1
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Aho A, Österlund T, Rahkila J, Virta PM. DNA‐templated formation and N,O‐transacetalization of N‐methoxyoxazolidines. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aapo Aho
- University of Turku: Turun Yliopisto Chemistry FINLAND
| | | | - Jani Rahkila
- Åbo Akademi: Abo Akademi Instrument Centre, Faculty of Science and Engineering FINLAND
| | - Pasi Markus Virta
- University of Turku department of chemistry Vatselankatu 2 20014 Turku FINLAND
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2
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Kühnlein A, Lanzmich SA, Braun D. tRNA sequences can assemble into a replicator. eLife 2021; 10:e63431. [PMID: 33648631 PMCID: PMC7924937 DOI: 10.7554/elife.63431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/28/2021] [Indexed: 11/29/2022] Open
Abstract
Can replication and translation emerge in a single mechanism via self-assembly? The key molecule, transfer RNA (tRNA), is one of the most ancient molecules and contains the genetic code. Our experiments show how a pool of oligonucleotides, adapted with minor mutations from tRNA, spontaneously formed molecular assemblies and replicated information autonomously using only reversible hybridization under thermal oscillations. The pool of cross-complementary hairpins self-selected by agglomeration and sedimentation. The metastable DNA hairpins bound to a template and then interconnected by hybridization. Thermal oscillations separated replicates from their templates and drove an exponential, cross-catalytic replication. The molecular assembly could encode and replicate binary sequences with a replication fidelity corresponding to 85-90 % per nucleotide. The replication by a self-assembly of tRNA-like sequences suggests that early forms of tRNA could have been involved in molecular replication. This would link the evolution of translation to a mechanism of molecular replication.
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Affiliation(s)
- Alexandra Kühnlein
- Systems Biophysics, Physics Department, Center for NanoScience, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Simon A Lanzmich
- Systems Biophysics, Physics Department, Center for NanoScience, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Dieter Braun
- Systems Biophysics, Physics Department, Center for NanoScience, Ludwig-Maximilians-Universität MünchenMunichGermany
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3
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Abstract
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The
potential of N(Me)-alkoxyamine glycosylation
as a DNA-templated ligation has been studied. On a hairpin stem-template
model, a notable rate enhancement and an increased equilibrium yield
are observed compared to the corresponding reaction without a DNA
catalyst. The N-glycosidic connection is dynamic
at pH 5, whereas it becomes irreversible at pH 7. The N(Me)-alkoxyamine glycosylation may hence be an attractive pH controlled
reaction for the assembly of DNA-based dynamic products.
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Affiliation(s)
- Tommi Österlund
- Department of Chemistry , University of Turku , 20014 Turku , Finland
| | - Heidi Korhonen
- Department of Chemistry , University of Turku , 20014 Turku , Finland
| | - Pasi Virta
- Department of Chemistry , University of Turku , 20014 Turku , Finland
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4
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Gimenez Molina A, Barvik I, Müller S, Vasseur JJ, Smietana M. RNA-based boronate internucleosidic linkages: an entry into reversible templated ligation and loop formation. Org Biomol Chem 2018; 16:8824-8830. [DOI: 10.1039/c8ob02182a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of a 5′-boronoribonucleotidic phosphoramidite building block has been achieved and incorporated at the 5′ extremities of RNA sequences for the templated assembly of RNA shortmers.
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Affiliation(s)
- Alejandro Gimenez Molina
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
| | - Ivan Barvik
- Institute of Physics
- Faculty of Mathematics and Physics
- Charles University
- 121 16 Prague 2
- Czech Republic
| | - Sabine Müller
- Institut für Biochemie
- Ernst-Moritz-Arndt-Universität Greifswald
- D-17489 Greifswald
- Germany
| | - Jean-Jacques Vasseur
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
| | - Michael Smietana
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
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5
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Beierle JM, Ura Y, Ghadiri MR, Leman LJ. Templated Self-Assembly of Dynamic Peptide Nucleic Acids. Biochemistry 2017; 57:160-172. [PMID: 28832127 DOI: 10.1021/acs.biochem.7b00656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Template-directed macromolecule synthesis is a hallmark of living systems. Inspired by this natural process, several fundamentally novel mechanisms for template-directed assembly of nucleic acid analogues have been developed. Although these approaches have broad significance, including potential applications in biotechnology and implications for the origins of life, there are unresolved challenges in how to characterize in detail the complex assembly equilibria associated with dynamic templated reactions. Here we describe mechanistic studies of template-directed dynamic assembly for thioester peptide nucleic acid (tPNA), an informational polymer that responds to selection pressures under enzyme-free conditions. To overcome some of the inherent challenges of mechanistic studies of dynamic oligomers, we designed, synthesized, and implemented tPNA-DNA conjugates. The DNA primer region affords a high level of control over the location and register of the tPNA backbone in relation to the template strand. We characterized the degree and kinetics of dynamic nucleobase mismatch correction at defined backbone positions. Furthermore, we report the fidelity of dynamic assembly in tPNA as a function of position along the peptide backbone. Finally, we present theoretical studies that explore the level of fidelity that can be expected for an oligomer having a given hybridization affinity in dynamic templated reactions and provide guidance for the future development of sequence self-editing polymers and materials. As our results demonstrate, the use of molecular conjugates of constitutionally static and dynamic polymers establishes a new methodology for expediting the characterization of the complex chemical equilibria that underlie the assembly of dynamic informational polymers.
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Affiliation(s)
- John M Beierle
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yasuyuki Ura
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - M Reza Ghadiri
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Luke J Leman
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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6
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He C, Gállego I, Laughlin B, Grover MA, Hud NV. A viscous solvent enables information transfer from gene-length nucleic acids in a model prebiotic replication cycle. Nat Chem 2016; 9:318-324. [PMID: 28338690 DOI: 10.1038/nchem.2628] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/23/2016] [Indexed: 11/09/2022]
Abstract
Many hypotheses concerning the nature of early life assume that genetic information was once transferred through the template-directed synthesis of RNA, before the emergence of coded enzymes. However, attempts to demonstrate enzyme-free, template-directed synthesis of nucleic acids have been limited by 'strand inhibition', whereby transferring information from a template strand in the presence of its complementary strand is inhibited by the stability of the template duplex. Here, we use solvent viscosity to circumvent strand inhibition, demonstrating information transfer from a gene-length template (>300 nt) within a longer (545 bp or 3 kb) duplex. These results suggest that viscous environments on the prebiotic Earth, generated periodically by water evaporation, could have facilitated nucleic acid replication-particularly of long, structured sequences such as ribozymes. Our approach works with DNA and RNA, suggesting that viscosity-mediated replication is possible for a range of genetic polymers, perhaps even for informational polymers that may have preceded RNA.
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Affiliation(s)
- Christine He
- School of Chemical &Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Isaac Gállego
- School of Chemistry &Biochemistry, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Brandon Laughlin
- School of Chemistry &Biochemistry, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Martha A Grover
- School of Chemical &Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Nicholas V Hud
- School of Chemistry &Biochemistry, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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7
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Catalano MJ, Price NE, Gates KS. Effective molarity in a nucleic acid-controlled reaction. Bioorg Med Chem Lett 2016; 26:2627-30. [PMID: 27117430 DOI: 10.1016/j.bmcl.2016.04.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 12/30/2022]
Abstract
Positioning of reactive functional groups within a DNA duplex can enable chemical reactions that otherwise would not occur to an appreciable extent. However, few studies have quantitatively defined the extent to which the enforced proximity of reaction partners in duplex DNA can favor chemical processes. Here, we measured substantial effective molarities (as high as 25M) afforded by duplex DNA to a reaction involving interstrand cross-link formation between 2'-deoxyadenosine and a 2-deoxyribose abasic (Ap) site.
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Affiliation(s)
- Michael J Catalano
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Nathan E Price
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States
| | - Kent S Gates
- University of Missouri, Department of Chemistry, 125 Chemistry Building, Columbia, MO 65211, United States; University of Missouri, Department of Biochemistry, 125 Chemistry Building, Columbia, MO 65211, United States.
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8
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Keefe AD, Clark MA, Hupp CD, Litovchick A, Zhang Y. Chemical ligation methods for the tagging of DNA-encoded chemical libraries. Curr Opin Chem Biol 2015; 26:80-8. [PMID: 25756406 DOI: 10.1016/j.cbpa.2015.02.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 11/28/2022]
Abstract
The generation of DNA-encoded chemical libraries requires the unimolecular association of multiple encoding oligonucleotides with encoded chemical entities during combinatorial synthesis processes. This has traditionally been achieved using enzymatic ligation. We discuss a range of chemical ligation methods that provide alternatives to enzymatic ligation. These chemical ligation methods include the generation of modified internucleotide linkages that support polymerase translocation and other modified linkages that while not supporting the translocation of polymerases can also be used to generate individual cDNA molecules containing encoded chemical information specifying individual library members. We also describe which of these approaches have been successfully utilized for the preparation of DNA-encoded chemical libraries and those that were subsequently used for the discovery of inhibitors.
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Affiliation(s)
- Anthony D Keefe
- X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA 02453, USA.
| | - Matthew A Clark
- X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA 02453, USA
| | | | | | - Ying Zhang
- X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA 02453, USA
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9
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Barbeyron R, Martin AR, Jean-Jacques Vasseur JJV, Michael Smietana MS. DNA-templated borononucleic acid self assembly: a study of minimal complexity. RSC Adv 2015. [DOI: 10.1039/c5ra20767c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The minimal degree of sequence complexity needed for DNA-templated self-assembly of bifunctional oligonucleotides able to form internucleosidic boronate linkages has been studied.
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Affiliation(s)
- Renaud Barbeyron
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- 34095 Montpellier
- France
| | - Anthony R. Martin
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- 34095 Montpellier
- France
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10
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Barbeyron R, Vasseur JJ, Smietana M. pH-controlled DNA- and RNA-templated assembly of short oligomers. Chem Sci 2015; 6:542-547. [PMID: 28936308 PMCID: PMC5588539 DOI: 10.1039/c4sc03028a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 10/24/2014] [Indexed: 01/04/2023] Open
Abstract
In the area of artificial genetics the development of non-enzymatic self-organization of synthetic building blocks is critical for both providing biopolymers with extended functions and understanding prebiotic processes. While reversibility is believed to have played a major role in early functional genetic materials, we previously reported an efficient DNA-templated ligation of suitably designed 5'-end boronic acid and 3'-end ribonucleosidic half-sequences. Here, we report the enzyme-free and activation-free DNA- and RNA-templated assembly of bifunctional hexamers. The reversible assembly was found to be regio- and sequence specific and the stabilities of the resulting duplexes were compared to their nicked counterparts. To go further with our understanding of this unprecedented process we also examined an auto-templated duplex self-assembly representing a key step toward the evolution of sequence-defined synthetic polymers.
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Affiliation(s)
- Renaud Barbeyron
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1 et Université Montpellier 2 , Place Bataillon , 34095 Montpellier , France . ;
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1 et Université Montpellier 2 , Place Bataillon , 34095 Montpellier , France . ;
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université Montpellier 1 et Université Montpellier 2 , Place Bataillon , 34095 Montpellier , France . ;
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11
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Birts CN, Sanzone AP, El-Sagheer AH, Blaydes JP, Brown T, Tavassoli A. Transcription of click-linked DNA in human cells. Angew Chem Int Ed Engl 2014; 53:2362-5. [PMID: 24452865 PMCID: PMC4016740 DOI: 10.1002/anie.201308691] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Indexed: 12/13/2022]
Abstract
Click DNA ligation promises an alternative to the current enzymatic approaches for DNA assembly, with the ultimate goal of using efficient chemical reactions for the total chemical synthesis and assembly of genes and genomes. Such an approach would enable the incorporation of various chemically modified bases throughout long stretches of DNA, a feat not possible with current polymerase-based methods. An unequivocal requirement for this approach is the biocompatibility of the resulting triazole-linked DNA. The correct function of this unnatural DNA linker in human cells is demonstrated here by using a click-linked gene encoding the fluorescent protein mCherry. Reverse transcription of mRNA isolated from these cells and subsequent sequencing of the mCherry cDNA shows error-free transcription. Nucleotide excision repair (NER) is shown to not play a role in the observed biocompatibility by using a NER-deficient human cell line. This is the first example of a non-natural DNA linker being functional in a eukaryotic cell.
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Affiliation(s)
- Charles N Birts
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD (UK)
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12
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Birts CN, Sanzone AP, El-Sagheer AH, Blaydes JP, Brown T, Tavassoli A. Transcription of Click-Linked DNA in Human Cells. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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13
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Vogel H, Gerlach C, Richert C. Reactions of buffers in cyanogen bromide-induced ligations. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2013; 32:17-27. [PMID: 23360292 DOI: 10.1080/15257770.2012.744036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Rapid, template-directed ligation reactions between a phosphate-terminated oligonucleotide and an unphosphorylated reaction partner may be induced by cyanogen bromide (BrCN). Frequently, however, the reaction is low yielding, and even a large excess of the condensing agent can fail to induce quantitative conversions. In this study, we used BrCN to induce chemical primer extension reactions. Here, we report that buffers containing hydroxyl groups react with short oligodeoxynucleotides in the presence of BrCN. One stable adduct between HEPBS buffer and cytosine was characterized by mass spectrometry and NMR after HPLC purification, indicating that a side reaction occurred at this nucleobase. Further, a first example of a primer extension reaction between an unmodified oligodeoxynucleotide as primer and dGMP is reported. Together, our results shed light on the potency, as well as the drawbacks of BrCN as a highly reactive condensing reagent for the ligation of unmodified nucleic acids.
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Affiliation(s)
- Heike Vogel
- Institute for Organic Chemistry, University of Stuttgart, Pfaffenwaldring, Germany
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14
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Barbeyron R, Wengel J, Vasseur JJ, Smietana M. Boronic acid-based autoligation of nucleic acids: influence of the nature of the 3′-end ribonucleotidic strand. MONATSHEFTE FUR CHEMIE 2012. [DOI: 10.1007/s00706-012-0881-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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