151
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Röthlisberger P, Levi-Acobas F, Leumann CJ, Hollenstein M. Enzymatic synthesis of biphenyl-DNA oligonucleotides. Bioorg Med Chem 2020; 28:115487. [PMID: 32284226 DOI: 10.1016/j.bmc.2020.115487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 12/25/2022]
Abstract
The incorporation of nucleotides equipped with C-glycosidic aromatic nucleobases into DNA and RNA is an alluring strategy for a number of practical applications including fluorescent labelling of oligonucleotides, expansion of the genetic alphabet for the generation of aptamers and semi-synthetic organisms, or the modulation of excess electron transfer within DNA. However, the generation of C-nucleoside containing oligonucleotides relies mainly on solid-phase synthesis which is quite labor intensive and restricted to short sequences. Here, we explore the possibility of constructing biphenyl-modified DNA sequences using enzymatic synthesis. The presence of multiple biphenyl-units or biphenyl residues modified with electron donors and acceptors permits the incorporation of a single dBphMP nucleotide. Moreover, templates with multiple abasic sites enable the incorporation of up to two dBphMP nucleotides, while TdT-mediated tailing reactions produce single-stranded DNA oligonucleotides with four biphenyl residues appended at the 3'-end.
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Affiliation(s)
- Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France.
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152
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Bacteria as genetically programmable producers of bioactive natural products. Nat Rev Chem 2020; 4:172-193. [PMID: 37128046 DOI: 10.1038/s41570-020-0176-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2020] [Indexed: 12/17/2022]
Abstract
Next to plants, bacteria account for most of the biomass on Earth. They are found everywhere, although certain species thrive only in specific ecological niches. These microorganisms biosynthesize a plethora of both primary and secondary metabolites, defined, respectively, as those required for the growth and maintenance of cellular functions and those not required for survival but offering a selective advantage for the producer under certain conditions. As a result, bacterial fermentation has long been used to manufacture valuable natural products of nutritional, agrochemical and pharmaceutical interest. The interactions of secondary metabolites with their biological targets have been optimized by millions of years of evolution and they are, thus, considered to be privileged chemical structures, not only for drug discovery. During the last two decades, functional genomics has allowed for an in-depth understanding of the underlying biosynthetic logic of secondary metabolites. This has, in turn, paved the way for the unprecedented use of bacteria as programmable biochemical workhorses. In this Review, we discuss the multifaceted use of bacteria as biological factories in diverse applications and highlight recent advances in targeted genetic engineering of bacteria for the production of valuable bioactive compounds. Emphasis is on current advances to access nature's abundance of natural products.
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153
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Marx A, Betz K. The Structural Basis for Processing of Unnatural Base Pairs by DNA Polymerases. Chemistry 2020; 26:3446-3463. [PMID: 31544987 PMCID: PMC7155079 DOI: 10.1002/chem.201903525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/17/2019] [Indexed: 12/16/2022]
Abstract
Unnatural base pairs (UBPs) greatly increase the diversity of DNA and RNA, furthering their broad range of molecular biological and biotechnological approaches. Different candidates have been developed whereby alternative hydrogen-bonding patterns and hydrophobic and packing interactions have turned out to be the most promising base-pairing concepts to date. The key in many applications is the highly efficient and selective acceptance of artificial base pairs by DNA polymerases, which enables amplification of the modified DNA. In this Review, computational as well as experimental studies that were performed to characterize the pairing behavior of UBPs in free duplex DNA or bound to the active site of KlenTaq DNA polymerase are highlighted. The structural studies, on the one hand, elucidate how base pairs lacking hydrogen bonds are accepted by these enzymes and, on the other hand, highlight the influence of one or several consecutive UBPs on the structure of a DNA double helix. Understanding these concepts facilitates optimization of future UBPs for the manifold fields of applications.
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Affiliation(s)
- Andreas Marx
- Department of ChemistryKonstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstrasse 1078464KonstanzGermany
| | - Karin Betz
- Department of ChemistryKonstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstrasse 1078464KonstanzGermany
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154
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Lutz JF. 100th Anniversary of Macromolecular Science Viewpoint: Toward Artificial Life-Supporting Macromolecules. ACS Macro Lett 2020; 9:185-189. [PMID: 35638671 DOI: 10.1021/acsmacrolett.9b00938] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Terrestrial Life is based on polymers. In all known living organisms, DNA stores genetic information, mutates, self-replicates, and guides the synthesis of messenger molecules. Although the function of nucleic acids is well-understood, the development of artificial macromolecular mimics remains very limited. Laboratory-synthesized nucleic acids still support Life, and some nucleic acids analogues exhibit biological functions. Yet, after hundred years of polymer science, no other type of Life-supporting macromolecule (i.e., non-nucleic acids) has ever been reported. In this context, the aim of the present viewpoint is to discuss important challenges that shall be addressed by polymer chemists to achieve artificial Life. Similarly to DNA, an artificial Life-supporting macromolecule shall store information, transfer information, and mutate. Many tools, such as sequence-defined polymer synthesis, polymer modification, supramolecular polymer chemistry, and dynamic chemistry, are already available to chemists to attain these properties. However, the design of artificial Life-supporting macromolecules is hindered by two main factors. First, the chemical search space is enormous, and it is difficult to predict promising structures, even with the help of combinatorial and chemoinformatic tools. Second, rational design is probably a limited approach to achieve macromolecules that shall be involved in nonequilibrium metabolic systems. Hence, a synergic combination of classical polymer chemistry with the more recent field of systems chemistry is probably the key toward the emergence of artificial Life-supporting macromolecules.
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Affiliation(s)
- Jean-François Lutz
- Université de Strasbourg, CNRS - UPR 22, Institut Charles Sadron, 23 rue du Loess, 67034 Strasbourg, France
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155
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Ledbetter MP, Craig JM, Karadeema RJ, Noakes MT, Kim HC, Abell SJ, Huang JR, Anderson BA, Krishnamurthy R, Gundlach JH, Romesberg FE. Nanopore Sequencing of an Expanded Genetic Alphabet Reveals High-Fidelity Replication of a Predominantly Hydrophobic Unnatural Base Pair. J Am Chem Soc 2020; 142:2110-2114. [PMID: 31985216 DOI: 10.1021/jacs.9b09808] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Unnatural base pairs (UBPs) have been developed and used for a variety of in vitro applications as well as for the engineering of semisynthetic organisms (SSOs) that store and retrieve increased information. However, these applications are limited by the availability of methods to rapidly and accurately determine the sequence of unnatural DNA. Here we report the development and application of the MspA nanopore to sequence DNA containing the dTPT3-dNaM UBP. Analysis of two sequence contexts reveals that DNA containing the UBP is replicated with an efficiency and fidelity similar to that of natural DNA and sufficient for use as the basis of an SSO that produces proteins with noncanonical amino acids.
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Affiliation(s)
- Michael P Ledbetter
- Department of Chemistry , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Jonathan M Craig
- Department of Physics , University of Washington , Seattle , Washington 98195 , United States
| | - Rebekah J Karadeema
- Department of Chemistry , The Scripps Research Institute , La Jolla , California 92037 , United States
| | - Matthew T Noakes
- Department of Physics , University of Washington , Seattle , Washington 98195 , United States
| | - Hwanhee C Kim
- Department of Physics , University of Washington , Seattle , Washington 98195 , United States
| | - Sarah J Abell
- Department of Physics , University of Washington , Seattle , Washington 98195 , United States
| | - Jesse R Huang
- Department of Physics , University of Washington , Seattle , Washington 98195 , United States
| | - Brooke A Anderson
- Department of Chemistry , The Scripps Research Institute , La Jolla , California 92037 , United States
| | | | - Jens H Gundlach
- Department of Physics , University of Washington , Seattle , Washington 98195 , United States
| | - Floyd E Romesberg
- Department of Chemistry , The Scripps Research Institute , La Jolla , California 92037 , United States
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156
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Dong Y, Sun F, Ping Z, Ouyang Q, Qian L. DNA storage: research landscape and future prospects. Natl Sci Rev 2020; 7:1092-1107. [PMID: 34692128 PMCID: PMC8288837 DOI: 10.1093/nsr/nwaa007] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/06/2020] [Accepted: 01/18/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract
The global demand for data storage is currently outpacing the world's storage capabilities. DNA, the carrier of natural genetic information, offers a stable, resource- and energy-efficient and sustainable data storage solution. In this review, we summarize the fundamental theory, research history, and technical challenges of DNA storage. From a quantitative perspective, we evaluate the prospect of DNA, and organic polymers in general, as a novel class of data storage medium.
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Affiliation(s)
- Yiming Dong
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Fajia Sun
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhi Ping
- Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Qi Ouyang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | - Long Qian
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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157
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Mukhopadhyay TK, Datta A. Screening two dimensional materials for the transportation and delivery of diverse genetic materials. NANOSCALE 2020; 12:703-719. [PMID: 31829380 DOI: 10.1039/c9nr05930j] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In spite of several reports of graphene and other 2D materials concerning their capacity for biomolecular adsorption and delivery, recent toxicity evaluations found them to be nanotoxic toward different biomolecules, especially nucleic acids. Therefore, there is urgent demand for the synthesis of 2D materials exhibiting biocompatible and non-nanotoxic features. In this article, employing classical molecular dynamics simulations, we provide a benchmarking of h2D-C2N, graphene and hexagonal boron nitride (h-BN) toward the adsorption, preservation, targeting and delivery of various classes of nucleic acids namely single stranded DNA, double stranded natural as well as unnatural base substituted DNA and two different types of human telomeric guanine quadruplexes, all comprising different secondary structures. Our simulations reveal that, while h2D-C2N preserves the structures of most of the nucleic acids, graphene and h-BN disrupt them through strong π-π stacking with aromatic nucleobases. Interestingly, for the first time we identified a 'quartet-by-quartet' disruption mechanism of guanine quadruplexes, but only on graphene and h-BN. The lateral diffusion of adsorbed nucleic acids over C2N is restricted unlike that over both graphene and h-BN, thereby increasing the targeting efficacy for C2N. Modeling of the delivery phenomena suggests orders of magnitude longer release times from graphene and h-BN compared to C2N, thereby demonstrating the preferential suitability of C2N for all the hierarchical steps of nucleic acid transportation.
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Affiliation(s)
- Titas Kumar Mukhopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India.
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158
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Affiliation(s)
- Jean‐François Lutz
- Université de Strasbourg, CNRSInstitut Charles Sadron, UPR22 23 rue du Loess 67034 Strasbourg Cedex 2 France
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159
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Jena NR. Electron and hole interactions with P, Z, and P:Z and the formation of mutagenic products by proton transfer reactions. Phys Chem Chem Phys 2020; 22:919-931. [DOI: 10.1039/c9cp05367k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Z would act as an electron acceptor and P would capture a hole in the unnatural DNA. The latter process would produce mutagenic products via a proton transfer reaction.
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Affiliation(s)
- N. R. Jena
- Discipline of Natural Sciences
- Indian Institute of Information Technology, Design, and Manufacturing
- Jabalpur-482005
- India
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160
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Zhou AXZ, Sheng K, Feldman AW, Romesberg FE. Progress toward Eukaryotic Semisynthetic Organisms: Translation of Unnatural Codons. J Am Chem Soc 2019; 141:20166-20170. [PMID: 31841336 PMCID: PMC6946121 DOI: 10.1021/jacs.9b09080] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have created a bacterial semisynthetic organism (SSO) that retains an unnatural base pair (UBP) in its DNA, transcribes it into mRNA and tRNA with cognate unnatural codons and anticodons, and after the tRNA is charged with a noncanonical amino acid synthesizes proteins containing the noncanonical amino acid. Here, we report the first progress toward the creation of eukaryotic SSOs. After demonstrating proof-of-concept with human HEK293 cells, we show that a variety of different unnatural codon-anticodon pairs can efficiently mediate the synthesis of unnatural proteins in CHO cells. Interestingly, we find that there are both similarities and significant differences between how the prokaryotic and eukaryotic ribosomes recognize the UBP, with the eukaryotic ribosome appearing more tolerant. The results represent the first progress toward eukaryotic SSOs and, in fact, suggest that such SSOs might be able to retain more unnatural information than their bacterial counterparts.
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Affiliation(s)
- Anne Xiao-Zhou Zhou
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Kai Sheng
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Aaron W. Feldman
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, United States
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161
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162
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Kobokovich A, West R, Montague M, Inglesby T, Gronvall GK. Strengthening Security for Gene Synthesis: Recommendations for Governance. Health Secur 2019; 17:419-429. [PMID: 31755783 DOI: 10.1089/hs.2019.0110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Since the inception of gene synthesis technologies, there have been concerns about possible misuse. Using gene synthesis, pathogens-particularly small viruses-may be assembled "from scratch" in the laboratory, evading the regulatory regimes many nations have in place to control unauthorized access to dangerous pathogens. Progress has been made to reduce these risks. In 2010, the US Department of Health and Human Services (HHS) published guidance for commercial gene synthesis providers that included sequence screening of the orders and customer screening. The industry-led International Gene Synthesis Consortium (IGSC) was formed in 2009 to share sequence and customer screening methods, and it now includes the major international gene synthesis providers among its members. Since the 2010 HHS Guidance was released, however, there have been changes in gene synthesis technologies and market conditions that have reduced the efficacy of these biosecurity protections, leading to questions about whether the 2010 HHS Guidance should be updated, what changes could make it more effective, and what other international governance efforts could be undertaken to reduce the risks of misuse of gene synthesis products. This article describes these conditions and recommends actions that governments should take to reduce these risks and engage other nations involved in gene synthesis research.
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Affiliation(s)
- Amanda Kobokovich
- Amanda Kobokovich, MPH, is an Analyst and Research Associate; Rachel West is a doctoral student; Michael Montague, PhD, is a Senior Scholar and Research Scientist; Tom Inglesby, MD, is the Center Director and Professor; and Gigi Kwik Gronvall, PhD, is a Senior Scholar and Associate Professor; all at the Johns Hopkins Center for Health Security and the Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Rachel West
- Amanda Kobokovich, MPH, is an Analyst and Research Associate; Rachel West is a doctoral student; Michael Montague, PhD, is a Senior Scholar and Research Scientist; Tom Inglesby, MD, is the Center Director and Professor; and Gigi Kwik Gronvall, PhD, is a Senior Scholar and Associate Professor; all at the Johns Hopkins Center for Health Security and the Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Michael Montague
- Amanda Kobokovich, MPH, is an Analyst and Research Associate; Rachel West is a doctoral student; Michael Montague, PhD, is a Senior Scholar and Research Scientist; Tom Inglesby, MD, is the Center Director and Professor; and Gigi Kwik Gronvall, PhD, is a Senior Scholar and Associate Professor; all at the Johns Hopkins Center for Health Security and the Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Tom Inglesby
- Amanda Kobokovich, MPH, is an Analyst and Research Associate; Rachel West is a doctoral student; Michael Montague, PhD, is a Senior Scholar and Research Scientist; Tom Inglesby, MD, is the Center Director and Professor; and Gigi Kwik Gronvall, PhD, is a Senior Scholar and Associate Professor; all at the Johns Hopkins Center for Health Security and the Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Gigi Kwik Gronvall
- Amanda Kobokovich, MPH, is an Analyst and Research Associate; Rachel West is a doctoral student; Michael Montague, PhD, is a Senior Scholar and Research Scientist; Tom Inglesby, MD, is the Center Director and Professor; and Gigi Kwik Gronvall, PhD, is a Senior Scholar and Associate Professor; all at the Johns Hopkins Center for Health Security and the Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
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163
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Gruber A, Haferkamp I. Nucleotide Transport and Metabolism in Diatoms. Biomolecules 2019; 9:E761. [PMID: 31766535 PMCID: PMC6995639 DOI: 10.3390/biom9120761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 01/01/2023] Open
Abstract
Plastids, organelles that evolved from cyanobacteria via endosymbiosis in eukaryotes, provide carbohydrates for the formation of biomass and for mitochondrial energy production to the cell. They generate their own energy in the form of the nucleotide adenosine triphosphate (ATP). However, plastids of non-photosynthetic tissues, or during the dark, depend on external supply of ATP. A dedicated antiporter that exchanges ATP against adenosine diphosphate (ADP) plus inorganic phosphate (Pi) takes over this function in most photosynthetic eukaryotes. Additional forms of such nucleotide transporters (NTTs), with deviating activities, are found in intracellular bacteria, and, surprisingly, also in diatoms, a group of algae that acquired their plastids from other eukaryotes via one (or even several) additional endosymbioses compared to algae with primary plastids and higher plants. In this review, we summarize what is known about the nucleotide synthesis and transport pathways in diatom cells, and discuss the evolutionary implications of the presence of the additional NTTs in diatoms, as well as their applications in biotechnology.
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Affiliation(s)
- Ansgar Gruber
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Ilka Haferkamp
- Pflanzenphysiologie, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany;
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164
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Abstract
To increase the scope of natural biosystem, nucleic acids have been intensively modified. One direction includes the development of a synthetic alternative to the native DNA and RNA, denoted Xenobiotic nucleic acids (XNAs) that are able to store and transfer genetic information either by base-modification or backbone-modification. Another line of research aims to develop alternative third base pair additional to natural A:T and G:C. These unnatural base pairs (UBPs) can store increased information content encoded in three base pairs. This review outlines the recent progress made towards XNA and UBP applications as new components of the genomic DNA as well as biostable aptamers. New achievements in the replacement of a bacterial genome by unnatural non-canonical nucleotides are also described.
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Affiliation(s)
- Elena Eremeeva
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, 3000 Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, 3000 Leuven, Belgium.
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165
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Johnson A, Karimi A, Luedtke NW. Enzymatic Incorporation of a Coumarin–Guanine Base Pair. Angew Chem Int Ed Engl 2019; 58:16839-16843. [DOI: 10.1002/anie.201910059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Aaron Johnson
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Ashkan Karimi
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Nathan W. Luedtke
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
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166
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Johnson A, Karimi A, Luedtke NW. Enzymatic Incorporation of a Coumarin–Guanine Base Pair. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Aaron Johnson
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Ashkan Karimi
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Nathan W. Luedtke
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
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167
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Levi-Acobas F, Röthlisberger P, Sarac I, Marlière P, Herdewijn P, Hollenstein M. On the Enzymatic Formation of Metal Base Pairs with Thiolated and pK a -Perturbed Nucleotides. Chembiochem 2019; 20:3032-3040. [PMID: 31216100 DOI: 10.1002/cbic.201900399] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Indexed: 12/15/2022]
Abstract
The formation of artificial metal base pairs is an alluring and versatile method for the functionalization of nucleic acids. Access to DNA functionalized with metal base pairs is granted mainly by solid-phase synthesis. An alternative, yet underexplored method, envisions the installation of metal base pairs through the polymerization of modified nucleoside triphosphates. Herein, we have explored the possibility of using thiolated and pKa -perturbed nucleotides for the enzymatic construction of artificial metal base pairs. The thiolated nucleotides S2C, S6G, and S4T as well as the fluorinated analogue 5FU are readily incorporated opposite a templating S4T nucleotide through the guidance of metal cations. Multiple incorporation of the modified nucleotides along with polymerase bypass of the unnatural base pairs are also possible under certain conditions. The thiolated nucleotides S4T, S4T, S2C, and S6G were also shown to be compatible with the synthesis of modified, high molecular weight single-stranded (ss)DNA products through TdT-mediated tailing reactions. Thus, sulfur-substitution and pKa perturbation represent alternative strategies for the design of modified nucleotides compatible with the enzymatic construction of metal base pairs.
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Affiliation(s)
- Fabienne Levi-Acobas
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Pascal Röthlisberger
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Ivo Sarac
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Philippe Marlière
- University of Paris Saclay, CNRS, iSSB, UEVE, Genopole, 5 Rue Henri Desbruères, 91030, Evry, France
| | - Piet Herdewijn
- Department of Medicinal Chemistry, Institute for Medical Research, KU Leuven, Herestraat, 49, Leuven, 3000, Belgium
| | - Marcel Hollenstein
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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168
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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169
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Galindo-Murillo R, Barroso-Flores J. Hydrophobic unnatural base pairs show a Watson-Crick pairing in micro-second molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:4098-4106. [PMID: 31542995 DOI: 10.1080/07391102.2019.1671898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two unnatural hydrophobic nucleotides, d5SICS (2,6-dimethyl-2H-isoquiniline-1-thione) and dNaM (2-methoxy-3-methylnaphthalene), were previously replicated in vivo by a modified E. coli strand, however, a consistent structure for their pairing in terms of specific and selective directional interactions remains elusive, as data from spectroscopy experiments and simulations are inconsistent. The proposed d5SICS-dNaM pairing has been suggested to be a stacked configuration as suggested by NMR data; simulations have failed to reproduce this configuration and a Watson-Crick like pairing is observed. Previously, we focused on reproducing the d5SICS-dNaM Unnatural Base Pair (UBP) paring using an older (bsc0) AMBER force field, which was not able to correctly reproduce the experimental data. We present our efforts to reproduce the experimental pairing using the current version of the AMBER DNA force fields (OL15 and bsc1), two water models (OPC and TIP3P) and external electrostatic stabilization by Mg2+ ions. Opposite to previously reported simulations, a Watson-Crick-like pairing with no hydrogen bonds persists throughout all our results. Despite our efforts to replicate the reported stacked conformation, we cannot confirm its plausibility nor obtain a consistent structure that is independent of the neighboring nucleotides. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Joaquín Barroso-Flores
- Centro Conjunto de Investigación en Química Sustentable UAEM-UNAM, Estado de México, C.P., México.,Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
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170
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Cleaves HJ, Butch C, Burger PB, Goodwin J, Meringer M. One Among Millions: The Chemical Space of Nucleic Acid-Like Molecules. J Chem Inf Model 2019; 59:4266-4277. [PMID: 31498614 DOI: 10.1021/acs.jcim.9b00632] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Biology encodes hereditary information in DNA and RNA, which are finely tuned to their biological functions and modes of biological production. The central role of nucleic acids in biological information flow makes them key targets of pharmaceutical research. Indeed, other nucleic acid-like polymers can play similar roles to natural nucleic acids both in vivo and in vitro; yet despite remarkable advances over the last few decades, much remains unknown regarding which structures are compatible with molecular information storage. Chemical space describes the structures and properties of molecules that could exist within a given molecular formula or other classification system. Using structure generation methods, we explore nucleic acid analogues within the formula ranges BC3-7H5-15O2-4 and BC3-6H5-15N1-2O0-4, where B is a recognition element (e.g., a nucleobase). Other restrictions included two obligatory points of attachment for inclusion into a linear polymer and substructures predicting chemical stability. These sets contain 86,007 (CHO) and 75,309 (CHNO) compositionally isomeric structures, representing 706,568 CHO and 454,422 CHNO stereoisomers, that diversely and densely occupy this space. These libraries point toward there being large spaces of unexplored chemistry relevant to pharmacology and biochemistry and efforts to understand the origins of life.
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Affiliation(s)
- Henderson James Cleaves
- Earth-Life Science Institute , Tokyo Institute of Technology , 2-12-IE-1 Ookayama , Meguro-ku , Tokyo 152-8551 , Japan.,Institute for Advanced Study , Princeton , New Jersey 08540 , United States.,Blue Marble Space Institute for Science , 1515 Gallatin St. NW , Washington , DC 20011 , United States
| | - Christopher Butch
- Earth-Life Science Institute , Tokyo Institute of Technology , 2-12-IE-1 Ookayama , Meguro-ku , Tokyo 152-8551 , Japan.,Blue Marble Space Institute for Science , 1515 Gallatin St. NW , Washington , DC 20011 , United States.,Department of Chemistry , Emory University , 1515 Dickey Dr. , Atlanta , Georgia 30322 , United States
| | - Pieter Buys Burger
- Department of Chemistry , Emory University , 1515 Dickey Dr. , Atlanta , Georgia 30322 , United States
| | - Jay Goodwin
- Department of Chemistry , Emory University , 1515 Dickey Dr. , Atlanta , Georgia 30322 , United States
| | - Markus Meringer
- German Aerospace Center (DLR) , Earth Observation Center (EOC) , Münchner Straße 20 , 82234 Oberpfaffenhofen-Wessling , Germany
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171
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Ledbetter MP, Malyshev DA, Romesberg FE. Site-Specific Labeling of DNA via PCR with an Expanded Genetic Alphabet. Methods Mol Biol 2019; 1973:193-212. [PMID: 31016704 DOI: 10.1007/978-1-4939-9216-4_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The polymerase chain reaction (PCR) is a universal and essential tool in molecular biology and biotechnology, but it is generally limited to the amplification of DNA with the four-letter genetic alphabet. Here, we describe PCR amplification with a six-letter alphabet that includes the two natural dA-dT and dG-dC base pairs and an unnatural base pair (UBP) formed between the synthetic nucleotides dNaM and d5SICS or dTPT3 or analogs of these synthetic nucleotides modified with linkers that allow for the site-specific labeling of the amplified DNA with different functional groups. Under standard conditions, the six-letter DNA may be amplified with high efficiency and with greater than 99.9% fidelity. This allows for the efficient production of DNA site-specifically modified with different functionalities of interest for use in a wide range of applications.
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Affiliation(s)
| | - Denis A Malyshev
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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172
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Cui Z, Wu Y, Mureev S, Alexandrov K. Oligonucleotide-mediated tRNA sequestration enables one-pot sense codon reassignment in vitro. Nucleic Acids Res 2019; 46:6387-6400. [PMID: 29846683 PMCID: PMC6158751 DOI: 10.1093/nar/gky365] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/26/2018] [Indexed: 12/17/2022] Open
Abstract
Sense codon reassignment to unnatural amino acids (uAAs) represents a powerful approach for introducing novel properties into polypeptides. The main obstacle to this approach is competition between the native isoacceptor tRNA(s) and orthogonal tRNA(s) for the reassigned codon. While several chromatographic and enzymatic procedures for selective deactivation of tRNA isoacceptors in cell-free translation systems exist, they are complex and not scalable. We designed a set of tRNA antisense oligonucleotides composed of either deoxy-, ribo- or 2′-O-methyl ribonucleotides and tested their ability to efficiently complex tRNAs of choice. Methylated oligonucleotides targeting sequence between the anticodon and variable loop of tRNASerGCU displayed subnanomolar binding affinity with slow dissociation kinetics. Such oligonucleotides efficiently and selectively sequestered native tRNASerGCU directly in translation-competent Escherichia coli S30 lysate, thereby, abrogating its translational activity and liberating the AGU/AGC codons. Expression of eGFP protein from the template harboring a single reassignable AGU codon in tRNASerGCU-depleted E. coli lysate allowed its homogeneous modification with n-propargyl-l-lysine or p-azido-l-phenylalanine. The strategy developed here is generic, as demonstrated by sequestration of tRNAArgCCU isoacceptor in E. coli translation system. Furthermore, this method is likely to be species-independent and was successfully applied to the eukaryotic Leishmania tarentolae in vitro translation system. This approach represents a new direction in genetic code reassignment with numerous practical applications.
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Affiliation(s)
- Zhenling Cui
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Yue Wu
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Sergey Mureev
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Kirill Alexandrov
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia.,Australian Institute for Bioengeneering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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173
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Behera B, Das P, Jena NR. Accurate Base Pair Energies of Artificially Expanded Genetic Information Systems (AEGIS): Clues for Their Mutagenic Characteristics. J Phys Chem B 2019; 123:6728-6739. [PMID: 31290661 DOI: 10.1021/acs.jpcb.9b04653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, several artificial nucleobases, such as B, S, J, V, X, K, P, and Z, have been proposed to help in the expansion of the genetic information system and diagnosis of diseases. Among these bases, P and Z were identified to form stable DNA and to participate in the replication. However, the stabilities of P:Z and other artificial base pairs are not fully understood. The abilities of these unnatural nucleobases in mispairing with themselves and with natural bases are also not known. Here, the ωB97X-D dispersion-corrected density functional theoretical and complete basis set (CBS-QB3) methods are used to obtain accurate structural and energetic data related to base pair interactions involving these unnatural nucleobases. The roles of protonation and deprotonation of certain artificial bases in inducing mutations are also studied. It is found that each artificial purine has a complementary artificial pyrimidine, the base pair interactions between which are similar to those of the natural Watson-Crick base pairs. Hence, these base pairs will function naturally and would not impart mutagenicity. Among these base pairs, the J:V complex is found to be the most stable and promising artificial base pair. Remarkably, the noncomplementary artificial nucleobases are found to form stable mispairs, which may generate mutagenic products in DNA. Similarly, the misinsertions of natural bases opposite artificial bases are also found to be mutagenic. The mechanisms of these mutations are explained in detail. These results are in agreement with earlier biochemical studies. It is thus expected that this study would aid in the advancement of the synthetic biology to design more robust artificial nucleotides.
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Affiliation(s)
- B Behera
- Discipline of Natural Sciences , Indian Institute of Information Technology, Design and Manufacturing , Jabalpur 482005 , India
| | - P Das
- Discipline of Natural Sciences , Indian Institute of Information Technology, Design and Manufacturing , Jabalpur 482005 , India
| | - N R Jena
- Discipline of Natural Sciences , Indian Institute of Information Technology, Design and Manufacturing , Jabalpur 482005 , India
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174
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Affiliation(s)
- John C. Chaput
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry University of California, Irvine CA USA
| | - Piet Herdewijn
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Leuven Belgien
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175
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Affiliation(s)
- John C. Chaput
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry University of California, Irvine CA USA
| | - Piet Herdewijn
- Medicinal Chemistry Rega Institute for Medical Research KU Leuven Leuven Belgium
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176
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Arranz-Gibert P, Patel JR, Isaacs FJ. The Role of Orthogonality in Genetic Code Expansion. Life (Basel) 2019; 9:E58. [PMID: 31284384 PMCID: PMC6789853 DOI: 10.3390/life9030058] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/01/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022] Open
Abstract
The genetic code defines how information in the genome is translated into protein. Aside from a handful of isolated exceptions, this code is universal. Researchers have developed techniques to artificially expand the genetic code, repurposing codons and translational machinery to incorporate nonstandard amino acids (nsAAs) into proteins. A key challenge for robust genetic code expansion is orthogonality; the engineered machinery used to introduce nsAAs into proteins must co-exist with native translation and gene expression without cross-reactivity or pleiotropy. The issue of orthogonality manifests at several levels, including those of codons, ribosomes, aminoacyl-tRNA synthetases, tRNAs, and elongation factors. In this concept paper, we describe advances in genome recoding, translational engineering and associated challenges rooted in establishing orthogonality needed to expand the genetic code.
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Affiliation(s)
- Pol Arranz-Gibert
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jaymin R Patel
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Farren J Isaacs
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA.
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177
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Singh I, Laos R, Hoshika S, Benner SA, Georgiadis MM. Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide. Nucleic Acids Res 2019; 46:7977-7988. [PMID: 29986111 PMCID: PMC6125688 DOI: 10.1093/nar/gky552] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/15/2018] [Indexed: 01/20/2023] Open
Abstract
The next challenge in synthetic biology is to be able to replicate synthetic nucleic acid sequences efficiently. The synthetic pair, 2-amino-8-(1-beta-d-2′- deoxyribofuranosyl) imidazo [1,2-a]-1,3,5-triazin-[8H]-4-one (trivially designated P) with 6-amino-3-(2′-deoxyribofuranosyl)-5-nitro-1H-pyridin-2-one (trivially designated Z), is replicated by certain Family A polymerases, albeit with lower efficiency. Through directed evolution, we identified a variant KlenTaq polymerase (M444V, P527A, D551E, E832V) that incorporates dZTP opposite P more efficiently than the wild-type enzyme. Here, we report two crystal structures of this variant KlenTaq, a post-incorporation complex that includes a template-primer with P:Z trapped in the active site (binary complex) and a pre-incorporation complex with dZTP paired to template P in the active site (ternary complex). In forming the ternary complex, the fingers domain exhibits a larger closure angle than in natural complexes but engages the template-primer and incoming dNTP through similar interactions. In the binary complex, although many of the interactions found in the natural complexes are retained, there is increased relative motion of the thumb domain. Collectively, our analyses suggest that it is the post-incorporation complex for unnatural substrates that presents a challenge to the natural enzyme and that more efficient replication of P:Z pairs requires a more flexible polymerase.
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Affiliation(s)
- Isha Singh
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Roberto Laos
- Foundation for Applied Molecular Evolution and the Westheimer Institute of Science & Technology, Alachua, FL 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution and the Westheimer Institute of Science & Technology, Alachua, FL 32615, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution and the Westheimer Institute of Science & Technology, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, Alachua, FL 32615, USA
| | - Millie M Georgiadis
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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178
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Luo M, Groaz E, Froeyen M, Pezo V, Jaziri F, Leonczak P, Schepers G, Rozenski J, Marlière P, Herdewijn P. Invading Escherichia coli Genetics with a Xenobiotic Nucleic Acid Carrying an Acyclic Phosphonate Backbone (ZNA). J Am Chem Soc 2019; 141:10844-10851. [PMID: 31251601 DOI: 10.1021/jacs.9b04714] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A synthetic orthogonal polymer embracing a chiral acyclic-phosphonate backbone [(S)-ZNA] is presented that uniquely adds to the emerging family of xenobiotic nucleic acids (XNAs). (S)-ZNA consists of reiterating six-atom structural units and can be accessed in few synthetic steps from readily available phophonomethylglycerol nucleoside (PMGN) precursors. Comparative thermal stability experiments conducted on homo- and heteroduplexes made of (S)-ZNA are described that evince its high self-hybridization efficiency in contrast to poor binding of natural complements. Although preliminary and not conclusive, circular dichroism data and dynamic modeling computations provide support to a left-handed geometry of double-stranded (S)-ZNA. Nonetheless, PMGN diphosphate monomers were recognized as substrates by Escherichia coli (E. coli) polymerase I as well as being imported into E. coli cells equipped with an algal nucleotide transporter. A further investigation into the in vivo propagation of (S)-ZNA culminated with the demonstration of the first synthetic nucleic acid with an acyclic backbone that can be transliterated to DNA by the E. coli cellular machinery.
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Affiliation(s)
- Min Luo
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Elisabetta Groaz
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Mathy Froeyen
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Valérie Pezo
- Génomique Métabolique, Genoscope, Institut François Jacob , CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux 91057 Evry , France
| | - Faten Jaziri
- Génomique Métabolique, Genoscope, Institut François Jacob , CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux 91057 Evry , France
| | - Piotr Leonczak
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Guy Schepers
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Jef Rozenski
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
| | - Philippe Marlière
- Génomique Métabolique, Genoscope, Institut François Jacob , CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux 91057 Evry , France
| | - Piet Herdewijn
- Medicinal Chemistry , KU Leuven, Rega Institute for Medical Research , Herestraat 49-box 1041, 3000 Leuven , Belgium
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179
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Feldman AW, Dien VT, Karadeema RJ, Fischer EC, You Y, Anderson BA, Krishnamurthy R, Chen JS, Li L, Romesberg FE. Optimization of Replication, Transcription, and Translation in a Semi-Synthetic Organism. J Am Chem Soc 2019; 141:10644-10653. [PMID: 31241334 DOI: 10.1021/jacs.9b02075] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Previously, we reported the creation of a semi-synthetic organism (SSO) that stores and retrieves increased information by virtue of stably maintaining an unnatural base pair (UBP) in its DNA, transcribing the corresponding unnatural nucleotides into the codons and anticodons of mRNAs and tRNAs, and then using them to produce proteins containing noncanonical amino acids (ncAAs). Here we report a systematic extension of the effort to optimize the SSO by exploring a variety of deoxy- and ribonucleotide analogues. Importantly, this includes the first in vivo structure-activity relationship (SAR) analysis of unnatural ribonucleoside triphosphates. Similarities and differences between how DNA and RNA polymerases recognize the unnatural nucleotides were observed, and remarkably, we found that a wide variety of unnatural ribonucleotides can be efficiently transcribed into RNA and then productively and selectively paired at the ribosome to mediate the synthesis of proteins with ncAAs. The results extend previous studies, demonstrating that nucleotides bearing no significant structural or functional homology to the natural nucleotides can be efficiently and selectively paired during replication, to include each step of the entire process of information storage and retrieval. From a practical perspective, the results identify the most optimal UBP for replication and transcription, as well as the most optimal unnatural ribonucleoside triphosphates for transcription and translation. The optimized SSO is now, for the first time, able to efficiently produce proteins containing multiple, proximal ncAAs.
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Affiliation(s)
- Aaron W Feldman
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Vivian T Dien
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Rebekah J Karadeema
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Emil C Fischer
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Yanbo You
- School of Chemistry and Chemical Engineering , Henan Normal University , Henan 453007 , P. R. China
| | - Brooke A Anderson
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Jason S Chen
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Lingjun Li
- School of Chemistry and Chemical Engineering , Henan Normal University , Henan 453007 , P. R. China
| | - Floyd E Romesberg
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
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180
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Hamashima K, Soong YT, Matsunaga KI, Kimoto M, Hirao I. DNA Sequencing Method Including Unnatural Bases for DNA Aptamer Generation by Genetic Alphabet Expansion. ACS Synth Biol 2019; 8:1401-1410. [PMID: 30995835 DOI: 10.1021/acssynbio.9b00087] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The creation of unnatural base pairs (UBPs) has rapidly advanced the genetic alphabet expansion technology of DNA, requiring a new sequencing method for UB-containing DNAs with five or more letters. The hydrophobic UBP, Ds-Px, exhibits high fidelity in PCR and has been applied to DNA aptamer generation involving Ds as a fifth base. Here, we present a sequencing method for Ds-containing DNAs, in which Ds bases are replaced with natural bases by PCR using intermediate UB substrates (replacement PCR) for conventional deep sequencing. The composition rates of the natural bases converted from Ds significantly varied, depending on the sequence contexts around Ds and two different intermediate substrates. Therefore, we made an encyclopedia of the natural-base composition rates for all sequence contexts in each replacement PCR using different intermediate substrates. The Ds positions in DNAs can be determined by comparing the natural-base composition rates in both the actual and encyclopedia data, at each position of the DNAs obtained by deep sequencing after replacement PCR. We demonstrated the sequence determination of DNA aptamers in the enriched Ds-containing DNA libraries isolated by aptamer generation procedures targeting proteins. This study also provides valuable information about the fidelity of the Ds-Px pair in replication.
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Affiliation(s)
- Kiyofumi Hamashima
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669
| | - Yun Ting Soong
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669
| | - Ken-ichiro Matsunaga
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669
| | - Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669
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181
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Ping Z, Ma D, Huang X, Chen S, Liu L, Guo F, Zhu SJ, Shen Y. Carbon-based archiving: current progress and future prospects of DNA-based data storage. Gigascience 2019; 8:giz075. [PMID: 31220251 PMCID: PMC6586197 DOI: 10.1093/gigascience/giz075] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/09/2018] [Accepted: 06/03/2019] [Indexed: 01/23/2023] Open
Abstract
The information explosion has led to a rapid increase in the amount of data requiring physical storage. However, in the near future, existing storage methods (i.e., magnetic and optical media) will be insufficient to store these exponentially growing data. Therefore, data scientists are continually looking for better, more stable, and space-efficient alternatives to store these huge datasets. Because of its unique biological properties, highly condensed DNA has great potential to become a storage material for the future. Indeed, DNA-based data storage has recently emerged as a promising approach for long-term digital information storage. This review summarizes state-of-the-art methods, including digital-to-DNA coding schemes and the media types used in DNA-based data storage, and provides an overview of recent progress achieved in this field and its exciting future.
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Affiliation(s)
- Zhi Ping
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Dongzhao Ma
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaoluo Huang
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Shihong Chen
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Longying Liu
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Fei Guo
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Sha Joe Zhu
- Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford OX3 7LF, UK
| | - Yue Shen
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518083, China
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182
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Gao W, Cho E, Liu Y, Lu Y. Advances and Challenges in Cell-Free Incorporation of Unnatural Amino Acids Into Proteins. Front Pharmacol 2019; 10:611. [PMID: 31191324 PMCID: PMC6549004 DOI: 10.3389/fphar.2019.00611] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/15/2019] [Indexed: 12/17/2022] Open
Abstract
Incorporation of unnatural amino acids (UNAAs) into proteins currently is an active biological research area for various fundamental and applied science. In this context, cell-free synthetic biology (CFSB) has been developed and recognized as a robust testing and biomanufacturing platform for highly efficient UNAA incorporation. It enables the orchestration of unnatural biological machinery toward an exclusive user-defined objective of unnatural protein synthesis. This review aims to overview the principles of cell-free unnatural protein synthesis (CFUPS) systems, their advantages, different UNAA incorporation approaches, and recent achievements. These have catalyzed cutting-edge research and diverse emerging applications. Especially, present challenges and future trends are focused and discussed. With the development of CFSB and the fusion with other advanced next-generation technologies, CFUPS systems would explicitly deliver their values for biopharmaceutical applications.
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Affiliation(s)
- Wei Gao
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- College of Life Science, Shenyang Normal University, Shenyang, China
| | - Eunhee Cho
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Yingying Liu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- College of Life Science, Shenyang Normal University, Shenyang, China
| | - Yuan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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183
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Abstract
Chemical damage to DNA is a key initiator of adverse biological consequences due to disruption of the faithful reading of the genetic code. For example, O6-alkylguanine ( O6-alkylG) DNA adducts are strongly miscoding during DNA replication when the damaged nucleobase is a template for polymerase-mediated translesion DNA synthesis. Thus, mutations derived from O6-alkylG adducts can have severe adverse effects on protein translation and function and are an early event in the initiation of carcinogenesis. However, the low abundance of these adducts places significant limitations on our ability to relate their presence and biological influences with resultant mutations or disease risk. As a consequence, there is a critical need for novel tools to detect and study the biological role of alkylation adducts. Incorporating DNA bases with altered structures that are derived synthetically is a strategy that has been used widely to interrogate biological processes involving DNA. Such synthetic nucleosides have contributed to our understanding of DNA structure, DNA polymerase (Pol) and repair enzyme function, and to the expansion of the genetic alphabet. This Account describes our efforts toward creating and applying synthetic nucleosides directed at DNA adducts. We synthesized a variety of nucleosides with altered base structures that complement the altered hydrogen bonding capacity and hydrophilicity of O6-alkylG adducts. The heterocyclic perimidinone-derived nucleoside Per was the first of such adduct-directed synthetic nucleosides; it specifically stabilized O6-benzylguanine ( O6-BnG) in a DNA duplex. Structural variants of Per were used to determine hydrogen bonding and base-stacking contributions to DNA duplex stability in templates containing O6-BnG as well as O6-methylguanine ( O6-MeG) adducts. We created synthetic probes able to stabilize damaged over undamaged templates and established how altered hydrogen bonding or base-stacking properties impact DNA duplex stability as a function of adduct structures. This knowledge was then applied to devise a hybridization-based detection strategy involving gold nanoparticles that distinguish damaged from undamaged DNA by colorimetric changes. Furthermore, synthetic nucleosides were used as mechanistic tools to understand chemical determinants such as hydrogen bonding, π-stacking, and size and shape deviations that impact the efficiency and fidelity of DNA adduct bypass by DNA Pols. Finally, we reported the first example of amplifying alkylated DNA, accomplished by combining an engineered polymerase and synthetic triphosphate for which incorporation is templated by a DNA adduct. The presence of the synthetic nucleoside in amplicons could serve as a marker for the presence and location of DNA damage at low levels in DNA strands. Adduct-directed synthetic nucleosides have opened new concepts to interrogate the levels, locations, and biological influences of DNA alkylation.
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Affiliation(s)
- Michael H. Räz
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zürich 8092, Switzerland
| | - Claudia M. N. Aloisi
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zürich 8092, Switzerland
| | - Hailey L. Gahlon
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zürich 8092, Switzerland
| | - Shana J. Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zürich 8092, Switzerland
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184
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Eggert F, Kurscheidt K, Hoffmann E, Kath‐Schorr S. Towards Reverse Transcription with an Expanded Genetic Alphabet. Chembiochem 2019; 20:1642-1645. [DOI: 10.1002/cbic.201800808] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Frank Eggert
- LIMES Institute, Chemical Biology and Medicinal Chemistry UnitUniversity of Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Katharina Kurscheidt
- LIMES Institute, Chemical Biology and Medicinal Chemistry UnitUniversity of Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Eva Hoffmann
- LIMES Institute, Chemical Biology and Medicinal Chemistry UnitUniversity of Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
| | - Stephanie Kath‐Schorr
- LIMES Institute, Chemical Biology and Medicinal Chemistry UnitUniversity of Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Germany
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185
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Xia PF, Ling H, Foo JL, Chang MW. Synthetic genetic circuits for programmable biological functionalities. Biotechnol Adv 2019; 37:107393. [PMID: 31051208 DOI: 10.1016/j.biotechadv.2019.04.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/09/2019] [Accepted: 04/28/2019] [Indexed: 02/06/2023]
Abstract
Living organisms evolve complex genetic networks to interact with the environment. Due to the rapid development of synthetic biology, various modularized genetic parts and units have been identified from these networks. They have been employed to construct synthetic genetic circuits, including toggle switches, oscillators, feedback loops and Boolean logic gates. Building on these circuits, complex genetic machines with capabilities in programmable decision-making could be created. Consequently, these accomplishments have led to novel applications, such as dynamic and autonomous modulation of metabolic networks, directed evolution of biological units, remote and targeted diagnostics and therapies, as well as biological containment methods to prevent release of engineered microorganisms and genetic materials. Herein, we outline the principles in genetic circuit design that have initiated a new chapter in transforming concepts to realistic applications. The features of modularized building blocks and circuit architecture that facilitate realization of circuits for a variety of novel applications are discussed. Furthermore, recent advances and challenges in employing genetic circuits to impart microorganisms with distinct and programmable functionalities are highlighted. We envision that this review gives new insights into the design of synthetic genetic circuits and offers a guideline for the implementation of different circuits in various aspects of biotechnology and bioengineering.
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Affiliation(s)
- Peng-Fei Xia
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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186
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Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins. Biophys J 2019; 116:2062-2072. [PMID: 31084902 DOI: 10.1016/j.bpj.2019.04.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/28/2019] [Accepted: 04/16/2019] [Indexed: 11/21/2022] Open
Abstract
Given by χ torsional angles, rotamers describe the side-chain conformations of amino acid residues in a protein based on the rotational isomers (hence the word rotamer). Constructed rotamer libraries, based on either protein crystal structures or dynamics studies, are the tools for classifying rotamers (torsional angles) in a way that reflect their frequency in nature. Rotamer libraries are routinely used in structure modeling and evaluation. In this perspective article, we would like to encourage researchers to apply rotamer analyses beyond their traditional use. Molecular dynamics (MD) of proteins highlight the in silico behavior of molecules in solution and thus can identify favorable side-chain conformations. In this article, we used simple computational tools to study rotamer dynamics (RD) in MD simulations. First, we isolated each frame in the MD trajectories in separate Protein Data Bank files via the cpptraj module in AMBER. Then, we extracted torsional angles via the Bio3D module in R language. The classification of torsional angles was also done in R according to the penultimate rotamer library. RD analysis is useful for various applications such as protein folding, study of rotamer-rotamer relationship in protein-protein interaction, real-time correlation between secondary structures and rotamers, study of flexibility of side chains in binding site for molecular docking preparations, use of RD as guide in functional analysis and study of structural changes caused by mutations, providing parameters for improving coarse-grained MD accuracy and speed, and many others. Major challenges facing RD to emerge as a new scientific field involve the validation of results via easy, inexpensive wet-lab methods. This realm is yet to be explored.
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187
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Arangundy-Franklin S, Taylor AI, Porebski BT, Genna V, Peak-Chew S, Vaisman A, Woodgate R, Orozco M, Holliger P. A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids. Nat Chem 2019; 11:533-542. [PMID: 31011171 DOI: 10.1038/s41557-019-0255-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 03/15/2019] [Indexed: 12/24/2022]
Abstract
The physicochemical properties of nucleic acids are dominated by their highly charged phosphodiester backbone chemistry. This polyelectrolyte structure decouples information content (base sequence) from bulk properties, such as solubility, and has been proposed as a defining trait of all informational polymers. However, this conjecture has not been tested experimentally. Here, we describe the encoded synthesis of a genetic polymer with an uncharged backbone chemistry: alkyl phosphonate nucleic acids (phNAs) in which the canonical, negatively charged phosphodiester is replaced by an uncharged P-alkyl phosphonodiester backbone. Using synthetic chemistry and polymerase engineering, we describe the enzymatic, DNA-templated synthesis of P-methyl and P-ethyl phNAs, and the directed evolution of specific streptavidin-binding phNA aptamer ligands directly from random-sequence mixed P-methyl/P-ethyl phNA repertoires. Our results establish an example of the DNA-templated enzymatic synthesis and evolution of an uncharged genetic polymer and provide a foundational methodology for their exploration as a source of novel functional molecules.
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Affiliation(s)
| | - Alexander I Taylor
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Benjamin T Porebski
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Vito Genna
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sew Peak-Chew
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Alexandra Vaisman
- Section on DNA Replication, Repair and Mutagenesis, Bethesda, MD, USA
| | - Roger Woodgate
- Section on DNA Replication, Repair and Mutagenesis, Bethesda, MD, USA
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona, Spain
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK.
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188
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Wang L, Liu B, Liu Y, Sun Y, Liu W, Yu D, Zhao ZK. Escherichia coli Strain Designed for Characterizing in Vivo Functions of Nicotinamide Adenine Dinucleotide Analogues. Org Lett 2019; 21:3218-3222. [PMID: 30995052 DOI: 10.1021/acs.orglett.9b00935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
An Escherichia coli strain was constructed for the efficient import of nicotinamide adenine dinucleotide (NAD) analogues into cells by limiting extracellular degradation while expressing an efficient NAD importer. In vivo functions of three NAD analogues were characterized. Nicotinamide hypoxanthine dinucleotide was identified as an inhibitor of NAD synthesis. Nicotinamide cytosine dinucleotide had excellent biocompatibility and was used for characterizing a growth-dependent degradation of in vivo nicotinamide cofactors.
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Affiliation(s)
- Lei Wang
- School of Chemical Engineering , Northeast Electric Power University , Jilin 132012 , China
| | - Bin Liu
- School of Chemical Engineering , Northeast Electric Power University , Jilin 132012 , China
| | - Yuxue Liu
- Division of Biotechnology , Dalian Institute of Chemical Physics , CAS, Dalian 116023 , China
| | - Yue Sun
- School of Chemical Engineering , Northeast Electric Power University , Jilin 132012 , China
| | - Wujun Liu
- Institute of Cancer Stem Cell , Dalian Medical University , Dalian 116044 , China
| | - Dayu Yu
- School of Chemical Engineering , Northeast Electric Power University , Jilin 132012 , China
| | - Zongbao K Zhao
- Division of Biotechnology , Dalian Institute of Chemical Physics , CAS, Dalian 116023 , China
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189
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Flamme M, McKenzie LK, Sarac I, Hollenstein M. Chemical methods for the modification of RNA. Methods 2019; 161:64-82. [PMID: 30905751 DOI: 10.1016/j.ymeth.2019.03.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
RNA is often considered as being the vector for the transmission of genetic information from DNA to the protein synthesis machinery. However, besides translation RNA participates in a broad variety of fundamental biological roles such as gene expression and regulation, protein synthesis, and even catalysis of chemical reactions. This variety of function combined with intricate three-dimensional structures and the discovery of over 100 chemical modifications in natural RNAs require chemical methods for the modification of RNAs in order to investigate their mechanism, location, and exact biological roles. In addition, numerous RNA-based tools such as ribozymes, aptamers, or therapeutic oligonucleotides require the presence of additional chemical functionalities to strengthen the nucleosidic backbone against degradation or enhance the desired catalytic or binding properties. Herein, the two main methods for the chemical modification of RNA are presented: solid-phase synthesis using phosphoramidite precursors and the enzymatic polymerization of nucleoside triphosphates. The different synthetic and biochemical steps required for each method are carefully described and recent examples of practical applications based on these two methods are discussed.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Luke K McKenzie
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Ivo Sarac
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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190
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Synthetic biology: Recent progress, biosafety and biosecurity concerns, and possible solutions. JOURNAL OF BIOSAFETY AND BIOSECURITY 2019. [DOI: 10.1016/j.jobb.2018.12.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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191
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Vecchi D, Miquel PA, Hernández I. From Biological Determination to Entangled Causation. Acta Biotheor 2019; 67:19-46. [PMID: 30182354 DOI: 10.1007/s10441-018-9339-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/29/2018] [Indexed: 11/27/2022]
Abstract
Biologists and philosophers often use the language of determination in order to describe the nature of developmental phenomena. Accounts in terms of determination have often been reductionist. One common idea is that DNA is supposed to play a special explanatory role in developmental explanations, namely, that DNA is a developmental determinant. In this article we try to make sense of determination claims in developmental biology. Adopting a manipulationist approach, we shall first argue that the notion of developmental determinant is causal. We suggest that two different theses concerning developmental determination can be articulated: determination of occurrence and structural determination. We shall argue that, while the first thesis is problematic, the second, opportunely qualified, is feasible. Finally, we shall argue that an analysis of biological causation in terms of determination cannot account for entangled dynamics. Characterising causal entanglement as a particular kind of interactive causation whereby difference-making causes ascribable to different levels of biological organisation influence a particular ontogenetic outcome, we shall, via two illustrative examples, diagnose some potential limits of a reductionist, molecular and intra-level understanding of biological causation.
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Affiliation(s)
- Davide Vecchi
- Centro de Filosofia das Ciências, Departamento de História e Filosofia das Ciências, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal.
- Departamento de Filosofía, Facultad de Humanidades, Universidad de Santiago de Chile, Avenida Libertador Bernardo O'Higgins #3677, Santiago, Chile.
| | - Paul-Antoine Miquel
- Laboratoire ERRAPHIS, PhSciVi, Université Toulouse Jean Jaurès, Maison de la Recherche 5 allée Antonio-Machado, 31058, Toulouse Cedex 9, France
| | - Isaac Hernández
- Laboratoire ERRAPHIS, PhSciVi, Université Toulouse Jean Jaurès, Maison de la Recherche 5 allée Antonio-Machado, 31058, Toulouse Cedex 9, France
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192
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Zhang Y, Kleiner RE. A Metabolic Engineering Approach to Incorporate Modified Pyrimidine Nucleosides into Cellular RNA. J Am Chem Soc 2019; 141:3347-3351. [PMID: 30735369 DOI: 10.1021/jacs.8b11449] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The incorporation of modified nucleotides into RNA is a powerful strategy to probe RNA structure and function. While a wide variety of modified nucleotides can be incorporated into RNA in vitro using chemical or enzymatic synthesis, strategies for the metabolic incorporation of artificial nucleotides into cellular RNA are limited, largely due to the incompatibility of modified nucleobases and nucleosides with nucleotide salvage pathways. In this work, we develop a metabolic engineering strategy to facilitate the labeling of cellular RNA with noncanonical pyrimidine nucleosides. First, we use structure-based protein engineering to alter the substrate specificity of uridine-cytidine kinase 2 (UCK2), a key enzyme in the pyrimidine nucleotide salvage pathway. Next, we show that expression of mutant UCK2 in HeLa and U2OS cells is sufficient to enable the incorporation of 5-azidomethyl uridine (5-AmU) into cellular RNA and promotes RNA labeling by other C5-modified pyrimidines. Finally, we apply UCK2-mediated RNA labeling with 5-AmU to study RNA trafficking and turnover during normal and stress conditions and find diminished RNA localization in the cytosol during arsenite stress. Taken together, our study provides a general strategy for the incorporation of modified pyrimidine nucleosides into cellular RNA and expands the chemical toolkit of modified bases for studying dynamic RNA behavior in living cells.
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Affiliation(s)
- Yu Zhang
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Ralph E Kleiner
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
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193
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Strazewski P. Low-Digit and High-Digit Polymers in the Origin of Life. Life (Basel) 2019; 9:life9010017. [PMID: 30717360 PMCID: PMC6463190 DOI: 10.3390/life9010017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/23/2019] [Accepted: 01/26/2019] [Indexed: 01/22/2023] Open
Abstract
Extant life uses two kinds of linear biopolymers that mutually control their own production, as well as the cellular metabolism and the production and homeostatic maintenance of other biopolymers. Nucleic acids are linear polymers composed of a relatively low structural variety of monomeric residues, and thus a low diversity per accessed volume. Proteins are more compact linear polymers that dispose of a huge compositional diversity even at the monomeric level, and thus bear a much higher catalytic potential. The fine-grained diversity of proteins makes an unambiguous information transfer from protein templates too error-prone, so they need to be resynthesized in every generation. But proteins can catalyse both their own reproduction as well as the efficient and faithful replication of nucleic acids, which resolves in a most straightforward way an issue termed “Eigen’s paradox”. Here the importance of the existence of both kinds of linear biopolymers is discussed in the context of the emergence of cellular life, be it for the historic orgin of life on Earth, on some other habitable planet, or in the test tube. An immediate consequence of this analysis is the necessity for translation to appear early during the evolution of life.
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Affiliation(s)
- Peter Strazewski
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (Unité Mixte de Recherche 5246), Université de Lyon, Claude Bernard Lyon 1, 43 bvd du 11 Novembre 1918, 69622 Villeurbanne CEDEX, France.
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194
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Affiliation(s)
- Floyd E. Romesberg
- Department of ChemistryThe Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
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195
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Müller TG, Sakin V, Müller B. A Spotlight on Viruses-Application of Click Chemistry to Visualize Virus-Cell Interactions. Molecules 2019; 24:molecules24030481. [PMID: 30700005 PMCID: PMC6385038 DOI: 10.3390/molecules24030481] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/18/2019] [Accepted: 01/19/2019] [Indexed: 01/03/2023] Open
Abstract
The replication of a virus within its host cell involves numerous interactions between viral and cellular factors, which have to be tightly controlled in space and time. The intricate interplay between viral exploitation of cellular pathways and the intrinsic host defense mechanisms is difficult to unravel by traditional bulk approaches. In recent years, novel fluorescence microscopy techniques and single virus tracking have transformed the investigation of dynamic virus-host interactions. A prerequisite for the application of these imaging-based methods is the attachment of a fluorescent label to the structure of interest. However, their small size, limited coding capacity and multifunctional proteins render viruses particularly challenging targets for fluorescent labeling approaches. Click chemistry in conjunction with genetic code expansion provides virologists with a novel toolbox for site-specific, minimally invasive labeling of virion components, whose potential has just recently begun to be exploited. Here, we summarize recent achievements, current developments and future challenges for the labeling of viral nucleic acids, proteins, glycoproteins or lipids using click chemistry in order to study dynamic processes in virus-cell interactions.
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Affiliation(s)
- Thorsten G Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
| | - Volkan Sakin
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
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196
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Blanco C, Janzen E, Pressman A, Saha R, Chen IA. Molecular Fitness Landscapes from High-Coverage Sequence Profiling. Annu Rev Biophys 2019; 48:1-18. [PMID: 30601678 DOI: 10.1146/annurev-biophys-052118-115333] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The function of fitness (or molecular activity) in the space of all possible sequences is known as the fitness landscape. Evolution is a random walk on the fitness landscape, with a bias toward climbing hills. Mapping the topography of real fitness landscapes is fundamental to understanding evolution, but previous efforts were hampered by the difficulty of obtaining large, quantitative data sets. The accessibility of high-throughput sequencing (HTS) has transformed this study, enabling large-scale enumeration of fitness for many mutants and even complete sequence spaces in some cases. We review the progress of high-throughput studies in mapping molecular fitness landscapes, both in vitro and in vivo, as well as opportunities for future research. Such studies are rapidly growing in number. HTS is expected to have a profound effect on the understanding of real molecular fitness landscapes.
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Affiliation(s)
- Celia Blanco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA; , , , ,
| | - Evan Janzen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA; , , , , .,Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106, USA
| | - Abe Pressman
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA; , , , , .,Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Ranajay Saha
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA; , , , ,
| | - Irene A Chen
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106, USA
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197
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Alternative Biochemistries for Alien Life: Basic Concepts and Requirements for the Design of a Robust Biocontainment System in Genetic Isolation. Genes (Basel) 2018; 10:genes10010017. [PMID: 30597824 PMCID: PMC6356944 DOI: 10.3390/genes10010017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 02/08/2023] Open
Abstract
The universal genetic code, which is the foundation of cellular organization for almost all organisms, has fostered the exchange of genetic information from very different paths of evolution. The result of this communication network of potentially beneficial traits can be observed as modern biodiversity. Today, the genetic modification techniques of synthetic biology allow for the design of specialized organisms and their employment as tools, creating an artificial biodiversity based on the same universal genetic code. As there is no natural barrier towards the proliferation of genetic information which confers an advantage for a certain species, the naturally evolved genetic pool could be irreversibly altered if modified genetic information is exchanged. We argue that an alien genetic code which is incompatible with nature is likely to assure the inhibition of all mechanisms of genetic information transfer in an open environment. The two conceivable routes to synthetic life are either de novo cellular design or the successive alienation of a complex biological organism through laboratory evolution. Here, we present the strategies that have been utilized to fundamentally alter the genetic code in its decoding rules or its molecular representation and anticipate future avenues in the pursuit of robust biocontainment.
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198
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Non canonical genetic material. Curr Opin Biotechnol 2018; 57:25-33. [PMID: 30554069 DOI: 10.1016/j.copbio.2018.12.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 11/13/2018] [Accepted: 12/03/2018] [Indexed: 01/20/2023]
Abstract
To increase the scope of natural biosystem, nucleic acids have been intensively modified. One direction includes the development of a synthetic alternative to the native DNA and RNA, denoted Xenobiotic nucleic acids (XNAs) that are able to store and transfer genetic information either by base-modification or backbone-modification. Another line of research aims to develop alternative third base pair additional to natural A:T and G:C. These unnatural base pairs (UBPs) can store increased information content encoded in three base pairs. This review outlines the recent progress made towards XNA and UBP applications as new components of the genomic DNA as well as biostable aptamers. New achievements in the replacement of a bacterial genome by unnatural non-canonical nucleotides are also described.
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Genetic Alphabet Expansion Provides Versatile Specificities and Activities of Unnatural-Base DNA Aptamers Targeting Cancer Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 14:158-170. [PMID: 30594072 PMCID: PMC6307347 DOI: 10.1016/j.omtn.2018.11.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/26/2018] [Accepted: 11/15/2018] [Indexed: 11/25/2022]
Abstract
The potential of genetic alphabet expansion technologies using artificial extra base pairs (unnatural base pairs) has been rapidly expanding and increasing. We present that the hydrophobic unnatural base, 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds), which acts as a fifth letter in a DNA library, provides a series of high-affinity DNA aptamers with versatile binding specificities and activities to cancer cells. These Ds-containing DNA aptamers were generated by a method called cell-ExSELEX to target three breast cancer cell lines: MCF7, MDA-MB-231, and T-47D. Aptamer 14A-MCF7, which targets MCF7 cells, specifically binds to MCF7 cells, but not other cancer cell lines. Aptamer 07-MB231, which targets MDA-MB-231 cells, binds to a series of metastatic bone and lung cancer cell lines. Aptamer 05-MB231 targets MDA-MB-231 cells, but it also binds to all of the cancer and leukemia cell lines that we examined. None of these aptamers bind to normal cell lines, such as MCF10A and HUVEC. In addition, aptamers 14A-MCF7 and 05-MB231 are internalized within the cancer cells, and aptamer 05-MB231 possesses anti-proliferative properties against most cancer cell lines that we examined. These aptamers and the generation method are broadly applicable to cancer cell imaging, biomarker discovery, cancer cell profiling, anti-cancer therapies, and drug delivery systems.
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Guo WW, Zhang TS, Fang WH, Cui G. QM/MM studies on the excited-state relaxation mechanism of a semisynthetic dTPT3 base. Phys Chem Chem Phys 2018; 20:5067-5073. [PMID: 29388994 DOI: 10.1039/c7cp08696b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Semisynthetic alphabets can potentially increase the genetic information stored in DNA through the formation of unusual base pairs. Recent experiments have shown that near-visible-light irradiation of the dTPT3 chromophore could lead to the formation of a reactive triplet state and of singlet oxygen in high quantum yields. However, the detailed excited-state relaxation paths that populate the lowest triplet state are unclear. Herein, we have for the first time employed the QM(MS-CASPT2//CASSCF)/MM method to explore the spectroscopic properties and excited-state relaxation mechanism of the aqueous dTPT3 chromophore. On the basis of the results, we have found that (1) the S2(1ππ*) state of dTPT3 is the initially populated excited singlet state upon near-visible light irradiation; and (2) there are two efficient relaxation pathways to populate the lowest triplet state, i.e. T1(3ππ*). In the first one, the S2(1ππ*) system first decays to the S1(1nπ*) state near the S2/S1 conical intersection, which is followed by an efficient S1 → T1 intersystem crossing process at the S1/T1 crossing point; in the second one, an efficient S2 → T2 intersystem crossing takes place first, and then, the T2(3nπ*) system hops to the T1(3ππ*) state through an internal conversion process at the T2/T1 conical intersection. Moreover, an S2/S1/T2 intersection region is found to play a vital role in the excited-state relaxation. These new mechanistic insights help in understanding the photophysics and photochemistry of unusual base pairs.
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Affiliation(s)
- Wei-Wei Guo
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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