1
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Han J, Kervio E, Richert C. High Fidelity Enzyme-Free Primer Extension with an Ethynylpyridone Thymidine Analog. Chemistry 2021; 27:15918-15921. [PMID: 34559417 PMCID: PMC9293356 DOI: 10.1002/chem.202102996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Indexed: 11/07/2022]
Abstract
High fidelity base pairing is important for the transmission of genetic information. Weak base pairs can lower fidelity, complicating sequencing, amplification and replication of DNA. Thymidine 5'-monophosphate (TMP) is the most weakly pairing nucleotide among the canonical deoxynucleotides, causing high errors rates in enzyme-free primer extension. Here we report the synthesis of an ethynylpyridone C-nucleoside analog of 3'-amino-2',3'-dideoxythymidine monophosphate and its incorporation in a growing strand by enzyme-free primer extension. The ethynylpyridone C-nucleotide accelerates extension more than five-fold, reduces misincorporation and readily displaces TMP in competition experiments. The results bode well for the use of the C-nucleoside as replacements for thymidine in practical applications.
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Affiliation(s)
- Jianyang Han
- Institut für Organische ChemieUniversität Stuttgart70569StuttgartGermany
| | - Eric Kervio
- Institut für Organische ChemieUniversität Stuttgart70569StuttgartGermany
| | - Clemens Richert
- Institut für Organische ChemieUniversität Stuttgart70569StuttgartGermany
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2
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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.
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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
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3
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Murayama K, Okita H, Kuriki T, Asanuma H. Nonenzymatic polymerase-like template-directed synthesis of acyclic L-threoninol nucleic acid. Nat Commun 2021; 12:804. [PMID: 33547322 PMCID: PMC7864931 DOI: 10.1038/s41467-021-21128-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/04/2021] [Indexed: 02/08/2023] Open
Abstract
Evolution of xeno nucleic acid (XNA) world essentially requires template-directed synthesis of XNA polymers. In this study, we demonstrate template-directed synthesis of an acyclic XNA, acyclic L-threoninol nucleic acid (L-aTNA), via chemical ligation mediated by N-cyanoimidazole. The ligation of an L-aTNA fragment on an L-aTNA template is significantly faster and occurs in considerably higher yield than DNA ligation. Both L-aTNA ligation on a DNA template and DNA ligation on an L-aTNA template are also observed. High efficiency ligation of trimer L-aTNA fragments to a template-bound primer is achieved. Furthermore, a pseudo primer extension reaction is demonstrated using a pool of random L-aTNA trimers as substrates. To the best of our knowledge, this is the first example of polymerase-like primer extension of XNA with all four nucleobases, generating phosphodiester bonding without any special modification. This technique paves the way for a genetic system of the L-aTNA world.
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Affiliation(s)
- Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
| | - Hikari Okita
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Takumi Kuriki
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
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4
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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: 20] [Impact Index Per Article: 5.0] [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.
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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
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5
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Walton T, Zhang W, Li L, Tam CP, Szostak JW. The Mechanism of Nonenzymatic Template Copying with Imidazole-Activated Nucleotides. Angew Chem Int Ed Engl 2019; 58:10812-10819. [PMID: 30908802 DOI: 10.1002/anie.201902050] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Indexed: 11/10/2022]
Abstract
The emergence of the replication of RNA oligonucleotides was a critical step in the origin of life. An important model for the study of nonenzymatic template copying, which would be a key part of any such pathway, involves the reaction of ribonucleoside-5'-phosphorimidazolides with an RNA primer/template complex. The mechanism by which the primer becomes extended by one nucleotide was assumed to be a classical in-line nucleophilic-substitution reaction in which the 3'-hydroxyl of the primer attacks the phosphate of the incoming activated monomer with displacement of the imidazole leaving group. Surprisingly, this simple model has turned out to be incorrect, and the dominant pathway has now been shown to involve the reaction of two activated nucleotides with each other to form a 5'-5'-imidazolium bridged dinucleotide intermediate. Here we review the discovery of this unexpected intermediate, and the chemical, kinetic, and structural evidence for its role in template copying chemistry.
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Affiliation(s)
- Travis Walton
- Howard Hughes Medical Institute and Dept. of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Wen Zhang
- Howard Hughes Medical Institute and Dept. of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Li Li
- Howard Hughes Medical Institute and Dept. of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Chun Pong Tam
- Howard Hughes Medical Institute and Dept. of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.,Present address: Moderna Inc., Cambridge, MA, 02139, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute and Dept. of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
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6
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Walton T, Zhang W, Li L, Tam CP, Szostak JW. The Mechanism of Nonenzymatic Template Copying with Imidazole‐Activated Nucleotides. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902050] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Travis Walton
- Howard Hughes Medical Institute and Dept. of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
| | - Wen Zhang
- Howard Hughes Medical Institute and Dept. of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
| | - Li Li
- Howard Hughes Medical Institute and Dept. of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
| | - Chun Pong Tam
- Howard Hughes Medical Institute and Dept. of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Dept. of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
- Present address: Moderna Inc. Cambridge MA 02139 USA
| | - Jack W. Szostak
- Howard Hughes Medical Institute and Dept. of Molecular Biology Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Dept. of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
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7
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Sosson M, Pfeffer D, Richert C. Enzyme-free ligation of dimers and trimers to RNA primers. Nucleic Acids Res 2019; 47:3836-3845. [PMID: 30869145 PMCID: PMC6486630 DOI: 10.1093/nar/gkz160] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/25/2019] [Accepted: 02/28/2019] [Indexed: 01/19/2023] Open
Abstract
The template-directed formation of phosphodiester bonds between two nucleic acid components is a pivotal process in biology. To induce such a reaction in the absence of enzymes is a challenge. This challenge has been met for the extension of a primer with mononucleotides, but the ligation of short oligonucleotides (dimers or trimers) has proven difficult. Here we report a method for ligating dimers and trimers of ribonucleotides using in situ activation in aqueous buffer. All 16 different dimers and two trimers were tested. Binding studies by NMR showed low millimolar dissociation constants for complexes between representative dimers and hairpins mimicking primer-template duplexes, confirming that a weak template effect is not the cause of the poor ligating properties of these short oligomers. Rather, cyclization was found to compete with ligation, with up to 90% of dimer being converted to the cyclic form during the course of an assay. This side reaction is strongly sequence dependent and more pronounced for dimers than for trimers. Under optimized reaction conditions, high yields were observed with strongly pairing purines at the 3'-terminus. These results show that short oligomers of ribonucleotides are competent reactants in enzyme-free copying.
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Affiliation(s)
- Marilyne Sosson
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Daniel Pfeffer
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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8
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Le Vay K, Weise LI, Libicher K, Mascarenhas J, Mutschler H. Templated Self‐Replication in Biomimetic Systems. ACTA ACUST UNITED AC 2019; 3:e1800313. [DOI: 10.1002/adbi.201800313] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/06/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Kristian Le Vay
- Biomimetic SystemsMax Planck Institute of Biochemistry Martinsried Germany
| | - Laura Isabel Weise
- Biomimetic SystemsMax Planck Institute of Biochemistry Martinsried Germany
| | - Kai Libicher
- Biomimetic SystemsMax Planck Institute of Biochemistry Martinsried Germany
| | - Judita Mascarenhas
- Department of Systems and Synthetic MicrobiologyMax Planck Institute for Terrestrial Microbiology Marburg Germany
| | - Hannes Mutschler
- Biomimetic SystemsMax Planck Institute of Biochemistry Martinsried Germany
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9
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Walton T, Pazienza L, Szostak JW. Template-Directed Catalysis of a Multistep Reaction Pathway for Nonenzymatic RNA Primer Extension. Biochemistry 2018; 58:755-762. [PMID: 30566332 PMCID: PMC7547881 DOI: 10.1021/acs.biochem.8b01156] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Before
the advent of polymerase enzymes, the copying of genetic
material during the origin of life may have involved the nonenzymatic
polymerization of RNA monomers that are more reactive than the biological
nucleoside triphosphates. Activated RNA monomers such as nucleotide
5′-phosphoro-2-aminoimidazolides spontaneously form an imidazolium-bridged
dinucleotide intermediate that undergoes rapid nonenzymatic template-directed
primer extension. However, it is unknown whether the intermediate
can form on the template or only in solution and whether the intermediate
is prone to hydrolysis when bound to the template or reacts preferentially
with the primer. Here we show that an activated monomer can first
bind the template and then form an imidazolium-bridged intermediate
by reacting with a 2-aminoimidazole-activated downstream oligonucleotide.
We have also characterized the partition of the template-bound intermediate
between hydrolysis and primer extension. In the presence of the catalytic
metal ion Mg2+, >90% of the template-bound intermediate
reacts with the adjacent primer to generate the primer extension product
while less than 10% reacts with competing water. Our results indicate
that an RNA template can catalyze a multistep phosphodiester bond
formation pathway while minimizing hydrolysis with a specificity reminiscent
of an enzyme-catalyzed reaction.
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Affiliation(s)
- Travis Walton
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology , Massachusetts General Hospital , Boston , Massachusetts 02114 , United States
| | - Lydia Pazienza
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , 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 , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
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10
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Affiliation(s)
- Elena Hänle
- Institut für Organische Chemie; Universität Stuttgart; 70569 Stuttgart Germany
| | - Clemens Richert
- Institut für Organische Chemie; Universität Stuttgart; 70569 Stuttgart Germany
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11
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Hänle E, Richert C. Enzyme-Free Replication with Two or Four Bases. Angew Chem Int Ed Engl 2018; 57:8911-8915. [PMID: 29779237 DOI: 10.1002/anie.201803074] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/27/2018] [Indexed: 11/10/2022]
Abstract
All known forms of life encode their genetic information in a sequence of bases of a genetic polymer and produce copies through replication. How this process started before polymerase enzymes had evolved is unclear. Enzyme-free copying of short stretches of DNA or RNA has been demonstrated using activated nucleotides, but not replication. We have developed a method for enzyme-free replication. It involves extension with reversible termination, enzyme-free ligation, and strand capture. We monitored nucleotide incorporation for a full helical turn of DNA, during both a first and a second round of copying, by using mass spectrometry. With all four bases (A/C/G/T), an "error catastrophe" occurred, with the correct sequence being "overwhelmed" by incorrect ones. When only C and G were used, approximately half of the daughter strands had the mass of the correct sequence after 20 copying steps. We conclude that enzyme-free replication is more likely to be successful with just the two strongly pairing bases than with all four bases of the genetic alphabet.
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Affiliation(s)
- Elena Hänle
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
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12
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Sosson M, Richert C. Enzyme-free genetic copying of DNA and RNA sequences. Beilstein J Org Chem 2018; 14:603-617. [PMID: 29623122 PMCID: PMC5870163 DOI: 10.3762/bjoc.14.47] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 02/20/2018] [Indexed: 11/23/2022] Open
Abstract
The copying of short DNA or RNA sequences in the absence of enzymes is a fascinating reaction that has been studied in the context of prebiotic chemistry. It involves the incorporation of nucleotides at the terminus of a primer and is directed by base pairing. The reaction occurs in aqueous medium and leads to phosphodiester formation after attack of a nucleophilic group of the primer. Two aspects of this reaction will be discussed in this review. One is the activation of the phosphate that drives what is otherwise an endergonic reaction. The other is the improved mechanistic understanding of enzyme-free primer extension that has led to a quantitative kinetic model predicting the yield of the reaction over the time course of an assay. For a successful modeling of the reaction, the strength of the template effect, the inhibitory effect of spent monomers, and the rate constants of the chemical steps have to be determined experimentally. While challenges remain for the high fidelity copying of long stretches of DNA or RNA, the available data suggest that enzyme-free primer extension is a more powerful reaction than previously thought.
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Affiliation(s)
- Marilyne Sosson
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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13
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Zhang W, Tam CP, Zhou L, Oh SS, Wang J, Szostak JW. Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide. J Am Chem Soc 2018; 140:2829-2840. [PMID: 29411978 PMCID: PMC6326529 DOI: 10.1021/jacs.7b11750] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Indexed: 01/28/2023]
Abstract
Nonenzymatic RNA primer extension by activated mononucleotides has long served as a model for the study of prebiotic RNA copying. We have recently shown that the rate of primer extension is greatly enhanced by the formation of an imidazolium-bridged dinucleotide between the incoming monomer and a second, downstream activated monomer. However, the rate of primer extension is further enhanced if the downstream monomer is replaced by an activated oligonucleotide. Even an unactivated downstream oligonucleotide provides a modest enhancement in the rate of reaction of a primer with a single activated monomer. Here we study the mechanism of these effects through crystallographic studies of RNA complexes with the recently synthesized nonhydrolyzable substrate analog, guanosine 5'-(4-methylimidazolyl)-phosphonate (ICG). ICG mimics 2-methylimidazole activated guanosine-5'-phosphate (2-MeImpG), a commonly used substrate in nonenzymatic primer extension experiments. We present crystal structures of primer-template complexes with either one or two ICG residues bound downstream of a primer. In both cases, the aryl-phosphonate moiety of the ICG adjacent to the primer is disordered. To investigate the effect of a downstream oligonucleotide, we transcribed a short RNA oligonucleotide with either a 5'-ICG residue, a 5'-phosphate or a 5'-hydroxyl. We then determined crystal structures of primer-template complexes with a bound ICG monomer sandwiched between the primer and each of the three downstream oligonucleotides. Surprisingly, all three oligonucleotides rigidify the ICG monomer conformation and position it for attack by the primer 3'-hydroxyl. Furthermore, when GpppG, an analog of the imidazolium-bridged intermediate, is sandwiched between an upstream primer and a downstream helper oligonucleotide, or covalently linked to the 5'-end of the downstream oligonucleotide, the complex is better preorganized for primer extension than in the absence of a downstream oligonucleotide. Our results suggest that a downstream helper oligonucleotide contributes to the catalysis of primer extension by favoring a reactive conformation of the primer-template-intermediate complex.
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Affiliation(s)
- Wen Zhang
- Howard
Hughes Medical Institute and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Chun Pong Tam
- Howard
Hughes Medical Institute 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 and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Seung Soo Oh
- Howard
Hughes Medical Institute and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Jiawei Wang
- School
of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jack W. Szostak
- Howard
Hughes Medical Institute and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
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14
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Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex. Proc Natl Acad Sci U S A 2017; 114:7659-7664. [PMID: 28673998 DOI: 10.1073/pnas.1704006114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nonenzymatic copying of RNA templates with imidazole-activated nucleotides is a well-studied model for the emergence of RNA self-replication during the origin of life. We have recently discovered that this reaction can proceed through the formation of an imidazolium-bridged dinucleotide intermediate that reacts rapidly with the primer. To gain insight into the relationship between the structure of this intermediate and its reactivity, we cocrystallized an RNA primer-template complex with a close analog of the intermediate, the triphosphate-bridged guanosine dinucleotide GpppG, and solved a high-resolution X-ray structure of the complex. The structure shows that GpppG binds the RNA template through two Watson-Crick base pairs, with the primer 3'-hydroxyl oriented to attack the 5'-phosphate of the adjacent G residue. Thus, the GpppG structure suggests that the bound imidazolium-bridged dinucleotide intermediate would be preorganized to react with the primer by in-line SN2 substitution. The structures of bound GppG and GppppG suggest that the length and flexibility of the 5'-5' linkage are important for optimal preorganization of the complex, whereas the position of the 5'-phosphate of bound pGpG explains the slow rate of oligonucleotide ligation reactions. Our studies provide a structural interpretation for the observed reactivity of the imidazolium-bridged dinucleotide intermediate in nonenzymatic RNA primer extension.
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15
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Tam CP, Fahrenbach AC, Björkbom A, Prywes N, Izgu EC, Szostak JW. Downstream Oligonucleotides Strongly Enhance the Affinity of GMP to RNA Primer-Template Complexes. J Am Chem Soc 2017; 139:571-574. [PMID: 28055190 PMCID: PMC7547879 DOI: 10.1021/jacs.6b09760] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Indexed: 11/29/2022]
Abstract
Origins of life hypotheses often invoke a transitional phase of nonenzymatic template-directed RNA replication prior to the emergence of ribozyme-catalyzed copying of genetic information. Here, using NMR and ITC, we interrogate the binding affinity of guanosine 5'-monophosphate (GMP) for primer-template complexes when either another GMP, or a helper oligonucleotide, can bind downstream. Binding of GMP to a primer-template complex cannot be significantly enhanced by the possibility of downstream monomer binding, because the affinity of the downstream monomer is weaker than that of the first monomer. Strikingly, GMP binding affinity can be enhanced by ca. 2 orders of magnitude when a helper oligonucleotide is stably bound downstream of the monomer binding site. We compare these thermodynamic parameters to those previously reported for T7 RNA polymerase-mediated replication to help address questions of binding affinity in related nonenzymatic processes.
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Affiliation(s)
- Chun Pong Tam
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Albert C. Fahrenbach
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Earth
Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Anders Björkbom
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Biosciences, Åbo Akademi University, Åbo FI-20520, Finland
| | - Noam Prywes
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Enver Cagri Izgu
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - 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, Massachusetts 02114, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
- Earth
Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
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16
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Reverte M, Barvik I, Vasseur JJ, Smietana M. RNA-directed off/on switch of RNase H activity using boronic ester formation. Org Biomol Chem 2017; 15:8204-8210. [DOI: 10.1039/c7ob02145c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new concept to modulate RNase H activity is presented based on the boronic acid/boronate switch.
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Affiliation(s)
- Maëva Reverte
- 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
| | - 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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17
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Hamlin TA, Poater J, Fonseca Guerra C, Bickelhaupt FM. B-DNA model systems in non-terran bio-solvents: implications for structure, stability and replication. Phys Chem Chem Phys 2017; 19:16969-16978. [DOI: 10.1039/c7cp01908d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We have computationally analyzed a comprehensive series of Watson–Crick and mismatched B-DNA base pairs, in the gas phase and in several solvents, including toluene, chloroform, ammonia, methanol and water, using dispersion-corrected density functional theory and implicit solvation.
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Affiliation(s)
- Trevor A. Hamlin
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM)
- Vrije Universiteit Amsterdam
- NL-1081 HV Amsterdam
- The Netherlands
| | - Jordi Poater
- Departament de Química Inorgànica i Orgánica & Institut de Química Teòrica i Computacional (IQTCUB)
- Universitat de Barcelona
- 08028 Barcelona
- Spain
- ICREA
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM)
- Vrije Universiteit Amsterdam
- NL-1081 HV Amsterdam
- The Netherlands
- Leiden Institute of Chemistry
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM)
- Vrije Universiteit Amsterdam
- NL-1081 HV Amsterdam
- The Netherlands
- Institute of Molecules and Materials
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18
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Taming Prebiotic Chemistry: The Role of Heterogeneous and Interfacial Catalysis in the Emergence of a Prebiotic Catalytic/Information Polymer System. Life (Basel) 2016; 6:life6040040. [PMID: 27827919 PMCID: PMC5198075 DOI: 10.3390/life6040040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 01/10/2023] Open
Abstract
Cellular life is based on interacting polymer networks that serve as catalysts, genetic information and structural molecules. The complexity of the DNA, RNA and protein biochemistry suggests that it must have been preceded by simpler systems. The RNA world hypothesis proposes RNA as the prime candidate for such a primal system. Even though this proposition has gained currency, its investigations have highlighted several challenges with respect to bulk aqueous media: (1) the synthesis of RNA monomers is difficult; (2) efficient pathways for monomer polymerization into functional RNAs and their subsequent, sequence-specific replication remain elusive; and (3) the evolution of the RNA function towards cellular metabolism in isolation is questionable in view of the chemical mixtures expected on the early Earth. This review will address the question of the possible roles of heterogeneous media and catalysis as drivers for the emergence of RNA-based polymer networks. We will show that this approach to non-enzymatic polymerizations of RNA from monomers and RNA evolution cannot only solve some issues encountered during reactions in bulk aqueous solutions, but may also explain the co-emergence of the various polymers indispensable for life in complex mixtures and their organization into primitive networks.
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19
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Göckel A, Richert C. Synthesis of an oligonucleotide with a nicotinamide mononucleotide residue and its molecular recognition in DNA helices. Org Biomol Chem 2016; 13:10303-9. [PMID: 26371420 DOI: 10.1039/c5ob01714a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD) is a pivotal redox cofactor of primary metabolism. Its redox reactivity is based on the nicotinamide mononucleotide (NMN) moiety. We investigated whether NMN(+) can engage in pairing interactions, when incorporated into an oligonucleotide. Here we describe the incorporation of NMN(+) at the 3'-terminus of an oligodeoxynucleotide via a phosphoramidate coupling in solution. The stability of duplexes and triplexes with the NMN(+)-containing strand was measured in UV-melting curves. While the melting points of duplexes with different bases facing the nicotinamide were similar, triplex stabilities varied greatly between different base combinations, suggesting specific pairing. The most stable triplexes were found when a guanine and an adenine were facing the NMN(+) residue. Their triplex melting points were higher than those of the corresponding triplexes with a thymidine residue at the same position. These results show that NMN(+) residues can be recognized selectively in DNA helices and are thus compatible with the molecular recognition in nucleic acids.
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Affiliation(s)
- A Göckel
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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20
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Kervio E, Sosson M, Richert C. The effect of leaving groups on binding and reactivity in enzyme-free copying of DNA and RNA. Nucleic Acids Res 2016; 44:5504-14. [PMID: 27235418 PMCID: PMC4937335 DOI: 10.1093/nar/gkw476] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 01/29/2023] Open
Abstract
The template-directed incorporation of nucleotides at the terminus of a growing primer is the basis of the transmission of genetic information. Nature uses polymerases-catalyzed reactions, but enzyme-free versions exist that employ nucleotides with organic leaving groups. The leaving group affects yields, but it was not clear whether inefficient extensions are due to poor binding, low reactivity toward the primer, or rapid hydrolysis. We have measured the binding of a total of 15 different activated nucleotides to DNA or RNA sequences. Further, we determined rate constants for the chemical step of primer extension involving methylimidazolides or oxyazabenzotriazolides of deoxynucleotides or ribonucleotides. Binding constants range from 10 to >500 mM and rate constants from 0.1 to 370 M(-1) h(-1) For aminoterminal primers, a fast covalent step and slow hydrolysis are the main factors leading to high yields. For monomers with weakly pairing bases, the leaving group can improve binding significantly. A detailed mechanistic picture emerges that explains why some enzyme-free primer extensions occur in high yield, while others remain recalcitrant to copying without enzymatic catalysis. A combination of tight binding and rapid extension, coupled with slow hydrolysis induces efficient enzyme-free copying.
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Affiliation(s)
- Eric Kervio
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Marilyne Sosson
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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21
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Prywes N, Blain JC, Del Frate F, Szostak JW. Nonenzymatic copying of RNA templates containing all four letters is catalyzed by activated oligonucleotides. eLife 2016; 5:e17756. [PMID: 27351102 PMCID: PMC4959843 DOI: 10.7554/elife.17756] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/27/2016] [Indexed: 01/26/2023] Open
Abstract
The nonenzymatic replication of RNA is a potential transitional stage between the prebiotic chemistry of nucleotide synthesis and the canonical RNA world in which RNA enzymes (ribozymes) catalyze replication of the RNA genomes of primordial cells. However, the plausibility of nonenzymatic RNA replication is undercut by the lack of a protocell-compatible chemical system capable of copying RNA templates containing all four nucleotides. We show that short 5'-activated oligonucleotides act as catalysts that accelerate primer extension, and allow for the one-pot copying of mixed sequence RNA templates. The fidelity of the primer extension products resulting from the sequential addition of activated monomers, when catalyzed by activated oligomers, is sufficient to sustain a genome long enough to encode active ribozymes. Finally, by immobilizing the primer and template on a bead and adding individual monomers in sequence, we synthesize a significant part of an active hammerhead ribozyme, forging a link between nonenzymatic polymerization and the RNA world.
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Affiliation(s)
- Noam Prywes
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States
| | - J Craig Blain
- Department of Molecular Biology and Center for Computational and Integrative Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States
| | - Francesca Del Frate
- Department of Molecular Biology and Center for Computational and Integrative Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States
| | - Jack W Szostak
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States
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22
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Pal A, Das RS, Zhang W, Lang M, McLaughlin LW, Szostak JW. Effect of terminal 3′-hydroxymethyl modification of an RNA primer on nonenzymatic primer extension. Chem Commun (Camb) 2016; 52:11905-11907. [DOI: 10.1039/c6cc06925h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Displacing the hydroxyl nucleophile at the 3′-end of a primer by a single methylene group drastically decreases the rate of primer extension, illustrating the importance of the precise position of the hydroxyl nucleophile.
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Affiliation(s)
- Ayan Pal
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- Boston
- USA
| | - Rajat S. Das
- Boston College
- Department of Chemistry
- Merkert Chemistry Center
- Chestnut Hill
- USA
| | - Weicheng Zhang
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- Boston
- USA
| | - Megan Lang
- Boston College
- Department of Chemistry
- Merkert Chemistry Center
- Chestnut Hill
- USA
| | - Larry W. McLaughlin
- Boston College
- Department of Chemistry
- Merkert Chemistry Center
- Chestnut Hill
- USA
| | - Jack W. Szostak
- Howard Hughes Medical Institute
- Department of Molecular Biology and Center for Computational and Integrative Biology
- Massachusetts General Hospital
- Boston
- USA
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23
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Jauker M, Griesser H, Richert C. Copying of RNA Sequences without Pre-Activation. Angew Chem Int Ed Engl 2015; 54:14559-63. [PMID: 26435291 PMCID: PMC4678514 DOI: 10.1002/anie.201506592] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/03/2015] [Indexed: 11/23/2022]
Abstract
Template-directed incorporation of nucleotides at the terminus of a growing complementary strand is the basis of replication. For RNA, this process can occur in the absence of enzymes, if the ribonucleotides are first converted to an active species with a leaving group. Thus far, the activation required a separate chemical step, complicating prebiotically plausible scenarios. Here we show that a combination of a carbodiimide and an organocatalyst induces near-quantitative incorporation of any of the four ribonucleotides. Upon in situ activation, adenosine monophosphate was found to also form oligomers in aqueous solution. So, both de novo strand formation and sequence-specific copying can occur without an artificial synthetic step.
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Affiliation(s)
- Mario Jauker
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
| | - Helmut Griesser
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany).
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24
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Jauker M, Griesser H, Richert C. Kopieren von RNA-Sequenzen ohne Voraktivierung. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506592] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Larsen AT, Fahrenbach AC, Sheng J, Pian J, Szostak JW. Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization. Nucleic Acids Res 2015; 43:7675-87. [PMID: 26240387 PMCID: PMC4652770 DOI: 10.1093/nar/gkv761] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/14/2015] [Indexed: 02/07/2023] Open
Abstract
Nucleobase modifications dramatically alter nucleic acid structure and thermodynamics. 2-thiouridine (s(2)U) is a modified nucleobase found in tRNAs and known to stabilize U:A base pairs and destabilize U:G wobble pairs. The recently reported crystal structures of s(2)U-containing RNA duplexes do not entirely explain the mechanisms responsible for the stabilizing effect of s(2)U or whether this effect is entropic or enthalpic in origin. We present here thermodynamic evaluations of duplex formation using ITC and UV thermal denaturation with RNA duplexes containing internal s(2)U:A and s(2)U:U pairs and their native counterparts. These results indicate that s(2)U stabilizes both duplexes. The stabilizing effect is entropic in origin and likely results from the s(2)U-induced preorganization of the single-stranded RNA prior to hybridization. The same preorganizing effect is likely responsible for structurally resolving the s(2)U:U pair-containing duplex into a single conformation with a well-defined H-bond geometry. We also evaluate the effect of s(2)U on single strand conformation using UV- and CD-monitored thermal denaturation and on nucleoside conformation using (1)H NMR spectroscopy, MD and umbrella sampling. These results provide insights into the effects that nucleobase modification has on RNA structure and thermodynamics and inform efforts toward improving both ribozyme-catalyzed and nonenzymatic RNA copying.
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Affiliation(s)
- Aaron T Larsen
- Howard Hughes Medical Institute, Center for Computational and Integrative Biology, and Department of Molecular Biology, Simches Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Albert C Fahrenbach
- Howard Hughes Medical Institute, Center for Computational and Integrative Biology, and Department of Molecular Biology, Simches Research Center, Massachusetts General Hospital, Boston, MA 02114, USA Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Jia Sheng
- University at Albany, State University of New York, Department of Chemistry, The RNA Institute, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Julia Pian
- Howard Hughes Medical Institute, Center for Computational and Integrative Biology, and Department of Molecular Biology, Simches Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Center for Computational and Integrative Biology, and Department of Molecular Biology, Simches Research Center, Massachusetts General Hospital, Boston, MA 02114, USA Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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26
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27
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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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28
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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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29
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Synergism and mutualism in non-enzymatic RNA polymerization. Life (Basel) 2014; 4:598-620. [PMID: 25370531 PMCID: PMC4284460 DOI: 10.3390/life4040598] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 01/19/2023] Open
Abstract
The link between non-enzymatic RNA polymerization and RNA self-replication is a key step towards the "RNA world" and still far from being solved, despite extensive research. Clay minerals, lipids and, more recently, peptides were found to catalyze the non-enzymatic synthesis of RNA oligomers. Herein, a review of the main models for the formation of the first RNA polymers is presented in such a way as to emphasize the cooperation between life's building blocks in their emergence and evolution. A logical outcome of the previous results is a combination of these models, in which RNA polymerization might have been catalyzed cooperatively by clays, lipids and peptides in one multi-component prebiotic soup. The resulting RNAs and oligopeptides might have mutualistically evolved towards functional RNAs and catalytic peptides, preceding the first RNA replication, thus supporting an RNA-peptide world. The investigation of such a system is a formidable challenge, given its complexity deriving from a tremendously large number of reactants and innumerable products. A rudimentary experimental design is outlined, which could be used in an initial attempt to study a quaternary component system.
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30
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Kervio E, Claasen B, Steiner UE, Richert C. The strength of the template effect attracting nucleotides to naked DNA. Nucleic Acids Res 2014; 42:7409-20. [PMID: 24875480 PMCID: PMC4066754 DOI: 10.1093/nar/gku314] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transmission of genetic information relies on Watson–Crick base pairing between nucleoside phosphates and template bases in template–primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequences is intimately linked to the origin of life and provides new opportunities for reading genetic information. Here, we report the dissociation constants for complexes between (deoxy)nucleotides and template–primer complexes, as determined by nuclear magnetic resonance and the inhibitory effect of unactivated nucleotides on enzyme-free primer extension. Depending on the sequence context, Kd′s range from 280 mM for thymidine monophosphate binding to a terminal adenine of a hairpin to 2 mM for a deoxyguanosine monophosphate binding in the interior of a sequence with a neighboring strand. Combined with rate constants for the chemical step of extension and hydrolytic inactivation, our quantitative theory explains why some enzyme-free copying reactions are incomplete while others are not. For example, for GMP binding to ribonucleic acid, inhibition is a significant factor in low-yielding reactions, whereas for amino-terminal DNA hydrolysis of monomers is critical. Our results thus provide a quantitative basis for enzyme-free copying.
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Affiliation(s)
- Eric Kervio
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Birgit Claasen
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Ulrich E Steiner
- Fachbereich Chemie, Universität Konstanz, 78457 Konstanz, Germany
| | - Clemens Richert
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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31
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Abstract
The complexity of even the simplest known life forms makes efforts to synthesize living cells from inanimate components seem like a daunting task. However, recent progress toward the creation of synthetic cells, ranging from simple protocells to artificial cells approaching the complexity of bacteria, suggests that the synthesis of life is now a realistic goal. Protocell research, fueled by advances in the biophysics of primitive membranes and the chemistry of nucleic acid replication, is providing new insights into the origin of cellular life. Parallel efforts to construct more complex artificial cells, incorporating translational machinery and protein enzymes, are providing information about the requirements for protein-based life. We discuss recent advances and remaining challenges in the synthesis of artificial cells, the possibility of creating new forms of life distinct from existing biology, and the promise of this research for gaining a deeper understanding of the nature of living systems.
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Affiliation(s)
- J Craig Blain
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114; ,
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32
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Kaiser A, Richert C. Nucleotide-based copying of nucleic acid sequences without enzymes. J Org Chem 2013; 78:793-9. [PMID: 23327991 DOI: 10.1021/jo3025779] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chemical primer extension is the enzyme-free incorporation of nucleotides at the end of an oligonucleotide, directed by a template. The reaction mimics the copying of sequences during replication but relies on recognition and reactivity of nucleic acids alone. Copying is low-yielding, particularly for long RNA. Hydrolysis of active esters and inhibition through hydrolysis products have been identified as factors that prevent high yields, and approaches to overcoming them have culminated in successful template-directed solid-phase syntheses for RNA and phosphoramidate DNA.
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Affiliation(s)
- Andreas Kaiser
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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33
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Leu K, Kervio E, Obermayer B, Turk-MacLeod RM, Yuan C, Luevano JM, Chen E, Gerland U, Richert C, Chen IA. Cascade of reduced speed and accuracy after errors in enzyme-free copying of nucleic acid sequences. J Am Chem Soc 2013; 135:354-66. [PMID: 23259600 PMCID: PMC3557965 DOI: 10.1021/ja3095558] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonenzymatic, template-directed synthesis of nucleic acids is a paradigm for self-replicating systems. The evolutionary dynamics of such systems depend on several factors, including the mutation rates, relative replication rates, and sequence characteristics of mutant sequences. We measured the kinetics of correct and incorrect monomer insertion downstream of a primer-template mismatch (mutation), using a range of backbone structures (RNA, DNA, and LNA templates and RNA and DNA primers) and two types of 5'-activated nucleotides (oxyazabenzotriazolides and imidazolides, i.e., nucleoside 5'-phosphorimidazolides). Our study indicated that for all systems studied, an initial mismatch was likely to be followed by another error (54-75% of the time), and extension after a single mismatch was generally 10-100 times slower than extension without errors. If the mismatch was followed by a matched base pair, the extension rate recovered to nearly normal levels. On the basis of these data, we simulated nucleic acid replication in silico, which indicated that a primer suffering an initial error would lag behind properly extended counterparts due to a cascade of subsequent errors and kinetic stalling, with the typical mutational event consisting of several consecutive errors. Our study also included different sequence contexts, which suggest the presence of cooperativity among monomers affecting both absolute rate (by up to 2 orders of magnitude) and fidelity. The results suggest that molecular evolution in enzyme-free replication systems would be characterized by large "leaps" through sequence space rather than isolated point mutations, perhaps enabling rapid exploration of diverse sequences. The findings may also be useful for designing self-replicating systems combining high fidelity with evolvability.
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Affiliation(s)
- Kevin Leu
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Eric Kervio
- Institute for Organic Chemistry, University of Stuttgart, Stuttgart, Germany
| | | | | | - Caterina Yuan
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | | | - Eric Chen
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
| | - Ulrich Gerland
- Physics Department and Center for Nanoscience, University of Munich, Munich, Germany
| | - Clemens Richert
- Institute for Organic Chemistry, University of Stuttgart, Stuttgart, Germany
| | - Irene A. Chen
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
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Choi JY, Kim YT, Byun JY, Ahn J, Chung S, Gweon DG, Kim MG, Seo TS. An integrated allele-specific polymerase chain reaction-microarray chip for multiplex single nucleotide polymorphism typing. LAB ON A CHIP 2012; 12:5146-5154. [PMID: 23037501 DOI: 10.1039/c2lc40878c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
An integrated allele-specific polymerase chain reaction (AS PCR) and microarray chip has been developed for multiplex single nucleotide polymorphism (SNP) typing on a portable genetic analyzer instrumentation. We applied the integrated PCR-microarray system for on-site Hanwoo (Korean indigenous beef cattle) identification. Eleven sets of primers were designed, among which ten sets of primers targeted ten SNP loci to discriminate Hanwoo from the imported beef cattle and one primer set was used as a positive PCR control. The AS PCR for multiplex SNP typing was conducted on a glass-based microchip consisting of four layers: a microchannel plate for microfluidic control, a Pt-electrode plate for a resistance temperature detector (RTD), a poly(dimethylsiloxane) (PDMS) membrane and a manifold glass for micropump and microvalve function. The resultant AS PCR products were mixed with a hybridization buffer in a micromixer channel through the micropumping operation, and then the microarray assay was performed in the downstream process. Eleven duplicate probes were spotted in a glass slide, which was connected at the end of the micromixer channel unit. When the mixed solution was injected into the disposable microarray chip, pneumatically actuated micropumping was executed to speed up the hybridization process by inducing the convective flow. The fluorescence signals on each spot were monitored by a miniaturized fluorescence scanner, and the Hanwoo was verified by detecting the number of fluorescent spots with three or fewer among eleven. An integrated portable PCR-microarray genetic analysis microsystem was first demonstrated for rapid, accurate, and on-site multiplex SNP typing to differentiate animal species.
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Affiliation(s)
- Jong Young Choi
- Department of Chemical and Biomolecular Engineering (BK21 Program), Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
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35
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Kaiser A, Spies S, Lommel T, Richert C. Template-Directed Synthesis in 3′- and 5′-Direction with Reversible Termination. Angew Chem Int Ed Engl 2012; 51:8299-303. [DOI: 10.1002/anie.201203859] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Indexed: 01/21/2023]
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36
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Kaiser A, Spies S, Lommel T, Richert C. Template-Directed Synthesis in 3′- and 5′-Direction with Reversible Termination. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203859] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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37
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Choi JY, Kim YT, Ahn J, Kim KS, Gweon DG, Seo TS. Integrated allele-specific polymerase chain reaction-capillary electrophoresis microdevice for single nucleotide polymorphism genotyping. Biosens Bioelectron 2012; 35:327-334. [PMID: 22464916 DOI: 10.1016/j.bios.2012.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 02/09/2012] [Accepted: 03/08/2012] [Indexed: 11/30/2022]
Abstract
An integrated allele-specific (AS) polymerase chain reaction (PCR) and capillary electrophoresis (CE) microdevice has been developed for multiplex single nucleotide polymorphism (SNP) genotyping on a portable instrumentation, which was applied for on-site identification of HANWOO (Korean indigenous beef cattle). Twelve sets of primers were designed for targeting beef cattle's eleven SNP loci for HANWOO verification and one primer set for a positive PCR control, and the success rate for identification of HANWOO was demonstrated statistically. The AS PCR and CE separation for multiplex SNP typing was carried out on a glass-based microchip consisting of four layers: a microchannel plate for microfluidic control, a Pt-electrode plate for a resistance temperature detector (RTD), a poly(dimethylsiloxane) (PDMS) membrane and a manifold glass for microvalve function. The operation of the sample loading, AS PCR, microvalve, and CE on a chip was automated with a portable genetic analyzer, and the laser-induced fluorescence detection was performed on a miniaturized fluorescence detector. The blind samples were correctly identified as a HANWOO by showing one or two amplicon peaks in the electropherogram, while the imported beef cattle revealed more than five peaks. Our genetic analysis platform provides rapid, accurate, and on-site multiplex SNP typing.
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Affiliation(s)
- Jong Young Choi
- Department of Chemical and Biomolecular Engineering (BK21 Program) and KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Yong Tae Kim
- Department of Chemical and Biomolecular Engineering (BK21 Program) and KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Jinwoo Ahn
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Dahak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Kwan Suk Kim
- College of Agriculture, Life and Environment Sciences, Chungbuk National University, 52 Naesudong-ro, Heungdeok-gu, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Dae-Gab Gweon
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Dahak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Tae Seok Seo
- Department of Chemical and Biomolecular Engineering (BK21 Program) and KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
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38
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Griesser H, Tolev M, Singh A, Sabirov T, Gerlach C, Richert C. Solution-phase synthesis of branched DNA hybrids based on dimer phosphoramidites and phenolic or nucleosidic cores. J Org Chem 2012; 77:2703-17. [PMID: 22369351 DOI: 10.1021/jo202505h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Branched oligonucleotides with "CG zippers" as DNA arms assemble into materials from micromolar solutions. Their synthesis has been complicated by low yields in solid-phase syntheses. Here we present a solution-phase synthesis based on phosphoramidites of dimers and phenolic cores that produces six-arm or four-arm hybrids in up to 61% yield. On the level of hybrids, only the final product has to be purified by precipitation or chromatography. A total of five different hybrids were prepared via the solution-phase route, including new hybrid (TCG)(4)TTPA with a tetrakis(triazolylphenyl)adamantane core and trimer DNA arms. The new method is more readily scaled up than solid-phase syntheses, uses no more than 4 equiv of phosphoramidite per phenolic alcohol, and provides routine access to novel materials that assemble via predictable base-pairing interactions.
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Affiliation(s)
- Helmut Griesser
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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39
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Leu K, Obermayer B, Rajamani S, Gerland U, Chen IA. The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA. Nucleic Acids Res 2011; 39:8135-47. [PMID: 21724606 PMCID: PMC3185426 DOI: 10.1093/nar/gkr525] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/07/2011] [Accepted: 06/07/2011] [Indexed: 11/13/2022] Open
Abstract
In the early 'RNA world' stage of life, RNA stored genetic information and catalyzed chemical reactions. However, the RNA world eventually gave rise to the DNA-RNA-protein world, and this transition included the 'genetic takeover' of information storage by DNA. We investigated evolutionary advantages for using DNA as the genetic material. The error rate of replication imposes a fundamental limit on the amount of information that can be stored in the genome, as mutations degrade information. We compared misincorporation rates of RNA and DNA in experimental non-enzymatic polymerization and calculated the lowest possible error rates from a thermodynamic model. Both analyses found that RNA replication was intrinsically error-prone compared to DNA, suggesting that total genomic information could increase after the transition to DNA. Analysis of the transitional RNA/DNA hybrid duplexes showed that copying RNA into DNA had similar fidelity to RNA replication, so information could be maintained during the genetic takeover. However, copying DNA into RNA was very error-prone, suggesting that attempts to return to the RNA world would result in a considerable loss of information. Therefore, the genetic takeover may have been driven by a combination of increased chemical stability, increased genome size and irreversibility.
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Affiliation(s)
- Kevin Leu
- FAS Center for Systems Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA and Department of Physics, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians Universität München, Munich, Germany
| | - Benedikt Obermayer
- FAS Center for Systems Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA and Department of Physics, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians Universität München, Munich, Germany
| | - Sudha Rajamani
- FAS Center for Systems Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA and Department of Physics, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians Universität München, Munich, Germany
| | - Ulrich Gerland
- FAS Center for Systems Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA and Department of Physics, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians Universität München, Munich, Germany
| | - Irene A. Chen
- FAS Center for Systems Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA and Department of Physics, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians Universität München, Munich, Germany
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40
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Poater J, Swart M, Fonseca Guerra C, Bickelhaupt FM. Selectivity in DNA replication. Interplay of steric shape, hydrogen bonds, π-stacking and solvent effects. Chem Commun (Camb) 2011; 47:7326-8. [PMID: 21611661 DOI: 10.1039/c0cc04707d] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our dispersion-corrected DFT computations reveal key factors behind the intrinsic affinity of a DNA template-primer complex to select the correct nucleotide.
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Affiliation(s)
- Jordi Poater
- Theoretical Chemistry and ACMM, VU University, 1081 HV Amsterdam, The Netherlands
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Guo Y, Deng L, Li J, Guo S, Wang E, Dong S. Hemin-graphene hybrid nanosheets with intrinsic peroxidase-like activity for label-free colorimetric detection of single-nucleotide polymorphism. ACS NANO 2011; 5:1282-90. [PMID: 21218851 DOI: 10.1021/nn1029586] [Citation(s) in RCA: 438] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This paper demonstrated for the first time a simple wet-chemical strategy for synthesizing hemin-graphene hybrid nanosheets (H-GNs) through the π-π interactions. Significantly, this new material possesses the advantages of both hemin and graphene and exhibits three interesting properties. First, H-GNs have intrinsic peroxidase-like activity, which can catalyze the reaction of peroxidase substrate, due to the existence of hemin on the graphene surface. Second, their dispersion follow the 2D Schulze-Hardy rule, that is to say, the coagulation of H-GNs in electrolyte solution results from the interplay between van der Waals attraction and electric double-layer repulsion. Third, H-GNs exhibit the ability to differentiate ss- and ds-DNA in optimum electrolyte concentration, owing to the different affinities of ss- and ds-DNA to the H-GNs. On the basis of these unique properties of the as-prepared H-GNs, we have developed a label-free colorimetric detection system for single-nucleotide polymorphisms (SNPs) in disease-associated DNA. To our knowledge, this is the first report concerning on SNPs detection using functionalized graphene nanosheets. Owing to its easy operation and high specificity, it was expected that the proposed procedure might hold great promise in the pathogenic diagnosis and genetic diseases.
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Affiliation(s)
- Yujing Guo
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, China
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42
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Röthlingshöfer M, Richert C. Chemical primer extension at submillimolar concentration of deoxynucleotides. J Org Chem 2010; 75:3945-52. [PMID: 20364862 DOI: 10.1021/jo1002467] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Template-directed primer extension usually requires a polymerase, nucleoside triphosphates, and magnesium ions as cofactors. Enzyme-free, chemical primer extensions are known for preactivated nucleotides at millimolar concentrations. Based on a screen of carbodiimides, heterocyclic catalysts, and reactions conditions, we now show that near-quantitative primer conversion can be achieved at submillimolar concentration of any of the four deoxynucleotides (dAMP, dCMP, dGMP and dTMP). The new protocol relies on in situ activation with EDC and 1-methylimidazole and a magnesium-free buffer that was tested successfully for different sequence motifs. The method greatly simplifies chemical primer extension assays, further reduces the cost of such assays, and demonstrates the potential of the in situ activation approach.
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Affiliation(s)
- Manuel Röthlingshöfer
- Institute for Organic Chemistry, University of Karlsruhe/K.I.T., 76131 Karlsruhe, Germany
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43
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Abstract
Template-directed synthesis of complementary strands is pivotal for life. Nature employs polymerases for this reaction, leaving the ability of DNA itself to direct the incorporation of individual nucleotides at the end of a growing primer difficult to assess. Using 64 sequences, we now find that any of the four nucleobases, in combination with any neighboring residue, support enzyme-free primer extension when primer and mononucleotide are sufficiently reactive, with >or=93% primer extension for all sequences. Between the 64 possible base triplets, the rate of extension for the poorest template, CAG, with A as templating base, and the most efficient template, TCT, with C as templating base, differs by less than two orders of magnitude. Further, primer extension with a balanced mixture of monomers shows >or=72% of the correct extension product in all cases, and >or=90% incorporation of the correct base for 46 out of 64 triplets in the presence of a downstream-binding strand. A mechanism is proposed with a binding equilibrium for the monomer, deprotonation of the primer, and two chemical steps, the first of which is most strongly modulated by the sequence. Overall, rates show a surprisingly smooth reactivity landscape, with similar incorporation on strongly and weakly templating sequences. These results help to clarify the substrate contribution to copying, as found in polymerase-catalyzed replication, and show an important feature of DNA as genetic material.
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44
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Bell NM, Wong R, Micklefield J. A non-enzymatic, DNA template-directed morpholino primer extension approach. Chemistry 2010; 16:2026-30. [PMID: 20087911 DOI: 10.1002/chem.200902237] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Neil M Bell
- School of Chemistry, The University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7ND, UK
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45
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Rajamani S, Ichida JK, Antal T, Treco DA, Leu K, Nowak MA, Szostak JW, Chen IA. Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replication. J Am Chem Soc 2010; 132:5880-5. [PMID: 20359213 PMCID: PMC2857888 DOI: 10.1021/ja100780p] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Indexed: 11/28/2022]
Abstract
The frequency of errors during genome replication limits the amount of functionally important information that can be passed on from generation to generation. During the origin of life, mutation rates are thought to have been quite high, raising a classic chicken-and-egg paradox: could nonenzymatic replication propagate sequences accurately enough to allow for the emergence of heritable function? Here we show that the theoretical limit on genomic information content may increase substantially as a consequence of dramatically slowed polymerization after mismatches. As a result of postmismatch stalling, accurate copies of a template tend to be completed more rapidly than mutant copies and the accurate copies can therefore begin a second round of replication more quickly. To quantify this effect, we characterized an experimental model of nonenzymatic, template-directed nucleic acid polymerization. We found that most mismatches decrease the rate of primer extension by more than 2 orders of magnitude relative to a matched (Watson-Crick) control. A chemical replication system with this property would be able to propagate sequences long enough to have function. Our study suggests that the emergence of functional sequences during the origin of life would be possible even in the face of the high intrinsic error rates of chemical replication.
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46
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Xue X, Xu W, Wang F, Liu X. Multiplex single-nucleotide polymorphism typing by nanoparticle-coupled DNA-templated reactions. J Am Chem Soc 2009; 131:11668-9. [PMID: 19642679 DOI: 10.1021/ja904728v] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel chip-based detection approach for single-nucleotide polymorphism (SNP) typing based on nanoparticle-coupled DNA-templated ligation reactions is reported. In contrast to conventional methods or recently developed techniques, this approach does not need costly instrumentation and complex stringency washing processes and offers both rapid multiplex SNP detection capability and ultrahigh sensitivity. The ability of the approach to quickly identify the precise location of the single-base mismatch may provide a time-efficient method for high-throughput multiplex SNP genotyping.
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Affiliation(s)
- Xuejia Xue
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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47
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Schrum JP, Ricardo A, Krishnamurthy M, Blain JC, Szostak JW. Efficient and rapid template-directed nucleic acid copying using 2'-amino-2',3'-dideoxyribonucleoside-5'-phosphorimidazolide monomers. J Am Chem Soc 2009; 131:14560-70. [PMID: 19757789 PMCID: PMC2759813 DOI: 10.1021/ja906557v] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of a sequence-general nucleic acid copying system is an essential step in the assembly of a synthetic protocell, an autonomously replicating spatially localized chemical system capable of spontaneous Darwinian evolution. Previously described nonenzymatic template-copying experiments have validated the concept of nonenzymatic replication, but have not yet achieved robust, sequence-general polynucleotide replication. The 5'-phosphorimidazolides of the 2'-amino-2',3'-dideoxyribonucleotides are attractive as potential monomers for such a system because they polymerize by forming 2'-->5' linkages, which are favored in nonenzymatic polymerization reactions using similarly activated ribonucleotides on RNA templates. Furthermore, the 5'-activated 2'-amino nucleotides do not cyclize. We recently described the rapid and efficient nonenzymatic copying of a DNA homopolymer template (dC(15)) encapsulated within fatty acid vesicles using 2'-amino-2',3'-dideoxyguanosine-5'-phosphorimidazolide as the activated monomer. However, to realize a true Darwinian system, the template-copying chemistry must be able to copy most sequences and their complements to allow for the transmission of information from generation to generation. Here, we describe the copying of a series of nucleic acid templates using 2'-amino-2',3'-dideoxynucleotide-5'-phosphorimidazolides. Polymerization reactions proceed rapidly to completion on short homopolymer RNA and LNA templates, which favor an A-type duplex geometry. We show that more efficiently copied sequences are generated by replacing the adenine nucleobase with diaminopurine, and uracil with C5-(1-propynyl)uracil. Finally, we explore the copying of longer, mixed-sequence RNA templates to assess the sequence-general copying ability of 2'-amino-2',3'-dideoxynucleoside-5'-phosphorimidazolides. Our results are a significant step forward in the realization of a self-replicating genetic polymer compatible with protocell template copying and suggest that N2'-->P5'-phosphoramidate DNA may have the potential to function as a self-replicating system.
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Affiliation(s)
- Jason P Schrum
- Howard Hughes Medical Institute and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Harvard Medical School, Boston, Massachusetts 02114, USA
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48
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Chen JJ, Cai X, Szostak JW. N2'-->p3' phosphoramidate glycerol nucleic acid as a potential alternative genetic system. J Am Chem Soc 2009; 131:2119-21. [PMID: 19166350 PMCID: PMC2722806 DOI: 10.1021/ja809069b] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Glycerol nucleic acid (GNA) is an interesting base-pairing system with an acyclic, three-carbon backbone. In the present study, GNA analogues with N2′→P3′ phosphoramidate linkages (npGNA) have been synthesized and their base-pairing properties examined. Thermal denaturation and circular dichroism studies show that npGNA can form stable duplexes with itself and with GNA. Furthermore, we show that npGNA can be assembled by template-directed ligation of 3′-imidazole-activated-2′-amino GNA dinucleotides. These results suggest that npGNA is a potential candidate for a self-replicating system based upon phosphoramidate linkages.
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Affiliation(s)
- Jesse J Chen
- Howard Hughes Medical Institute, and Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
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49
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Röthlingshöfer M, Kervio E, Lommel T, Plutowski U, Hochgesand A, Richert C. Chemical primer extension in seconds. Angew Chem Int Ed Engl 2008; 47:6065-8. [PMID: 18613189 DOI: 10.1002/anie.200801260] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Manuel Röthlingshöfer
- Institut für Organische Chemie, Universität Karlsruhe (TH), 76131 Karlsruhe, Germany
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50
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Röthlingshöfer M, Kervio E, Lommel T, Plutowski U, Hochgesand A, Richert C. Chemical Primer Extension in Seconds. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801260] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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