial organic material from unknown life. The instrument uses chromogenic assay-based detection of various hydrolytic catalytic activities, which are matched to corresponding artificial substrates having the same, chromogenic (preferably fluorescent) upon release, group; D- and L-enantiomers of these substrates can be used to also answer the question whether unknown life is chiral. Since catalysis is a time-proportional product-concentration amplification process, hydrolytic catalytic activity can be measured on a sample of even a minute size, and with instruments based on, for example, optofluidic chip technology.
Collapse
Affiliation(s)
| | | | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| |
Collapse
|
15
|
Park SJ, Callaghan KL, Ellis AV. Role of helicity in the nonenzymatic template-directed primer extension of DNA. Org Biomol Chem 2023; 21:6702-6706. [PMID: 37555399 DOI: 10.1039/d3ob01179h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Complexing a DNA primer with an RNA template showed improved nonenzymatic template-directed primer extension, attributed to a shift in the DNA helicity from a B-type towards an A-type helix. A 2-fold (deoxyadenosine) and 4.5-fold (deoxycytidine) increase in conversion from initial DNA primer to a primer + 1 nucleotide product was observed.
Collapse
Affiliation(s)
- Sung Joon Park
- School of Chemical and Biomedical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Kimberley Laura Callaghan
- School of Chemical and Biomedical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Amanda Vera Ellis
- School of Chemical and Biomedical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
| |
Collapse
|
16
|
Dagar S, Sarkar S, Rajamani S. Nonenzymatic Template-Directed Primer Extension Using 2'-3' Cyclic Nucleotides Under Wet-Dry Cycles. ORIGINS LIFE EVOL B 2023; 53:43-60. [PMID: 37243884 DOI: 10.1007/s11084-023-09636-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/15/2023] [Indexed: 05/29/2023]
Abstract
RNA World Hypothesis is centred around the idea of a period in the early history of life's origin, wherein nonenzymatic oligomerization and replication of RNA resulted in functional ribozymes. Previous studies in this endeavour have demonstrated template-directed primer extension using chemically modified nucleotides and primers. Nonetheless, similar studies that used non-activated nucleotides led to the formation of RNA only with abasic sites. In this study, we report template-directed primer extension with prebiotically relevant cyclic nucleotides, under dehydration-rehydration (DH-RH) cycles occurring at high temperature (90 °C) and alkaline conditions (pH 8). 2'-3' cyclic nucleoside monophosphates (cNMP) resulted in primer extension, while 3'-5' cNMP failed to do so. Intact extension of up to two nucleotide additions was observed with both canonical hydroxy-terminated (OH-primer) and activated amino-terminated (NH2-primer) primers. We demonstrate primer extension reactions using both purine and pyrimidine 2'-3' cNMPs, with higher product yield observed during cAMP additions. Further, the presence of lipid was observed to significantly enhance the extended product in cCMP reactions. In all, our study provides a proof-of-concept for nonenzymatic primer extension of RNA, using intrinsically activated prebiotically relevant cyclic nucleotides as monomers.
Collapse
Affiliation(s)
- Shikha Dagar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Susovan Sarkar
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India
| | - Sudha Rajamani
- Department of Biology, Indian Institute of Science Education and Research, Pune, 411008, India.
| |
Collapse
|
17
|
Ding D, Zhang SJ, Szostak JW. Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides. Nucleic Acids Res 2023:7184164. [PMID: 37247941 PMCID: PMC10359593 DOI: 10.1093/nar/gkad439] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 04/28/2023] [Accepted: 05/10/2023] [Indexed: 05/31/2023] Open
Abstract
The nonenzymatic copying of RNA is thought to have been necessary for the transition between prebiotic chemistry and ribozyme-catalyzed RNA replication in the RNA World. We have previously shown that a potentially prebiotic nucleotide activation pathway based on phospho-Passerini chemistry can lead to the efficient synthesis of 2-aminoimidazole activated mononucleotides when carried out under freeze-thaw cycling conditions. Such activated nucleotides react with each other to form 5'-5' 2-aminoimidazolium bridged dinucleotides, enabling template-directed primer extension to occur within the same reaction mixture. However, mononucleotides linked to oligonucleotides by a 5'-5' 2-aminoimidazolium bridge are superior substrates for nonenzymatic primer extension; their higher intrinsic reactivity and their higher template affinity enable faster template copying at lower substrate concentrations. Here we show that eutectic phase phospho-Passerini chemistry efficiently activates short oligonucleotides and promotes the formation of monomer-bridged-oligonucleotide species during freeze-thaw cycles. We then demonstrate that in-situ generated monomer-bridged-oligonucleotides lead to efficient nonenzymatic template copying in the same reaction mixture. Our demonstration that multiple steps in the pathway from activation chemistry to RNA copying can occur together in a single complex environment simplifies this aspect of the origin of life.
Collapse
Affiliation(s)
- Dian Ding
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA02114, USA
| | - Stephanie J Zhang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA02114, USA
| | - Jack W Szostak
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA02114, USA
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA02115, USA
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL60637, USA
| |
Collapse
|
18
|
Green NJ, Russell DA, Tanner SH, Sutherland JD. Prebiotic Synthesis of N-Formylaminonitriles and Derivatives in Formamide. J Am Chem Soc 2023; 145:10533-10541. [PMID: 37146260 DOI: 10.1021/jacs.2c13306] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Amino acids and their derivatives were probably instrumental in the transition of prebiotic chemistry to early biology. Accordingly, amino acid formation under prebiotic conditions has been intensively investigated. Unsurprisingly, most of these studies have taken place with water as the solvent. Herein, we describe an investigation into the formation and subsequent reactions of aminonitriles and their formylated derivatives in formamide. We find that N-formylaminonitriles form readily from aldehydes and cyanide in formamide, even in the absence of added ammonia, suggesting a potentially prebiotic source of amino acid derivatives. Alkaline processing of N-formylaminonitriles proceeds with hydration at the nitrile group faster than deformylation, protecting aminonitrile derivatives from reversion of the Strecker condensation equilibrium during hydration/hydrolysis and furnishing mixtures of N-formylated and unformylated amino acid derivatives. Furthermore, the facile synthesis of N-formyldehydroalanine nitrile is observed in formamide from glycolaldehyde and cyanide without intervention. Dehydroalanine derivatives have been proposed as important compounds for prebiotic peptide synthesis, and we demonstrate both a synthesis suggesting that they are potentially plausible components of a prebiotic inventory, and reactions showing their utility as abiotic precursors to a range of compounds of prebiological interest.
Collapse
Affiliation(s)
- Nicholas J Green
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
- Department of Chemistry, University of Otago, Dunedin 9054, New Zealand
| | - David A Russell
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | - Sasha H Tanner
- Department of Chemistry, University of Otago, Dunedin 9054, New Zealand
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| |
Collapse
|
19
|
Ding D, Zhou L, Mittal S, Szostak JW. Experimental Tests of the Virtual Circular Genome Model for Nonenzymatic RNA Replication. J Am Chem Soc 2023; 145:7504-7515. [PMID: 36963403 PMCID: PMC10080680 DOI: 10.1021/jacs.3c00612] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
The virtual circular genome (VCG) model was proposed as a means of going beyond template copying to indefinite cycles of nonenzymatic RNA replication during the origin of life. In the VCG model, the protocellular genome is a collection of short oligonucleotides that map to both strands of a virtual circular sequence. Replication is driven by templated nonenzymatic primer extensions on a subset of kinetically trapped partially base-paired configurations, followed by the shuffling of these configurations to enable continued oligonucleotide elongation. Here, we describe initial experimental studies of the feasibility of the VCG model for replication. We designed a small 12-nucleotide model VCG and synthesized all 247 oligonucleotides of lengths 2 to 12 corresponding to this genome. We experimentally monitored the fate of individual labeled primers in the pool of VCG oligonucleotides following the addition of activated nucleotides and investigated the effect of factors such as oligonucleotide length, concentration, composition, and temperature on the extent of primer extension. We observe a surprisingly prolonged equilibration process in the VCG system that enables a considerable extent of reaction. We find that environmental fluctuations would be essential for continuous templated extension of the entire VCG system since the shortest oligonucleotides can only bind to templates at low temperatures, while the longest oligonucleotides require high-temperature spikes to escape from inactive configurations. Finally, we demonstrate that primer extension is significantly enhanced when the mix of VCG oligonucleotides is preactivated. We discuss the necessity of ongoing in situ activation chemistry for continuous and accurate VCG replication.
Collapse
Affiliation(s)
- Dian Ding
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Lijun Zhou
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Shriyaa Mittal
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jack W Szostak
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
20
|
Todisco M, Szostak JW. Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides. Nucleic Acids Res 2022; 50:9647-9662. [PMID: 36099434 PMCID: PMC9508827 DOI: 10.1093/nar/gkac784] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/23/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
Hybridization and strand displacement kinetics determine the evolution of the base paired configurations of mixtures of oligonucleotides over time. Although much attention has been focused on the thermodynamics of DNA and RNA base pairing in the scientific literature, much less work has been done on the time dependence of interactions involving multiple strands, especially in RNA. Here we provide a study of oligoribonucleotide interaction kinetics and show that it is possible to calculate the association, dissociation and strand displacement rates displayed by short oligonucleotides (5nt–12nt) that exhibit no expected secondary structure as simple functions of oligonucleotide length, CG content, ΔG of hybridization and ΔG of toehold binding. We then show that the resultant calculated kinetic parameters are consistent with the experimentally observed time dependent changes in concentrations of the different species present in mixtures of multiple competing RNA strands. We show that by changing the mixture composition, it is possible to create and tune kinetic traps that extend by orders of magnitude the typical sub-second hybridization timescale of two complementary oligonucleotides. We suggest that the slow equilibration of complex oligonucleotide mixtures may have facilitated the nonenzymatic replication of RNA during the origin of life.
Collapse
Affiliation(s)
- Marco Todisco
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| |
Collapse
|
21
|
Fontana F, Bellini T, Todisco M. Liquid Crystal Ordering in DNA Double Helices with Backbone Discontinuities. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francesco Fontana
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, via Vanvitelli 32, 20129 Milano, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, via Vanvitelli 32, 20129 Milano, Italy
| | - Marco Todisco
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano, via Vanvitelli 32, 20129 Milano, Italy
| |
Collapse
|
22
|
Closs AC, Bechtel M, Trapp O. Dynamischer Austausch von Substituenten in einem präbiotischen Organokatalysator: Erste Schritte auf dem Weg zu einem evolutionären System. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Anna C. Closs
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 München Deutschland
- Max-Planck-Institut für Astronomie Königstuhl 17 69117 Heidelberg Deutschland
| | - Maximilian Bechtel
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 München Deutschland
| | - Oliver Trapp
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 München Deutschland
- Max-Planck-Institut für Astronomie Königstuhl 17 69117 Heidelberg Deutschland
| |
Collapse
|
23
|
Lin H, Jiménez EI, Arriola JT, Müller UF, Krishnamurthy R. Concurrent Prebiotic Formation of Nucleoside‐Amidophosphates and Nucleoside‐Triphosphates Potentiates Transition from Abiotic to Biotic Polymerization. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Huacan Lin
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| | - Eddy I. Jiménez
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Joshua T. Arriola
- Department of Chemistry and Biochemistry UC San Diego 9500 Gilman Drive La Jolla CA 92037 USA
| | - Ulrich F. Müller
- Department of Chemistry and Biochemistry UC San Diego 9500 Gilman Drive La Jolla CA 92037 USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
- NSF-NASA Center for Chemical Evolution Atlanta GA 30332 USA
| |
Collapse
|
24
|
Mangalath S, Karunakaran SC, Newnam G, Schuster GB, Hud NV. Supramolecular assembly-enabled homochiral polymerization of short (dA) n oligonucleotides. Chem Commun (Camb) 2021; 57:13602-13605. [PMID: 34852364 DOI: 10.1039/d1cc05420a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A goal of supramolecular chemistry is to create covalent polymers of precise composition and stereochemistry from complex mixtures by the reversible assembly of specific monomers prior to covalent bond formation. We illustrate the power of this approach with short oligomers of deoxyadenosine monophosphate ((dA)n3'p), n ≥ 3, which form supramolecular assemblies with cyanuric acid. The addition of a condensing agent to these assemblies results in their selective, non-enzymatic polymerization to form long polymers (e.g., (dA)1003'p). Significantly, mixtures of D- and L-(dA)53'p form homochiral covalent polymers, which demonstrates self-sorting of racemic monomers and covalent bond formation exclusively in homochiral assemblies.
Collapse
Affiliation(s)
- Sreejith Mangalath
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
| | - Suneesh C Karunakaran
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
| | - Gary Newnam
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
| | - Gary B Schuster
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, USA.
| |
Collapse
|
25
|
Lin H, Jiménez EI, Arriola JT, Müller UF, Krishnamurthy R. Concurrent Prebiotic Formation of Nucleoside-Amidophosphates and Nucleoside-Triphosphates Potentiates Transition from Abiotic to Biotic Polymerization. Angew Chem Int Ed Engl 2021; 61:e202113625. [PMID: 34738300 DOI: 10.1002/anie.202113625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Indexed: 11/10/2022]
Abstract
Polymerization of nucleic acids in biology utilizes 5'-nucleoside triphosphates (NTPs) as substrates. The prebiotic availability of NTPs has been unresolved and other derivatives of nucleoside-monophosphates (NMPs) have been studied. However, this latter approach necessitates a change in chemistries when transitioning to biology. Herein we show that diamidophosphate (DAP), in a one-pot amidophosphorylation-hydrolysis setting converts NMPs into the corresponding NTPs via 5'-nucleoside amidophosphates (NaPs). The resulting crude mixture of NTPs are accepted by proteinaceous- and ribozyme-polymerases as substrates for nucleic acid polymerization. This phosphorylation also operates at the level of oligonucleotides enabling ribozyme-mediated ligation. This one-pot protocol for simultaneous generation of NaPs and NTPs suggests that the transition from prebiotic-phosphorylation and oligomerization to an enzymatic processive-polymerization can be more continuous than previously anticipated.
Collapse
Affiliation(s)
- Huacan Lin
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.,NSF-NASA Center for Chemical Evolution, Atlanta, GA, 30332, USA
| | - Eddy I Jiménez
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Joshua T Arriola
- Department of Chemistry and Biochemistry, UC San Diego, 9500 Gilman Drive, La Jolla, CA, 92037, USA
| | - Ulrich F Müller
- Department of Chemistry and Biochemistry, UC San Diego, 9500 Gilman Drive, La Jolla, CA, 92037, USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.,NSF-NASA Center for Chemical Evolution, Atlanta, GA, 30332, USA
| |
Collapse
|
26
|
Wunnava S, Dirscherl CF, Výravský J, Kovařík A, Matyášek R, Šponer J, Braun D, Šponer JE. Acid-Catalyzed RNA-Oligomerization from 3',5'-cGMP. Chemistry 2021; 27:17581-17585. [PMID: 34726799 PMCID: PMC9299008 DOI: 10.1002/chem.202103672] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 11/28/2022]
Abstract
The assembly of ancient informational polymers from nucleotide precursors is the central challenge of life's origin on our planet. Among the possible solutions, dry polymerization of 3’,5’‐cyclic guanosine monophosphate (3’,5’‐cGMP) has been proposed as a candidate to create oligonucleotides of 15–20 units in length. However, the reported sensitivity of the reaction to the presence of cations raised questions of whether this chemistry could be relevant in a geological context. The experiments in this study show that the presence of cations is not restrictive as long as the reaction is conducted in an acidic environment, in contrast to previous reports that suggested optimal conditions at pH 9.
Collapse
Affiliation(s)
- Sreekar Wunnava
- Department of Physics, NanoSystems Initiative Munich and Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstrasse 54, 80799, Munich, Germany
| | - Christina F Dirscherl
- Department of Physics, NanoSystems Initiative Munich and Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstrasse 54, 80799, Munich, Germany
| | - Jakub Výravský
- Tescan Brno s.r.o., Libušina třída 1, 62300, Brno, Czech Republic.,Department of Geological Sciences, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Roman Matyášek
- Institute of Biophysics Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Dieter Braun
- Department of Physics, NanoSystems Initiative Munich and Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstrasse 54, 80799, Munich, Germany
| | - Judit E Šponer
- Institute of Biophysics Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| |
Collapse
|
27
|
Closs AC, Bechtel M, Trapp O. Dynamic Exchange of Substituents in a Prebiotic Organocatalyst: Initial Steps towards an Evolutionary System. Angew Chem Int Ed Engl 2021; 61:e202112563. [PMID: 34705315 PMCID: PMC9298921 DOI: 10.1002/anie.202112563] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Indexed: 11/07/2022]
Abstract
All evolutionary biological processes lead to a change in heritable traits over successive generations. The responsible genetic information encoded in DNA is altered, selected, and inherited by mutation of the base sequence. While this is well known at the biological level, an evolutionary change at the molecular level of small organic molecules is unknown but represents an important prerequisite for the emergence of life. Here, we present a class of prebiotic imidazolidine-4-thione organocatalysts able to dynamically change their constitution and potentially capable to form an evolutionary system. These catalysts functionalize their building blocks and dynamically adapt to their (self-modified) environment by mutation of their own structure. Depending on the surrounding conditions, they show pronounced and opposing selectivity in their formation. Remarkably, the preferentially formed species can be associated with different catalytic properties, which enable multiple pathways for the transition from abiotic matter to functional biomolecules.
Collapse
Affiliation(s)
- Anna C Closs
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.,Max-Planck-Institute for Astronomy, Königstuhl 17, 69117, Heidelberg, Germany
| | - Maximilian Bechtel
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Oliver Trapp
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.,Max-Planck-Institute for Astronomy, Königstuhl 17, 69117, Heidelberg, Germany
| |
Collapse
|
28
|
Schuster GB, Cafferty BJ, Karunakaran SC, Hud NV. Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA. J Am Chem Soc 2021; 143:9279-9296. [PMID: 34152760 DOI: 10.1021/jacs.0c13081] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hypothesis that RNA and DNA are products of chemical and biological evolution has motivated our search for alternative nucleic acids that may have come earlier in the emergence of life-polymers that possess a proclivity for covalent and non-covalent self-assembly not exhibited by RNA. Our investigations have revealed a small set of candidate ancestral nucleobases that self-assemble into hexameric rosettes that stack in water to form long, twisted, rigid supramolecular polymers. These structures exhibit properties that provide robust solutions to long-standing problems that have stymied the search for a prebiotic synthesis of nucleic acids. Moreover, their examination by experimental and computational methods provides insight into the chemical and physical principles that govern a particular class of water-soluble one-dimensional supramolecular polymers. In addition to efficient self-assembly, their lengths and polydispersity are modulated by a wide variety of positively charged, planar compounds; their assembly and disassembly are controlled over an exceedingly narrow pH range; they exhibit spontaneous breaking of symmetry; and homochirality emerges through non-covalent cross-linking during hydrogel formation. Some of these candidate ancestral nucleobases spontaneously form glycosidic bonds with ribose and other sugars, and, most significantly, functionalized forms of these heterocycles form supramolecular structures and covalent polymers under plausibly prebiotic conditions. This Perspective recounts a journey of discovery that continues to reveal attractive answers to questions concerning the origins of life and to uncover the principles that control the structure and properties of water-soluble supramolecular polymers.
Collapse
Affiliation(s)
- Gary B Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Brian J Cafferty
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Suneesh C Karunakaran
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| |
Collapse
|
29
|
Wang Y, Wang Y, Song D, Sun X, Zhang Z, Li X, Li Z, Yu H. A Threose Nucleic Acid Enzyme with RNA Ligase Activity. J Am Chem Soc 2021; 143:8154-8163. [PMID: 34028252 DOI: 10.1021/jacs.1c02895] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Threose nucleic acid (TNA) has been considered a potential RNA progenitor in evolution due to its chemical simplicity and base pairing property. Catalytic TNA sequences with RNA ligase activities might have facilitated the transition to the RNA world. Here we report the isolation of RNA ligase TNA enzymes by in vitro selection. The identified TNA enzyme T8-6 catalyzes the formation of a 2'-5' phosphoester bond between a 2',3'-diol and a 5'-triphosphate group, with a kobs of 1.1 × 10-2 min-1 (40 mM Mg2+, pH 9.0). For efficient reaction, T8-6 requires UA|GA at the ligation junction and tolerates variations at other substrate positions. Functional RNAs such as hammerhead ribozyme can be prepared by T8-6-catalyzed ligation, with site-specific introduction of a 2'-5' linkage. Together, this work provides experimental support for TNA as a plausible pre-RNA genetic polymer and also offers an alternative molecular tool for biotechnology.
Collapse
Affiliation(s)
- Yao Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yueyao Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China.,Applied Adaptome Immunology Institute, Jiangsu Industrial Technology Research Institute, Nanjing, Jiangsu 210023, China
| | - Dongfan Song
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xin Sun
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
| | - Ze Zhang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xintong Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Zhe Li
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hanyang Yu
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
| |
Collapse
|
30
|
Duzdevich D, Carr CE, Ding D, Zhang SJ, Walton TS, Szostak JW. Competition between bridged dinucleotides and activated mononucleotides determines the error frequency of nonenzymatic RNA primer extension. Nucleic Acids Res 2021; 49:3681-3691. [PMID: 33744957 PMCID: PMC8053118 DOI: 10.1093/nar/gkab173] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/12/2021] [Accepted: 03/05/2021] [Indexed: 12/15/2022] Open
Abstract
Nonenzymatic copying of RNA templates with activated nucleotides is a useful model for studying the emergence of heredity at the origin of life. Previous experiments with defined-sequence templates have pointed to the poor fidelity of primer extension as a major problem. Here we examine the origin of mismatches during primer extension on random templates in the simultaneous presence of all four 2-aminoimidazole-activated nucleotides. Using a deep sequencing approach that reports on millions of individual template-product pairs, we are able to examine correct and incorrect polymerization as a function of sequence context. We have previously shown that the predominant pathway for primer extension involves reaction with imidazolium-bridged dinucleotides, which form spontaneously by the reaction of two mononucleotides with each other. We now show that the sequences of correctly paired products reveal patterns that are expected from the bridged dinucleotide mechanism, whereas those associated with mismatches are consistent with direct reaction of the primer with activated mononucleotides. Increasing the ratio of bridged dinucleotides to activated mononucleotides, either by using purified components or by using isocyanide-based activation chemistry, reduces the error frequency. Our results point to testable strategies for the accurate nonenzymatic copying of arbitrary RNA sequences.
Collapse
Affiliation(s)
- Daniel Duzdevich
- To whom correspondence should be addressed. Tel: +1 617 726 5102; Fax: +1 617 643 332;
| | - Christopher E Carr
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Dian Ding
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Stephanie J Zhang
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Travis S Walton
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jack W Szostak
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
31
|
Colville BWF, Powner MW. Selective Prebiotic Synthesis of α‐Threofuranosyl Cytidine by Photochemical Anomerization. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
32
|
Colville BWF, Powner MW. Selective Prebiotic Synthesis of α-Threofuranosyl Cytidine by Photochemical Anomerization. Angew Chem Int Ed Engl 2021; 60:10526-10530. [PMID: 33644959 PMCID: PMC8252090 DOI: 10.1002/anie.202101376] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Indexed: 11/23/2022]
Abstract
The structure of life's first genetic polymer is a question of intense ongoing debate. The “RNA world theory” suggests RNA was life's first nucleic acid. However, ribonucleotides are complex chemical structures, and simpler nucleic acids, such as threose nucleic acid (TNA), can carry genetic information. In principle, nucleic acids like TNA could have played a vital role in the origins of life. The advent of any genetic polymer in life requires synthesis of its monomers. Here we demonstrate a high‐yielding, stereo‐, regio‐ and furanosyl‐selective prebiotic synthesis of threo‐cytidine 3, an essential component of TNA. Our synthesis uses key intermediates and reactions previously exploited in the prebiotic synthesis of the canonical pyrimidine ribonucleoside cytidine 1. Furthermore, we demonstrate that erythro‐specific 2′,3′‐cyclic phosphate synthesis provides a mechanism to photochemically select TNA cytidine. These results suggest that TNA may have coexisted with RNA during the emergence of life.
Collapse
Affiliation(s)
- Ben W F Colville
- Department of Chemistry, UCL, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Matthew W Powner
- Department of Chemistry, UCL, 20 Gordon Street, London, WC1H 0AJ, UK
| |
Collapse
|
33
|
Kim SC, O'Flaherty DK, Giurgiu C, Zhou L, Szostak JW. The Emergence of RNA from the Heterogeneous Products of Prebiotic Nucleotide Synthesis. J Am Chem Soc 2021; 143:3267-3279. [PMID: 33636080 DOI: 10.1021/jacs.0c12955] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in prebiotic chemistry are beginning to outline plausible pathways for the synthesis of the canonical ribonucleotides and their assembly into oligoribonucleotides. However, these reaction pathways suggest that many noncanonical nucleotides are likely to have been generated alongside the standard ribonucleotides. Thus, the oligomerization of prebiotically synthesized nucleotides is likely to have led to a highly heterogeneous collection of oligonucleotides comprised of a wide range of types of nucleotides connected by a variety of backbone linkages. How then did relatively homogeneous RNA emerge from this primordial heterogeneity? Here we focus on nonenzymatic template-directed primer extension as a process that would have strongly enriched for homogeneous RNA over the course of multiple cycles of replication. We review the effects on copying the kinetics of nucleotides with altered nucleobase and sugar moieties, when they are present as activated monomers and when they are incorporated into primer and template oligonucleotides. We also discuss three variations in backbone connectivity, all of which are nonheritable and regenerate native RNA upon being copied. The kinetic superiority of RNA synthesis suggests that nonenzymatic copying served as a chemical selection mechanism that allowed relatively homogeneous RNA to emerge from a complex mixture of prebiotically synthesized nucleotides and oligonucleotides.
Collapse
Affiliation(s)
- Seohyun Chris Kim
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Derek K O'Flaherty
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| |
Collapse
|
34
|
Kunnev D. Origin of Life: The Point of No Return. Life (Basel) 2020; 10:life10110269. [PMID: 33153087 PMCID: PMC7693465 DOI: 10.3390/life10110269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/01/2020] [Accepted: 11/01/2020] [Indexed: 12/13/2022] Open
Abstract
Origin of life research is one of the greatest scientific frontiers of mankind. Many hypotheses have been proposed to explain how life began. Although different hypotheses emphasize different initial phenomena, all of them agree around one important concept: at some point, along with the chain of events toward life, Darwinian evolution emerged. There is no consensus, however, how this occurred. Frequently, the mechanism leading to Darwinian evolution is not addressed and it is assumed that this problem could be solved later, with experimental proof of the hypothesis. Here, the author first defines the minimum components required for Darwinian evolution and then from this standpoint, analyzes some of the hypotheses for the origin of life. Distinctive features of Darwinian evolution and life rooted in the interaction between information and its corresponding structure/function are then reviewed. Due to the obligatory dependency of the information and structure subject to Darwinian evolution, these components must be locked in their origin. One of the most distinctive characteristics of Darwinian evolution in comparison with all other processes is the establishment of a fundamentally new level of matter capable of evolving and adapting. Therefore, the initiation of Darwinian evolution is the "point of no return" after which life begins. In summary: a definition and a mechanism for Darwinian evolution are provided together with a critical analysis of some of the hypotheses for the origin of life.
Collapse
Affiliation(s)
- Dimiter Kunnev
- Department of Oral Biology, University at Buffalo, Buffalo, NY 14263, USA
| |
Collapse
|
35
|
Hanopolskyi AI, Smaliak VA, Novichkov AI, Semenov SN. Autocatalysis: Kinetics, Mechanisms and Design. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000026] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Anton I. Hanopolskyi
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Viktoryia A. Smaliak
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Alexander I. Novichkov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| | - Sergey N. Semenov
- Department of Organic Chemistry Weizmann Institute of Science Herzl, 234 7610001 Rehovot Israel
| |
Collapse
|
36
|
Zhang SJ, Duzdevich D, Szostak JW. Potentially Prebiotic Activation Chemistry Compatible with Nonenzymatic RNA Copying. J Am Chem Soc 2020; 142:14810-14813. [PMID: 32794700 PMCID: PMC9594304 DOI: 10.1021/jacs.0c05300] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
The nonenzymatic replication of ribonucleic
acid (RNA) may have
enabled the propagation of genetic information during the origin of
life. RNA copying can be initiated in the laboratory with chemically
activated nucleotides, but continued copying requires a source of
chemical energy for in situ nucleotide activation.
Recent work has illuminated a potentially prebiotic cyanosulfidic
chemistry that activates nucleotides, but its application to nonenzymatic
RNA copying had not been demonstrated. Here, we report a novel pathway
that activates RNA nucleotides in a manner compatible with template-directed
nonenzymatic copying. We show that this pathway, which we refer to
as bridge-forming activation, selectively yields the reactive imidazolium-bridged
dinucleotide intermediate required for copying. Our results will enable
more realistic simulations of RNA propagation based on continuous in situ nucleotide activation.
Collapse
Affiliation(s)
- Stephanie J Zhang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Daniel Duzdevich
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jack W Szostak
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States.,Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| |
Collapse
|
37
|
Duzdevich D, Carr CE, Szostak JW. Deep sequencing of non-enzymatic RNA primer extension. Nucleic Acids Res 2020; 48:e70. [PMID: 32427335 PMCID: PMC7337528 DOI: 10.1093/nar/gkaa400] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/02/2020] [Accepted: 05/05/2020] [Indexed: 12/02/2022] Open
Abstract
Life emerging in an RNA world is expected to propagate RNA as hereditary information, requiring some form of primitive replication without enzymes. Non-enzymatic template-directed RNA primer extension is a model of the copying step in this posited form of replication. The sequence space accessed by primer extension dictates potential pathways to self-replication and, eventually, ribozymes. Which sequences can be accessed? What is the fidelity of the reaction? Does the recently illuminated mechanism of primer extension affect the distribution of sequences that can be copied? How do sequence features respond to experimental conditions and prebiotically relevant contexts? To help answer these and related questions, we here introduce a deep-sequencing methodology for studying RNA primer extension. We have designed and vetted special RNA constructs for this purpose, honed a protocol for sample preparation and developed custom software that analyzes sequencing data. We apply this new methodology to proof-of-concept controls, and demonstrate that it works as expected and reports on key features of the sequences accessed by primer extension.
Collapse
Affiliation(s)
- Daniel Duzdevich
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christopher E Carr
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jack W Szostak
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
38
|
|
39
|
Walton T, DasGupta S, Duzdevich D, Oh SS, Szostak JW. In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole-activated substrates. Proc Natl Acad Sci U S A 2020; 117:5741-5748. [PMID: 32123094 PMCID: PMC7084097 DOI: 10.1073/pnas.1914367117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The hypothesized central role of RNA in the origin of life suggests that RNA propagation predated the advent of complex protein enzymes. A critical step of RNA replication is the template-directed synthesis of a complementary strand. Two experimental approaches have been extensively explored in the pursuit of demonstrating protein-free RNA synthesis: template-directed nonenzymatic RNA polymerization using intrinsically reactive monomers and ribozyme-catalyzed polymerization using more stable substrates such as biological 5'-triphosphates. Despite significant progress in both approaches in recent years, the assembly and copying of functional RNA sequences under prebiotic conditions remains a challenge. Here, we explore an alternative approach to RNA-templated RNA copying that combines ribozyme catalysis with RNA substrates activated with a prebiotically plausible leaving group, 2-aminoimidazole (2AI). We applied in vitro selection to identify ligase ribozymes that catalyze phosphodiester bond formation between a template-bound primer and a phosphor-imidazolide-activated oligomer. Sequencing revealed the progressive enrichment of 10 abundant sequences from a random sequence pool. Ligase activity was detected in all 10 RNA sequences; all required activation of the ligator with 2AI and generated a 3'-5' phosphodiester bond. We propose that ribozyme catalysis of phosphodiester bond formation using intrinsically reactive RNA substrates, such as imidazolides, could have been an evolutionary step connecting purely nonenzymatic to ribozyme-catalyzed RNA template copying during the origin of life.
Collapse
Affiliation(s)
- Travis Walton
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Saurja DasGupta
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Daniel Duzdevich
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology, 37673 Pohang, Gyeongbuk, South Korea
| | - Jack W Szostak
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114;
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| |
Collapse
|
40
|
Motsch S, Pfeffer D, Richert C. 2'/3' Regioselectivity of Enzyme-Free Copying of RNA Detected by NMR. Chembiochem 2020; 21:2013-2018. [PMID: 32017335 PMCID: PMC7497262 DOI: 10.1002/cbic.202000014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Indexed: 11/06/2022]
Abstract
The RNA-templated extension of oligoribonucleotides by nucleotides produces either a 3',5' or a 2',5'-phosphodiester. Nature controls the regioselectivity during RNA chain growth with polymerases, but enzyme-free versions of genetic copying have modest specificity. Thus far, enzymatic degradation of products, combined with chromatography or electrophoresis, has been the preferred mode of detecting 2',5'-diesters produced in enzyme-free reactions. This approach hinges on the substrate specificity of nucleases, and is not suitable for in situ monitoring. Here we report how 1 H NMR spectroscopy can be used to detect the extension of self-templating RNA hairpins and that this reveals the regioisomeric nature of the newly formed phosphodiesters. We studied several modes of activating nucleotides, including imidazolides, a pyridinium phosphate, an active ester, and in situ activation with carbodiimide and organocatalyst. Conversion into the desired extension product ranged from 20 to 90 %, depending on the leaving group. Integration of the resonances of H1' protons of riboses and H5 protons of pyrimidines gave regioselectivities ranging from 40:60 to 85:15 (3',5' to 2',5' diester), but no simple correlation between 3',5' selectivity and yield. Our results show how monitoring with a high-resolution technique sheds a new light on a process that may have played an important role during the emergence of life.
Collapse
Affiliation(s)
- Sebastian Motsch
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Daniel Pfeffer
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| |
Collapse
|
41
|
Sui YF, Li D, Wang J, Bheemanaboina RRY, Ansari MF, Gan LL, Zhou CH. Design and biological evaluation of a novel type of potential multi-targeting antimicrobial sulfanilamide hybrids in combination of pyrimidine and azoles. Bioorg Med Chem Lett 2020; 30:126982. [DOI: 10.1016/j.bmcl.2020.126982] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/03/2020] [Accepted: 01/17/2020] [Indexed: 12/12/2022]
|
42
|
Johnson EO, Hung DT. A Point of Inflection and Reflection on Systems Chemical Biology. ACS Chem Biol 2019; 14:2497-2511. [PMID: 31613592 DOI: 10.1021/acschembio.9b00714] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
For the past several decades, chemical biologists have been leveraging chemical principles for understanding biology, tackling disease, and biomanufacturing, while systems biologists have holistically applied computation and genome-scale experimental tools to the same problems. About a decade ago, the benefit of combining the philosophies of chemical biology with systems biology into systems chemical biology was advocated, with the potential to systematically understand the way small molecules affect biological systems. Recently, there has been an explosion in new technologies that permit massive expansion in the scale of biological experimentation, increase access to more diverse chemical space, and enable powerful computational interpretation of large datasets. Fueled by these rapidly increasing capabilities, systems chemical biology is now at an inflection point, poised to enter a new era of more holistic and integrated scientific discovery. Systems chemical biology is primed to reveal an integrated understanding of fundamental biology and to discover new chemical probes to comprehensively dissect and systematically understand that biology, thereby providing a path to novel strategies for discovering therapeutics, designing drug combinations, avoiding toxicity, and harnessing beneficial polypharmacology. In this Review, we examine the emergence of new capabilities driving us to this inflection point in systems chemical biology, and highlight holistic approaches and opportunities that are arising from integrating chemical biology with a systems-level understanding of the intersection of biology and chemistry.
Collapse
Affiliation(s)
- Eachan O. Johnson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Deborah T. Hung
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| |
Collapse
|