1
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Banfalvi G. The Origin of RNA and the Formose-Ribose-RNA Pathway. Int J Mol Sci 2024; 25:6727. [PMID: 38928433 PMCID: PMC11203418 DOI: 10.3390/ijms25126727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Prebiotic pre-Darwinian reactions continued throughout biochemical or Darwinian evolution. Early chemical processes could have occurred on Earth between 4.5 and 3.6 billion years ago when cellular life was about to come into being. Pre-Darwinian evolution assumes the development of hereditary elements but does not regard them as self-organizing processes. The presence of biochemical self-organization after the pre-Darwinian evolution did not justify distinguishing between different types of evolution. From the many possible solutions, evolution selected from among those stable reactions that led to catalytic networks, and under gradually changing external conditions produced a reproducible, yet constantly evolving and adaptable, living system. Major abiotic factors included sunlight, precipitation, air, minerals, soil and the Earth's atmosphere, hydrosphere and lithosphere. Abiotic sources of chemicals contributed to the formation of prebiotic RNA, the development of genetic RNA, the RNA World and the initial life forms on Earth and the transition of genRNA to the DNA Empire, and eventually to the multitude of life forms today. The transition from the RNA World to the DNA Empire generated new processes such as oxygenic photosynthesis and the hierarchical arrangement of processes involved in the transfer of genetic information. The objective of this work is to unite earlier work dealing with the formose, the origin and synthesis of ribose and RNA reactions that were published as a series of independent reactions. These reactions are now regarded as the first metabolic pathway.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, 4032 Debrecen, Hungary
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2
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Jena NR, Shukla PK. Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA. Sci Rep 2023; 13:19246. [PMID: 37935822 PMCID: PMC10630353 DOI: 10.1038/s41598-023-46572-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023] Open
Abstract
A triple helical DNA can control gene expression, help in homologous recombination, induce mutations to facilitate DNA repair mechanisms, suppress oncogene formations, etc. However, the structure and function of semisynthetic triple helical DNA are not known. To understand this, various triplets formed between eight artificial nucleobases (P, Z, J, V, B, S, X, and K) and four natural DNA bases (G, C, A, and T) are studied herein by employing a reliable density functional theoretic (DFT) method. Initially, the triple helix-forming artificial nucleobases interacted with the duplex DNA containing GC and AT base pairs, and subsequently, triple helix-forming natural bases (G and C) interacted with artificial duplex DNA containing PZ, JV, BS, and XK base pairs. Among the different triplets formed in the first category, the C-JV triplet is found to be the most stable with a binding energy of about - 31 kcal/mol. Similarly, among the second category of triplets, the Z-GC and V-GC triplets are the most stable. Interestingly, Z-GC and V-GC are found to be isoenergetic with a binding energy of about - 30 kcal/mol. The C-JV, and Z-GC or V-GC triplets are about 12-14 kcal/mol more stable than the JV and GC base pairs respectively. Microsolvation of these triplets in 5 explicit water molecules further enhanced their stability by 16-21 kcal/mol. These results along with the consecutive stacking of the C-JV triplet (C-JV/C-JV) data indicate that the synthetic nucleobases can form stable semisynthetic triple helical DNA. However, consideration of a full-length DNA containing one or more semisynthetic bases or base pairs is necessary to understand the formation of semisynthetic DNA in living cells.
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Affiliation(s)
- N R Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design, and Manufacturing, Dumna Airport Road, Khamaria, Jabalpur, 482005, India.
| | - P K Shukla
- Department of Physics, Assam University, Silchar, Assam, 788 011, India
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3
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Enya K, Yamagishi A, Kobayashi K, Yoshimura Y, Tasker EJ. A Comparative Study of Methods for Detecting Extraterrestrial Life in Exploration Missions to Mars and the Solar System II: Targeted Characteristics, Detection Techniques, and Their Combination for Survey, Detection, and Analysis. ASTROBIOLOGY 2023; 23:1099-1117. [PMID: 37768711 PMCID: PMC10616949 DOI: 10.1089/ast.2022.0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 08/15/2023] [Indexed: 09/29/2023]
Abstract
We present a comparative study of the methods used in the search for extraterrestrial microorganism life, including a summary table where different life-detection techniques can be easily compared as an aid to mission and instrument design aimed at life detection. This is an extension of previous study, where detection techniques for a series of target characteristics and molecules that could constitute a positive life detection were evaluated. This comparison has been extended with a particular consideration to sources of false positives, the causes of negative detection, the results of detection techniques when presented regarding terrestrial life, and additional science objectives that could be achieved outside the primary aim of detecting life. These additions address both the scientific and programmatic side of exploration mission design, where a successful proposal must demonstrate probable outcomes and be able to return valuable results even if no life is found. The applicability of the life detection techniques is considered for Earth life, Earth-independent life (life emerging independently from that on Earth,) and Earth-kin life (sharing a common ancestor with life on Earth), and techniques effective in detecting Earth life should also be useful in the detection of Earth-kin life. However, their applicability is not guaranteed for Earth-independent life. As found in our previous study, there exists no realistic single detection method that can conclusively determine the discovery of extraterrestrial life, and no method is superior to all others. In this study, we further consider combinations of detection techniques and identify imaging as a valuable addition to molecule detection methods, even in cases where there is insufficient resolution to observe the detailed morphology of a microbial cell. The search for extraterrestrial life is further divided into a survey-and-detection and analysis-and-conclusion step. These steps benefit from different detection techniques, but imaging is necessary for both parts.
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Affiliation(s)
- Keigo Enya
- Department of Solar System Sciences, Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Sagamihara, Japan
- Space and Astronautical Science, Graduate Institute for Advanced Studies, SOKENDAI, Hayama, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Science, School of Life Science, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Kensei Kobayashi
- Department of Chemistry, Yokohama National University, Yokohama, Japan
- Department of Earth and Planetary Science, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Elizabeth J. Tasker
- Department of Solar System Sciences, Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Sagamihara, Japan
- Space and Astronautical Science, Graduate Institute for Advanced Studies, SOKENDAI, Hayama, Japan
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4
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Carr CE, Ramírez-Colón JL, Duzdevich D, Lee S, Taniguchi M, Ohshiro T, Komoto Y, Soderblom JM, Zuber MT. Solid-State Single-Molecule Sensing with the Electronic Life-Detection Instrument for Enceladus/Europa (ELIE). ASTROBIOLOGY 2023; 23:1056-1070. [PMID: 37782210 DOI: 10.1089/ast.2022.0119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Growing evidence of the potential habitability of Ocean Worlds across our solar system is motivating the advancement of technologies capable of detecting life as we know it-sharing a common ancestry or physicochemical origin with life on Earth-or don't know it, representing a distinct emergence of life different than our one known example. Here, we propose the Electronic Life-detection Instrument for Enceladus/Europa (ELIE), a solid-state single-molecule instrument payload that aims to search for life based on the detection of amino acids and informational polymers (IPs) at the parts per billion to trillion level. As a first proof-of-principle in a laboratory environment, we demonstrate the single-molecule detection of the amino acid L-proline at a 10 μM concentration in a compact system. Based on ELIE's solid-state quantum electronic tunneling sensing mechanism, we further propose the quantum property of the HOMO-LUMO gap (energy difference between a molecule's highest energy-occupied molecular orbital and lowest energy-unoccupied molecular orbital) as a novel metric to assess amino acid complexity. Finally, we assess the potential of ELIE to discriminate between abiotically and biotically derived α-amino acid abundance distributions to reduce the false positive risk for life detection. Nanogap technology can also be applied to the detection of nucleobases and short sequences of IPs such as, but not limited to, RNA and DNA. Future missions may utilize ELIE to target preserved biosignatures on the surface of Mars, extant life in its deep subsurface, or life or its biosignatures in a plume, surface, or subsurface of ice moons such as Enceladus or Europa. One-Sentence Summary: A solid-state nanogap can determine the abundance distribution of amino acids, detect nucleic acids, and shows potential for detecting life as we know it and life as we don't know it.
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Affiliation(s)
- Christopher E Carr
- Daniel Guggenheim School of Aerospace Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - José L Ramírez-Colón
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Daniel Duzdevich
- Massachusetts General Hospital, Department of Molecular Biology, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
- Current address: Department of Chemistry, University of Chicago, Chicago, Illinois, USA
| | - Sam Lee
- MIT Department of Electrical Engineering and Computer Science, Cambridge, Massachusetts, USA
| | - Masateru Taniguchi
- Osaka University, Institute of Scientific and Industrial Research, Osaka, Japan
| | - Takahito Ohshiro
- Osaka University, Institute of Scientific and Industrial Research, Osaka, Japan
| | - Yuki Komoto
- Osaka University, Institute of Scientific and Industrial Research, Osaka, Japan
| | - Jason M Soderblom
- MIT Department of Earth, Atmospheric and Planetary Sciences, Cambridge, Massachusetts, USA
| | - M T Zuber
- MIT Department of Earth, Atmospheric and Planetary Sciences, Cambridge, Massachusetts, USA
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5
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Thomas CA, Craig JM, Hoshika S, Brinkerhoff H, Huang JR, Abell SJ, Kim HC, Franzi MC, Carrasco JD, Kim HJ, Smith DC, Gundlach JH, Benner SA, Laszlo AH. Assessing Readability of an 8-Letter Expanded Deoxyribonucleic Acid Alphabet with Nanopores. J Am Chem Soc 2023; 145:8560-8568. [PMID: 37036666 DOI: 10.1021/jacs.3c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Chemists have now synthesized new kinds of DNA that add nucleotides to the four standard nucleotides (guanine, adenine, cytosine, and thymine) found in standard Terran DNA. Such "artificially expanded genetic information systems" are today used in molecular diagnostics; to support directed evolution to create medically useful receptors, ligands, and catalysts; and to explore issues related to the early evolution of life. Further applications are limited by the inability to directly sequence DNA containing nonstandard nucleotides. Nanopore sequencing is well-suited for this purpose, as it does not require enzymatic synthesis, amplification, or nucleotide modification. Here, we take the first steps to realize nanopore sequencing of an 8-letter "hachimoji" expanded DNA alphabet by assessing its nanopore signal range using the MspA (Mycobacterium smegmatis porin A) nanopore. We find that hachimoji DNA exhibits a broader signal range in nanopore sequencing than standard DNA alone and that hachimoji single-base substitutions are distinguishable with high confidence. Because nanopore sequencing relies on a molecular motor to control the motion of DNA, we then assessed the compatibility of the Hel308 motor enzyme with nonstandard nucleotides by tracking the translocation of single Hel308 molecules along hachimoji DNA, monitoring the enzyme kinetics and premature enzyme dissociation from the DNA. We find that Hel308 is compatible with hachimoji DNA but dissociates more frequently when walking over C-glycoside nucleosides, compared to N-glycosides. C-glycocide nucleosides passing a particular site within Hel308 induce a higher likelihood of dissociation. This highlights the need to optimize nanopore sequencing motors to handle different glycosidic bonds. It may also inform designs of future alternative DNA systems that can be sequenced with existing motors and pores.
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Affiliation(s)
- Christopher A Thomas
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Henry Brinkerhoff
- 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
| | - Sarah J Abell
- 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
| | - Michaela C Franzi
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jessica D Carrasco
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Hyo-Joong Kim
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Drew C Smith
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
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6
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Jena NR, Das P, Shukla PK. Complementary base pair interactions between different rare tautomers of the second-generation artificial genetic alphabets. J Mol Model 2023; 29:125. [PMID: 37014428 DOI: 10.1007/s00894-023-05537-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/29/2023] [Indexed: 04/05/2023]
Abstract
The functionality of a semisynthetic DNA in the biological environment will depend on the base pair nature of its complementary base pairs. To understand this, base pair interactions between complementary bases of recently proposed eight second-generation artificial nucleobases are studied herein by considering their rare tautomeric conformations and a dispersion-corrected density functional theoretic method. It is found that the binding energies of two hydrogen-bonded complementary base pairs are more negative than those of the three hydrogen-bonded base pairs. However, as the former base pairs are endothermic, the semisynthetic duplex DNA would involve the latter base pairs.
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Affiliation(s)
- N R Jena
- 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
| | - P K Shukla
- Department of Physics, Assam University, Silchar, 788011, India
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7
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Shukla MS, Hoshika S, Benner SA, Georgiadis MM. Crystal structures of 'ALternative Isoinformational ENgineered' DNA in B-form. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220028. [PMID: 36633282 PMCID: PMC9835606 DOI: 10.1098/rstb.2022.0028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The first structural model of duplex DNA reported in 1953 by Watson & Crick presented the double helix in B-form, the form that genomic DNA exists in much of the time. Thus, artificial DNA seeking to mimic the properties of natural DNA should also be able to adopt B-form. Using a host-guest system in which Moloney murine leukemia virus reverse transcriptase serves as the host and DNA as the guests, we determined high-resolution crystal structures of three complexes including 5'-CTTBPPBBSSZZSAAG, 5'-CTTSSPBZPSZBBAAG and 5'-CTTZZPBSBSZPPAAG with 10 consecutive unnatural nucleobase pairs in B-form within self-complementary 16 bp duplex oligonucleotides. We refer to this ALternative Isoinformational ENgineered (ALIEN) genetic system containing two nucleobase pairs (P:Z, pairing 2-amino-imidazo-[1,2-a]-1,3,5-triazin-(8H)-4-one with 6-amino-5-nitro-(1H)-pyridin-2-one, and B:S, 6-amino-4-hydroxy-5-(1H)-purin-2-one with 3-methyl-6-amino-pyrimidin-2-one) as ALIEN DNA. We characterized both position- and sequence-specific helical, nucleobase pair and dinucleotide step parameters of P:Z and B:S pairs in the context of B-form DNA. We conclude that ALIEN DNA exhibits structural features that vary with sequence. Further, Z can participate in alternative stacking modes within a similar sequence context as captured in two different structures. This finding suggests that ALIEN DNA may have a larger repertoire of B-form structures than natural DNA. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Madhura S. Shukla
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, no. 7, Alachua, FL 32615, USA
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, no. 7, Alachua, FL 32615, USA
| | - Millie M. Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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8
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Samokhvalova S, Lutz JF. Macromolecular Information Transfer. Angew Chem Int Ed Engl 2023; 62:e202300014. [PMID: 36696359 DOI: 10.1002/anie.202300014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/26/2023]
Abstract
Macromolecular information transfer can be defined as the process by which a coded monomer sequence is communicated from one macromolecule to another. In such a transfer process, the information sequence can be kept identical, transformed into a complementary sequence or even translated into a different molecular language. Such mechanisms are crucial in biology and take place in DNA→DNA replication, DNA→RNA transcription and RNA→protein translation. In fact, there would be no life on Earth without macromolecular information transfer. Mimicking such processes with synthetic macromolecules would also be of major scientific relevance because it would open up new avenues for technological applications (e.g. data storage and processing) but also for the creation of artificial life. In this important context, this minireview summarizes recent research about information transfer in synthetic oligomers and polymers. Medium- and long-term perspectives are also discussed.
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Affiliation(s)
- Svetlana Samokhvalova
- Université de Strasbourg, CNRS, ISIS, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Jean-François Lutz
- Université de Strasbourg, CNRS, ISIS, 8 allée Gaspard Monge, 67000, Strasbourg, France
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9
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Vos E, Hoehn SJ, Krul SE, Crespo-Hernández CE, González-Vázquez J, Corral I. Disclosing the Role of C4-Oxo Substitution in the Photochemistry of DNA and RNA Pyrimidine Monomers: Formation of Photoproducts from the Vibrationally Excited Ground State. J Phys Chem Lett 2022; 13:2000-2006. [PMID: 35191712 PMCID: PMC8900130 DOI: 10.1021/acs.jpclett.2c00052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Oxo and amino substituted purines and pyrimidines have been suggested as protonucleobases participating in ancient pre-RNA forms. Considering electromagnetic radiation as a key environmental selection pressure on early Earth, the investigation of the photophysics of modified nucleobases is crucial to determine their viability as nucleobases' ancestors and to understand the factors that rule the photostability of natural nucleobases. In this Letter, we combine femtosecond transient absorption spectroscopy and quantum mechanical simulations to reveal the photochemistry of 4-pyrimidinone, a close relative of uracil. Irradiation of 4-pyrimidinone with ultraviolet radiation populates the S1(ππ*) state, which decays to the vibrationally excited ground state in a few hundred femtoseconds. Analysis of the postirradiated sample in water reveals the formation of a 6-hydroxy-5H-photohydrate and 3-(N-(iminomethyl)imino)propanoic acid as the primary photoproducts. 3-(N-(Iminomethyl)imino)propanoic acid originates from the hydrolysis of an unstable ketene species generated from the C4-N3 photofragmentation of the pyrimidine core.
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Affiliation(s)
- Eva Vos
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
| | - Sean J. Hoehn
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Sarah E. Krul
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Carlos E. Crespo-Hernández
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Jesús González-Vázquez
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Inés Corral
- Departamento
de Química, Módulo 13, Universidad
Autónoma de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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10
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Romeo-Gella F, Arpa EM, Corral I. A molecular insight into the photophysics of barbituric acid, a candidate for canonical nucleobases' ancestor. Phys Chem Chem Phys 2022; 24:1405-1414. [PMID: 34982082 DOI: 10.1039/d1cp04987a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This work investigates the photophysics of barbituric acid at different pH conditions using ab initio methods. Our calculations ascribe the most intense bands at ca. 260 nm at neutral pH and 210 nm at acidic pH conditions in the absorption spectra of this chromophore to the lowest lying ππ* transitions. Consistently with the ultrashort excited state lifetimes experimentally registered, the potential energy landscapes of both the neutral and deprotonated forms of barbituric acid combined with the interpretation of their transient absorption spectra suggest the deactivation of these systems along the singlet manifold. Compared to uracil, its closest natural nucleobase, barbituric acid presents a red shifted absorption spectrum, due to the lowering by more than 0.5 eV of the lowest-energy ππ* excited state, and a much more complex topography of the S1 potential energy surface, with several energetically accessible local minima. This fact, however, does not affect the excited state lifetimes, which for barbituric acid were experimentally registered in the sub-ps time scale.
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Affiliation(s)
- Fernando Romeo-Gella
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Enrique M Arpa
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Inés Corral
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049, Madrid, Spain. .,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain
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11
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Jena NR. Rare Tautomers of Artificially Expanded Genetic Letters and their Effects on the Base pair Stabilities. Chemphyschem 2022; 23:e202100908. [PMID: 35029036 DOI: 10.1002/cphc.202100908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Indexed: 11/11/2022]
Abstract
To expand the existing genetic letters, it is necessary to design robust nucleotides that can function naturally in living cells. Therefore, it is desirable to examine the roles of recently proposed second-generation artificially expanded genetic letters in producing stable duplex DNA. Here, a reliable dispersion-corrected density functional theory method is used to understand the electronic structures and properties of different rare tautomers of proposed expanded genetic letters and their effects on the base pair stabilities in the duplex DNA. It is found that the rare tautomers are not only stable in the aqueous medium but can also base pair with natural bases to produce stable mispairs. Except for J and V, all the artificial genetic letters are found to produce mispairs that are about 1-7 kcal/mol more stable than their complementary counterparts. They are also appreciably more stable than the naturally occurring G:C, A:T, and G:T pairs. The higher base pair stabilities are found to be mainly because of the polarity of monomers and attractive electrostatic interactions.
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Affiliation(s)
- N R Jena
- IIITDM Jabalpur, Discipline of Natural Sciences, Dumna Airport Road, Khamaria, India, 482005, Jabalpur, INDIA
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12
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Larghi EL, Bruneau A, Sauvage F, Alami M, Vergnaud-Gauduchon J, Messaoudi S. Synthesis and Biological Activity of 3-(Heteroaryl)quinolin-2(1 H)-ones Bis-Heterocycles as Potential Inhibitors of the Protein Folding Machinery Hsp90. Molecules 2022; 27:412. [PMID: 35056725 PMCID: PMC8778022 DOI: 10.3390/molecules27020412] [Citation(s) in RCA: 2] [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: 12/28/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 01/02/2023] Open
Abstract
In the context of our SAR study concerning 6BrCaQ analogues as C-terminal Hsp90 inhibitors, we designed and synthesized a novel series of 3-(heteroaryl)quinolin-2(1H), of types 3, 4, and 5, as a novel class of analogues. A Pd-catalyzed Liebeskind-Srogl cross-coupling was developed as a convenient approach for easy access to complex purine architectures. This series of analogues showed a promising biological effect against MDA-MB231 and PC-3 cancer cell lines. This study led to the identification of the best compounds, 3b (IC50 = 28 µM) and 4e, which induce a significant decrease of CDK-1 client protein and stabilize the levels of Hsp90 and Hsp70 without triggering the HSR response.
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Affiliation(s)
- Enrique L. Larghi
- CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France;
- Instituto de Química Rosario (IQUIR) CONICET/UNR, FBioyF, Rosario S2002LRK, Argentina;
| | - Alexandre Bruneau
- Instituto de Química Rosario (IQUIR) CONICET/UNR, FBioyF, Rosario S2002LRK, Argentina;
| | - Félix Sauvage
- CNRS, Institut Galien-Paris Saclay, Université Paris-Saclay, 92296 Châtenay-Malabry, France; (F.S.); (J.V.-G.)
| | - Mouad Alami
- CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France;
| | - Juliette Vergnaud-Gauduchon
- CNRS, Institut Galien-Paris Saclay, Université Paris-Saclay, 92296 Châtenay-Malabry, France; (F.S.); (J.V.-G.)
| | - Samir Messaoudi
- CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France;
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13
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Kashida H, Asanuma H. Pseudo Base Pairs that Exhibit High Duplex Stability and Orthogonality through Covalent and Non-covalent Interactions. J SYN ORG CHEM JPN 2021. [DOI: 10.5059/yukigoseikyokaishi.79.1013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hiromu Kashida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University
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14
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Miao S, Bhunia D, Devari S, Liang Y, Munyaradzi O, Rundell S, Bong D. Bifacial PNAs Destabilize MALAT1 by 3' A-Tail Displacement from the U-Rich Internal Loop. ACS Chem Biol 2021; 16:1600-1609. [PMID: 34382766 DOI: 10.1021/acschembio.1c00575] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report herein a new class of synthetic reagents for targeting the element for nuclear expression (ENE) in MALAT1, a long noncoding RNA upregulated in many cancers. The cis-acting ENE contains a U-rich internal loop (URIL) that forms an 11 base UAU-rich triplex stem with the truncated 3' oligo-A tail of MALAT1, protecting the terminus from exonuclease digestion and greatly extending transcript lifetime. Bifacial peptide nucleic acids (bPNAs) similarly bind URILs via base triple formation between two uracil bases and a synthetic base, melamine. We synthesized a set of low molecular weight bPNAs composed of α-linked peptide, isodipeptide, and diketopiperazine backbones and evaluated their ENE binding efficacy in vitro via oligo-A strand displacement and consequent exonuclease sensitivity. Degradation was greatly enhanced by bPNA treatment in the presence of exonucleases, with ENE half-life plunging to 6 min from >24 h. RNA digestion kinetics could clearly distinguish between bPNAs with similar URIL affinities, highlighting the utility of functional assays for evaluating synthetic RNA binders. In vitro activity was mirrored by a 50% knockdown of MALAT1 expression in pancreatic cancer (PANC-1) cells upon treatment with bPNAs, consistent with intracellular digestion triggered by a similar ENE A-tail displacement mechanism. Pulldown from PANC-1 total RNA with biotinylated bPNA enriched MALAT1 > 4000× , supportive of bPNA-URIL selectivity. Together, these experiments establish the feasibility of native transcript targeting by bPNA in both in vitro and intracellular contexts. Reagents such as bPNAs may be useful tools for the investigation of transcripts stabilized by cis-acting poly(A) binding RNA elements.
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Affiliation(s)
- Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Debmalya Bhunia
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shekaraiah Devari
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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15
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Danielsen MB, Wengel J. Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides. Beilstein J Org Chem 2021; 17:1828-1848. [PMID: 34386102 PMCID: PMC8329367 DOI: 10.3762/bjoc.17.125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/14/2021] [Indexed: 12/20/2022] Open
Abstract
Antisense oligonucleotides (ASOs) have the ability of binding to endogenous nucleic acid targets, thereby inhibiting the gene expression. Although ASOs have great potential in the treatment of many diseases, the search for favorable toxicity profiles and distribution has been challenging and consequently impeded the widespread use of ASOs as conventional medicine. One strategy that has been employed to optimize the delivery profile of ASOs, is the functionalization of ASOs with cationic amine groups, either by direct conjugation onto the sugar, nucleobase or internucleotide linkage. The introduction of these positively charged groups has improved properties like nuclease resistance, increased binding to the nucleic acid target and improved cell uptake for oligonucleotides (ONs) and ASOs. The modifications highlighted in this review are some of the most prevalent cationic amine groups which have been attached as single modifications onto ONs/ASOs. The review has been separated into three sections, nucleobase, sugar and backbone modifications, highlighting what impact the cationic amine groups have on the ONs/ASOs physiochemical and biological properties. Finally, a concluding section has been added, summarizing the important knowledge from the three chapters, and examining the future design for ASOs.
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Affiliation(s)
- Mathias B Danielsen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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16
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Schuster GB, Cafferty BJ, Karunakaran SC, Hud NV. Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA. J Am Chem Soc 2021; 143:9279-9296. [PMID: 34152760 DOI: 10.1021/jacs.0c13081] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hypothesis that RNA and DNA are products of chemical and biological evolution has motivated our search for alternative nucleic acids that may have come earlier in the emergence of life-polymers that possess a proclivity for covalent and non-covalent self-assembly not exhibited by RNA. Our investigations have revealed a small set of candidate ancestral nucleobases that self-assemble into hexameric rosettes that stack in water to form long, twisted, rigid supramolecular polymers. These structures exhibit properties that provide robust solutions to long-standing problems that have stymied the search for a prebiotic synthesis of nucleic acids. Moreover, their examination by experimental and computational methods provides insight into the chemical and physical principles that govern a particular class of water-soluble one-dimensional supramolecular polymers. In addition to efficient self-assembly, their lengths and polydispersity are modulated by a wide variety of positively charged, planar compounds; their assembly and disassembly are controlled over an exceedingly narrow pH range; they exhibit spontaneous breaking of symmetry; and homochirality emerges through non-covalent cross-linking during hydrogel formation. Some of these candidate ancestral nucleobases spontaneously form glycosidic bonds with ribose and other sugars, and, most significantly, functionalized forms of these heterocycles form supramolecular structures and covalent polymers under plausibly prebiotic conditions. This Perspective recounts a journey of discovery that continues to reveal attractive answers to questions concerning the origins of life and to uncover the principles that control the structure and properties of water-soluble supramolecular polymers.
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Affiliation(s)
- Gary B Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Brian J Cafferty
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Suneesh C Karunakaran
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
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17
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Ghosh P, Ghosh A, Ghosh D. Radiationless Decay Processes of an Unnatural DNA Base: Pyrrole 2-Carbaldehyde. J Phys Chem A 2021; 125:5556-5561. [PMID: 34133168 DOI: 10.1021/acs.jpca.1c03875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyrrole-2-carbaldehyde (Pa) forms one of the unnatural nucleic acid bases, and as a base pair with 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds), it has been known to be stable in DNA. The Ds-Pa pair is stabilized in DNA via van der Waals' interaction and shape fitting. There are some studies on the origin of its stability and reactivity in the ground state. However, for a successful unnatural base pair, it needs to be stable not only in the ground state but also upon irradiation with UV-visible light. To understand the photoinduced reactivity, we investigate the excited-state properties of the Pa base and understand the energetically feasible photoprocesses that can occur upon excitation in the UV region. Two distinct pathways are obtained. One of the pathways involves an out-of-plane mode and has some similarities with the deactivation channels in the natural pyrimidine bases. On the other hand, the second pathway involves an excited-state proton transfer.
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Affiliation(s)
- Paulami Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Arpita Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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18
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Method for Rapid Analysis of Mutant RNA Polymerase Activity on Templates Containing Unnatural Nucleotides. Int J Mol Sci 2021; 22:ijms22105186. [PMID: 34069057 PMCID: PMC8155940 DOI: 10.3390/ijms22105186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/10/2021] [Indexed: 11/17/2022] Open
Abstract
Pairs of unnatural nucleotides are used to expand the genetic code and create artificial DNA or RNA templates. In general, an approach is used to engineer orthogonal systems capable of reading codons comprising artificial nucleotides; however, DNA and RNA polymerases capable of recognizing unnatural nucleotides are required for amplification and transcription of templates. Under favorable conditions, in the presence of modified nucleotide triphosphates, DNA polymerases are able to synthesize unnatural DNA with high efficiency; however, the currently available RNA polymerases reveal high specificity to the natural nucleotides and may not easily recognize the unnatural nucleotides. Due to the absence of simple and rapid methods for testing the activity of mutant RNA polymerases, the development of RNA polymerase recognizing unnatural nucleotides is limited. To fill this gap, we developed a method for rapid analysis of mutant RNA polymerase activity on templates containing unnatural nucleotides. Herein, we optimized a coupled cell-free translation system and tested the ability of three unnatural nucleotides to be transcribed by different T7 RNA polymerase mutants, by demonstrating high sensitivity and simplicity of the developed method. This approach can be applied to various unnatural nucleotides and can be simultaneously scaled up to determine the activity of numerous polymerases on different templates. Due to the simplicity and small amounts of material required, the developed cell-free system provides a highly scalable and versatile tool to study RNA polymerase activity.
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19
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Franco A, da Silva JAL. Boron in Prebiological Evolution. Angew Chem Int Ed Engl 2021; 60:10458-10468. [PMID: 32997879 DOI: 10.1002/anie.202010616] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Indexed: 01/02/2023]
Abstract
Boron(III), as borate (or boric acid), mediates the synthesis of ribose, ribonucleosides, and ribonucleotides. These reactions are carried out under moderate temperatures (typically 70-95 °C) with organic molecules (or their derivatives) detected in interstellar space and inorganic ions found in minerals on Earth (and could occur during early stages of prebiotic evolution). Research in this century suggests that borate was a relevant prebiological reagent, thus reinforcing the RNA world hypothesis as an explanation for the origin of life. Herein, these developments on prebiological chemistry related to boron species are reviewed.
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Affiliation(s)
- Ana Franco
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - José Armando L da Silva
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
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20
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Affiliation(s)
- Ana Franco
- Centro de Química Estrutural Instituto Superior Técnico, Universidade de Lisboa Av. Rovisco Pais 1049-001 Lisbon Portugal
| | - José Armando L. Silva
- Centro de Química Estrutural Instituto Superior Técnico, Universidade de Lisboa Av. Rovisco Pais 1049-001 Lisbon Portugal
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21
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Bains W, Petkowski JJ, Zhan Z, Seager S. Evaluating Alternatives to Water as Solvents for Life: The Example of Sulfuric Acid. Life (Basel) 2021; 11:400. [PMID: 33925658 PMCID: PMC8145300 DOI: 10.3390/life11050400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 12/18/2022] Open
Abstract
The chemistry of life requires a solvent, which for life on Earth is water. Several alternative solvents have been suggested, but there is little quantitative analysis of their suitability as solvents for life. To support a novel (non-terrestrial) biochemistry, a solvent must be able to form a stable solution of a diverse set of small molecules and polymers, but must not dissolve all molecules. Here, we analyze the potential of concentrated sulfuric acid (CSA) as a solvent for biochemistry. As CSA is a highly effective solvent but a reactive substance, we focused our analysis on the stability of chemicals in sulfuric acid, using a model built from a database of kinetics of reaction of molecules with CSA. We consider the sulfuric acid clouds of Venus as a test case for this approach. The large majority of terrestrial biochemicals have half-lives of less than a second at any altitude in Venus's clouds, but three sets of human-synthesized chemicals are more stable, with average half-lives of days to weeks at the conditions around 60 km altitude on Venus. We show that sufficient chemical structural and functional diversity may be available among those stable chemicals for life that uses concentrated sulfuric acid as a solvent to be plausible. However, analysis of meteoritic chemicals and possible abiotic synthetic paths suggests that postulated paths to the origin of life on Earth are unlikely to operate in CSA. We conclude that, contrary to expectation, sulfuric acid is an interesting candidate solvent for life, but further work is needed to identify a plausible route for life to originate in it.
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Affiliation(s)
- William Bains
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (J.J.P.); (Z.Z.); (S.S.)
- School of Physics & Astronomy, Cardiff University, 4 The Parade, Cardiff CF24 3AA, UK
| | - Janusz Jurand Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (J.J.P.); (Z.Z.); (S.S.)
| | - Zhuchang Zhan
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (J.J.P.); (Z.Z.); (S.S.)
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (J.J.P.); (Z.Z.); (S.S.)
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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22
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Abstract
The encoded biosynthesis of proteins provides the ultimate paradigm for high-fidelity synthesis of long polymers of defined sequence and composition, but it is limited to polymerizing the canonical amino acids. Recent advances have built on genetic code expansion - which commonly permits the cellular incorporation of one type of non-canonical amino acid into a protein - to enable the encoded incorporation of several distinct non-canonical amino acids. Developments include strategies to read quadruplet codons, use non-natural DNA base pairs, synthesize completely recoded genomes and create orthogonal translational components with reprogrammed specificities. These advances may enable the genetically encoded synthesis of non-canonical biopolymers and provide a platform for transforming the discovery and evolution of new materials and therapeutics.
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Affiliation(s)
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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23
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Ouaray Z, Benner SA, Georgiadis MM, Richards NGJ. Building better polymerases: Engineering the replication of expanded genetic alphabets. J Biol Chem 2020; 295:17046-17059. [PMID: 33004440 PMCID: PMC7863901 DOI: 10.1074/jbc.rev120.013745] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/30/2020] [Indexed: 11/30/2022] Open
Abstract
DNA polymerases are today used throughout scientific research, biotechnology, and medicine, in part for their ability to interact with unnatural forms of DNA created by synthetic biologists. Here especially, natural DNA polymerases often do not have the "performance specifications" needed for transformative technologies. This creates a need for science-guided rational (or semi-rational) engineering to identify variants that replicate unnatural base pairs (UBPs), unnatural backbones, tags, or other evolutionarily novel features of unnatural DNA. In this review, we provide a brief overview of the chemistry and properties of replicative DNA polymerases and their evolved variants, focusing on the Klenow fragment of Taq DNA polymerase (Klentaq). We describe comparative structural, enzymatic, and molecular dynamics studies of WT and Klentaq variants, complexed with natural or noncanonical substrates. Combining these methods provides insight into how specific amino acid substitutions distant from the active site in a Klentaq DNA polymerase variant (ZP Klentaq) contribute to its ability to replicate UBPs with improved efficiency compared with Klentaq. This approach can therefore serve to guide any future rational engineering of replicative DNA polymerases.
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Affiliation(s)
- Zahra Ouaray
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida, USA
| | - Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom; Foundation for Applied Molecular Evolution, Alachua, Florida, USA.
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24
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Skinner A, Yang C, Hincks K, Wang H, Resendiz MJE. Experimental and theoretical rationalization for the base pairing abilities of inosine, guanosine, adenosine, and their corresponding 8-oxo-7,8-dihydropurine, and 8-bromopurine analogues within A-form duplexes of RNA. Biopolymers 2020; 111:e23410. [PMID: 33216981 PMCID: PMC7780609 DOI: 10.1002/bip.23410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/30/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022]
Abstract
Inosine is an important RNA modification, furthermore RNA oxidation has gained interest due, in part, to its potential role in the development/progression of disease as well as on its impact on RNA structure and function. In this report we established the base pairing abilities of purine nucleobases G, I, A, as well as their corresponding, 8-oxo-7,8-dihydropurine (common products of oxidation at the C8-position of purines), and 8-bromopurine (as probes to explore conformational changes), derivatives, namely 8-oxoG, 8-oxoI, 8-oxoA, 8-BrG, and 8-BrI. Dodecamers of RNA were obtained using standard phosphoramidite chemistry via solid-phase synthesis, and used as models to establish the impact that each of these nucleobases have on the thermal stability of duplexes, when base pairing to canonical and noncanonical nucleobases. Thermal stabilities were obtained from thermal denaturation transition (Tm ) measurements, via circular dichroism (CD). The results were then rationalized using models of base pairs between two monomers, via density functional theory (DFT), that allowed us to better understand potential contributions from H-bonding patterns arising from distinct conformations. Overall, some of the important results indicate that: (a) an anti-I:syn-A base pair provides thermal stability, due to the absence of the exocyclic amine; (b) 8-oxoG base pairs like U, and does not induce destabilization within the duplex when compared to the pyrimidine ring; (c) a U:G wobble-pair is only stabilized by G; and (d) 8-oxoA displays an inherited base pairing promiscuity in this sequence context. Gaining a better understanding of how this oxidatively generated lesions potentially base pair with other nucleobases will be useful to predict various biological outcomes, as well as in the design of biomaterials and/or nucleotide derivatives with biological potential.
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Affiliation(s)
- Austin Skinner
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | - Chou‐Hsun Yang
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | - Kazuki Hincks
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
| | - Haobin Wang
- Department of ChemistryUniversity of Colorado DenverDenverColoradoUSA
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25
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Light-induced formation of silver(I)-mediated base pairs in DNA: Possibilities and limitations. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119856] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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26
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Escher D, Müller J. Silver(I) Coordination in Silver(I)-Mediated Homo Base Pairs of 6-Pyrazolylpurine in DNA Duplexes Involves the Watson-Crick Edge. Chemistry 2020; 26:16043-16048. [PMID: 32627879 PMCID: PMC7756626 DOI: 10.1002/chem.202002803] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Indexed: 12/18/2022]
Abstract
DNA duplexes comprising 6‐(1H‐pyrazol‐1‐yl)‐9H‐purine (6PP), 1‐deaza‐6PP (1D6PP), 7‐deaza‐6PP (7D6PP) and 1,7‐dideaza‐6PP (1,7D6PP) 2′‐deoxyribonucleosides, respectively, were investigated towards their ability to form metal‐mediated base pairs in the presence of AgI. In 6PP and 7D6PP, the AgI ion can coordinate to the nucleobase via the endocyclic N1 nitrogen atom, that is, via the Watson–Crick edge. In contrast, this nitrogen atom is not available in 1D6PP and 1,7D6PP, so that in 1D6PP an AgI coordination is only possible via the Hoogsteen edge (N7). Reference duplexes with either adenine:adenine mispairs or canonical adenine:thymine base pairs were used to investigate the impact of the pyrazolyl moiety on the AgI‐binding properties. To determine the thermal and structural duplex stabilities in the absence or presence of AgI, all duplexes were examined by UV and circular dichroism spectroscopic studies. These investigations shed light on the question of whether N1‐ or N7‐coordination is preferred in purine‐based metal‐mediated base pairs.
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Affiliation(s)
- Daniela Escher
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 30, 48149, Münster, Germany
| | - Jens Müller
- Westfälische Wilhelms-Universität Münster, Institut für Anorganische und Analytische Chemie, Corrensstr. 30, 48149, Münster, Germany
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27
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Kimoto M, Hirao I. Genetic alphabet expansion technology by creating unnatural base pairs. Chem Soc Rev 2020; 49:7602-7626. [PMID: 33015699 DOI: 10.1039/d0cs00457j] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent advancements in the creation of artificial extra base pairs (unnatural base pairs, UBPs) are opening the door to a new research area, xenobiology, and genetic alphabet expansion technologies. UBPs that function as third base pairs in replication, transcription, and/or translation enable the site-specific incorporation of novel components into DNA, RNA, and proteins. Here, we describe the UBPs developed by three research teams and their application in PCR-based diagnostics, high-affinity DNA aptamer generation, site-specific labeling of RNAs, semi-synthetic organism creation, and unnatural-amino-acid-containing protein synthesis.
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Affiliation(s)
- Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore.
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28
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Mukba SA, Vlasov PK, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems. Mol Biol 2020. [DOI: 10.1134/s0026893320040111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Nie P, Bai Y, Mei H. Synthetic Life with Alternative Nucleic Acids as Genetic Materials. Molecules 2020; 25:E3483. [PMID: 32751873 PMCID: PMC7435384 DOI: 10.3390/molecules25153483] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
DNA, the fundamental genetic polymer of all living organisms on Earth, can be chemically modified to embrace novel functions that do not exist in nature. The key chemical and structural parameters for genetic information storage, heredity, and evolution have been elucidated, and many xenobiotic nucleic acids (XNAs) with non-canonical structures are developed as alternative genetic materials in vitro. However, it is still particularly challenging to replace DNAs with XNAs in living cells. This review outlines some recent studies in which the storage and propagation of genetic information are achieved in vivo by expanding genetic systems with XNAs.
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Affiliation(s)
| | | | - Hui Mei
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; (P.N.); (Y.B.)
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30
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Abstract
DNA polymerases play a central role in biology by transferring genetic information from one generation to the next during cell division. Harnessing the power of these enzymes in the laboratory has fueled an increase in biomedical applications that involve the synthesis, amplification, and sequencing of DNA. However, the high substrate specificity exhibited by most naturally occurring DNA polymerases often precludes their use in practical applications that require modified substrates. Moving beyond natural genetic polymers requires sophisticated enzyme-engineering technologies that can be used to direct the evolution of engineered polymerases that function with tailor-made activities. Such efforts are expected to uniquely drive emerging applications in synthetic biology by enabling the synthesis, replication, and evolution of synthetic genetic polymers with new physicochemical properties.
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31
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Eberlein L, Beierlein FR, van Eikema Hommes NJR, Radadiya A, Heil J, Benner SA, Clark T, Kast SM, Richards NGJ. Tautomeric Equilibria of Nucleobases in the Hachimoji Expanded Genetic Alphabet. J Chem Theory Comput 2020; 16:2766-2777. [PMID: 32125859 DOI: 10.1021/acs.jctc.9b01079] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Evolution has yielded biopolymers that are constructed from exactly four building blocks and are able to support Darwinian evolution. Synthetic biology aims to extend this alphabet, and we recently showed that 8-letter (hachimoji) DNA can support rule-based information encoding. One source of replicative error in non-natural DNA-like systems, however, is the occurrence of alternative tautomeric forms, which pair differently. Unfortunately, little is known about how structural modifications impact free-energy differences between tautomers of the non-natural nucleobases used in the hachimoji expanded genetic alphabet. Determining experimental tautomer ratios is technically difficult, and so, strategies for improving hachimoji DNA replication efficiency will benefit from accurate computational predictions of equilibrium tautomeric ratios. We now report that high-level quantum-chemical calculations in aqueous solution by the embedded cluster reference interaction site model, benchmarked against free-energy molecular simulations for solvation thermodynamics, provide useful quantitative information on the tautomer ratios of both Watson-Crick and hachimoji nucleobases. In agreement with previous computational studies, all four Watson-Crick nucleobases adopt essentially only one tautomer in water. This is not the case, however, for non-natural nucleobases and their analogues. For example, although the enols of isoguanine and a series of related purines are not populated in water, these heterocycles possess N1-H and N3-H keto tautomers that are similar in energy, thereby adversely impacting accurate nucleobase pairing. These robust computational strategies offer a firm basis for improving experimental measurements of tautomeric ratios, which are currently limited to studying molecules that exist only as two tautomers in solution.
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Affiliation(s)
- Lukas Eberlein
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Frank R Beierlein
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Nico J R van Eikema Hommes
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Ashish Radadiya
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Jochen Heil
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Timothy Clark
- Computer-Chemistry-Centre and Interdisciplinary Centre for Molecular Materials, Department of Chemistry & Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Dortmund 44227, Germany
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K.,Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
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32
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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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33
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Seio K, Yamaguchi K, Yamazaki A, Kanamori T, Masaki Y. Transcription of DNA duplex containing deoxypseudouridine and deoxypseudoisocytidine, and inhibition of transcription by triplex forming oligonucleotide that recognizes the modified duplex. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:892-904. [PMID: 32126878 DOI: 10.1080/15257770.2020.1714652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
We developed new DNA triplexes that contain four base triads T-A·T, A-ψ·CBr, G-PIC·YO, and C-G·Py+, where CBr, YO, Py, ψ, and PIC are 5-bromocytosine, 5-methyl-4-pyrimidone, 2-aminopyridine, the aglycons of deoxypseudouridine, and deoxypseudoisocytidine, respectively. DNA duplex incorporating T-A, A-ψ, G-PIC, and C-G, and triplex forming oligonucleotide incorporating T, CBr, YO, and Py formed the triplex as evaluated by Tm measurements. The triplex formation was successfully applied to the inhibition of transcription of the DNA duplex incorporating T7-promoter sequence modified by the above modified bases.
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Affiliation(s)
- Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kei Yamaguchi
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ayano Yamazaki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Takashi Kanamori
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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34
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Ouaray Z, Singh I, Georgiadis MM, Richards NGJ. Building better enzymes: Molecular basis of improved non-natural nucleobase incorporation by an evolved DNA polymerase. Protein Sci 2020; 29:455-468. [PMID: 31654473 PMCID: PMC6954703 DOI: 10.1002/pro.3762] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/17/2019] [Accepted: 10/23/2019] [Indexed: 01/02/2023]
Abstract
Obtaining semisynthetic microorganisms that exploit the information density of "hachimoji" DNA requires access to engineered DNA polymerases. A KlenTaq variant has been reported that incorporates the "hachimoji" P:Z nucleobase pair with a similar efficiency to that seen for Watson-Crick nucleobase incorporation by the wild type (WT) KlenTaq DNA polymerase. The variant polymerase differs from WT KlenTaq by only four amino acid substitutions, none of which are located within the active site. We now report molecular dynamics (MD) simulations on a series of binary complexes aimed at elucidating the contributions of the four amino acid substitutions to altered catalytic activity. These simulations suggest that WT KlenTaq is insufficiently flexible to be able to bind AEGIS DNA correctly, leading to the loss of key protein/DNA interactions needed to position the binary complex for efficient incorporation of the "hachimoji" Z nucleobase. In addition, we test literature hypotheses about the functional roles of each amino acid substitution and provide a molecular description of how individual residue changes contribute to the improved activity of the KlenTaq variant. We demonstrate that MD simulations have a clear role to play in systematically screening DNA polymerase variants capable of incorporating different types of nonnatural nucleobases thereby limiting the number that need to be characterized by experiment. It is now possible to build DNA molecules containing nonnatural nucleobase pairs in addition to A:T and G:C. Exploiting this development in synthetic biology requires engineered DNA polymerases that can replicate nonnatural nucleobase pairs. Computational studies on a DNA polymerase variant reveal how amino acid substitutions outside of the active site yield an enzyme that replicates nonnatural nucleobase pairs with high efficiency. This work will facilitate efforts to obtain bacteria possessing an expanded genetic alphabet.
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Affiliation(s)
| | - Isha Singh
- Department of Biochemistry & Molecular BiologyIndiana University School of MedicineIndianapolisIndiana
| | - Millie M. Georgiadis
- Department of Biochemistry & Molecular BiologyIndiana University School of MedicineIndianapolisIndiana
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35
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Romero-Pérez S, López-Martín I, Martos-Maldonado MC, Somoza Á, González-Rodríguez D. Synthesis of Phosphoramidite Monomers Equipped with Complementary Bases for Solid-Phase DNA Oligomerization. Org Lett 2020; 22:41-45. [PMID: 31860314 DOI: 10.1021/acs.orglett.9b03801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe the preparation of two monomers that bear complementary nucleobases at the edges (guanine-2'-deoxycytidine and 2-aminoadenine-2'-deoxyuridine) and that are conveniently protected and activated for solid-phase automated DNA synthesis. We report the optimized synthetic routes leading to the four nucleobase derivatives involved, their cross-coupling reactions into dinucleobase-containing monomers, and their oligomerization in the DNA synthesizer.
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Affiliation(s)
- Sonia Romero-Pérez
- Nanostructured Molecular Systems and Materials Group, Departamento de Química Orgánica , Universidad Autónoma de Madrid , 28049 Madrid , Spain.,NanoBiotechnology Research Group , Instituto IMDEA Nanociencia , 28049 Madrid , Spain
| | - Isabel López-Martín
- Nanostructured Molecular Systems and Materials Group, Departamento de Química Orgánica , Universidad Autónoma de Madrid , 28049 Madrid , Spain
| | - Manuel C Martos-Maldonado
- Nanostructured Molecular Systems and Materials Group, Departamento de Química Orgánica , Universidad Autónoma de Madrid , 28049 Madrid , Spain
| | - Álvaro Somoza
- NanoBiotechnology Research Group , Instituto IMDEA Nanociencia , 28049 Madrid , Spain
| | - David González-Rodríguez
- Nanostructured Molecular Systems and Materials Group, Departamento de Química Orgánica , Universidad Autónoma de Madrid , 28049 Madrid , Spain.,Institute for Advanced Research in Chemical Sciences (IAdChem) , Universidad Autónoma de Madrid , 28049 Madrid , Spain
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36
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Bhai S, Ganguly B. Role of the backbone of nucleic acids in the stability of Hg2+-mediated canonical base pairs and thymine–thymine mispair: a DFT study. RSC Adv 2020; 10:40969-40982. [PMID: 35519218 PMCID: PMC9057718 DOI: 10.1039/d0ra07526d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/26/2020] [Indexed: 11/21/2022] Open
Abstract
Metal-mediated base pairs have attracted attention in nucleic acid research and molecular devices. Herein, we report a systematic computational study on Hg2+-mediated base pairs with canonical and TT mispair dimers. The computed results revealed that the model DTTD (thymine–thymine with DNA backbone) mispair is more energetically favored than the canonical base pairs. The DTTTTD mispair dimer is more energetically stable by ∼36.0 kcal mol−1 than the corresponding canonical DATGCD base pairs. The Hg⋯Hg metallophilic interaction was observed with the DTTTTD mispair and not the canonical base pairs. The DATGCD (adenine: thymine, guanine: cytosine) base pairs were significantly perturbed upon interaction with the mercury ion; however, the TTTT mispairs were aligned upon interaction with the Hg2+ ion. The DTTTTD mispair adopts a B-type conformation with proper alignment of its nucleobases along the axis. The MESP calculations showed a larger Vmin value for the interacting nitrogen centers of the thymine nucleobase, supporting its stronger binding with the Hg2+ ion compared to the other nucleobases. The role of the backbone is crucial in nucleic acids to determine many useful properties, and PNAs have been exploited extensively in the literature. Thus, this study was further extended to metal-mediated PNA-containing dimer mispairs such as DTTTTP (thymine–thymine dimer model with hybrid DNA and PNA backbone) and PTTTTP (thymine–thymine dimer model with PNA backbone). The calculated results showed that the PTTTTP PNA mispair is thermodynamically more stable than the canonical dimers. The enthalpy calculated for DTTTTD and PTTTTP at the B3LYP-D3/6-31G* level of theory showed that PTTTTP is ∼3.0 kcal mol−1 more stable than DTTTTD. The metallophilic interaction of Hg2+ ions in the PTTTTP mispair was not observed; however, the metal ions interact with the nitrogen of the thymine bases, presumably enhancing the stability of this mispair by strong electrostatic interactions. These interactions arise due to the P-type conformations of PNAs, which lack metallophilic interactions between the metal ions and can adopt a wider and more unwounded helix. The interaction of the mispair dimers with the explicit water molecules also showed a similar stability trend to that observed with the implicit solvation model. The metallophilic interaction (Hg⋯Hg) was found to be conserved in DTTTTD. The AIM analysis performed for these dimers revealed that the interactions are primarily electrostatic in nature. The UV-vis absorption spectra of the mispair systems calculated at the B3LYP-D3/6-31G* level of theory using the TD-DFT method in the aqueous phase suggested that the absorption maximum is located at a longer wavelength in the case of PTTTTP compared to the corresponding DTTTTD and can be a signature to identify the formation of metal-mediated nucleic acid systems. Hg2+-mediated PNA–PNA mispair duplex (PTTTTP) is more energetically favoured compared to DNA–DNA mispair duplex (DTTTTD).![]()
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Affiliation(s)
- Surjit Bhai
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility)
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar
- India-364 002
- Academy of Scientific and Innovative Research (AcSIR)
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility)
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar
- India-364 002
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37
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38
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Abstract
The chemical or prebiotic evolution referred also to as pre-Darwinian evolution describes chemical reactions up to the origin of a self-replicating system that was capable of Darwinian evolution. These chemical processes took place on Earth between about 3.7 and 4.5 billion years ago when cellular life came into being. The pre-Darwinian chemical evolution usually assumes hereditary elements, but does not regard them as self-organizing processes. Physical and chemical self-organization led to uninterrupted pre-Darwinian and Darwinian evolution. Thus, it is not justified to distinguish between different types of evolution. From the many possible solutions, evolution selected among those reactions that generated catalytic networks incorporating chemical sequence information and under gradually changing circumstances produced a reproducible and stable living system that adapted to these conditions. Major issues in this review involve prebiotic reactions leading to genetic evolution involving (1) abiotic sources of components of ribonucleotides and xenobiotic nucleotides, (2) formation of prebiotic RNA, (3) development of genetic RNA from random-sequence noncoding RNA, (4) transition from RNA World to DNA Empire, (5) the role of oxygenic photosynthesis in genetic transitions, and (6) hierarchical arrangement of processes involved in the optimized genetic system.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
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39
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Zhang L, Wang S, Yang Z, Hoshika S, Xie S, Li J, Chen X, Wan S, Li L, Benner SA, Tan W. An Aptamer-Nanotrain Assembled from Six-Letter DNA Delivers Doxorubicin Selectively to Liver Cancer Cells. Angew Chem Int Ed Engl 2019; 59:663-668. [PMID: 31650689 DOI: 10.1002/anie.201909691] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/16/2019] [Indexed: 12/30/2022]
Abstract
Expanding the number of nucleotides in DNA increases the information density of functional DNA molecules, creating nanoassemblies that cannot be invaded by natural DNA/RNA in complex biological systems. Here, we show how six-letter GACTZP DNA contributes this property in two parts of a nanoassembly: 1) in an aptamer evolved from a six-letter DNA library to selectively bind liver cancer cells; and 2) in a six-letter self-assembling GACTZP nanotrain that carries the drug doxorubicin. The aptamer-nanotrain assembly, charged with doxorubicin, selectively kills liver cancer cells in culture, as the selectivity of the aptamer binding directs doxorubicin into the aptamer-targeted cells. The assembly does not kill untransformed cells that the aptamer does not bind. This architecture, built with an expanded genetic alphabet, is reminiscent of antibodies conjugated to drugs, which presumably act by this mechanism as well, but with the antibody replaced by an aptamer.
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Affiliation(s)
- Liqin Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China.,Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Sai Wang
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.,Current address: College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, Box 7, Alachua, FL, 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL, 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, Box 7, Alachua, FL, 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL, 32615, USA
| | - Sitao Xie
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Jin Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Xigao Chen
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Shuo Wan
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Long Li
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, Box 7, Alachua, FL, 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL, 32615, USA
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China.,Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
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40
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Zhang L, Wang S, Yang Z, Hoshika S, Xie S, Li J, Chen X, Wan S, Li L, Benner SA, Tan W. An Aptamer‐Nanotrain Assembled from Six‐Letter DNA Delivers Doxorubicin Selectively to Liver Cancer Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Liqin Zhang
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
| | - Sai Wang
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
- Current address: College of Food Science and Engineering Ocean University of China Qingdao Shandong 266003 China
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution 13709 Progress Boulevard, Box 7 Alachua FL 32615 USA
- Firebird Biomolecular Sciences LLC 13709 Progress Boulevard, Box 17 Alachua FL 32615 USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution 13709 Progress Boulevard, Box 7 Alachua FL 32615 USA
- Firebird Biomolecular Sciences LLC 13709 Progress Boulevard, Box 17 Alachua FL 32615 USA
| | - Sitao Xie
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Jin Li
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Xigao Chen
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
| | - Shuo Wan
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
| | - Long Li
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution 13709 Progress Boulevard, Box 7 Alachua FL 32615 USA
- Firebird Biomolecular Sciences LLC 13709 Progress Boulevard, Box 17 Alachua FL 32615 USA
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
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41
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Leonczak P, Srivastava P, Bande O, Schepers G, Lescrinier E, Herdewijn P. N8-Glycosylated 8-Azapurine and Methylated Purine Nucleobases: Synthesis and Study of Base Pairing Properties. J Org Chem 2019; 84:13394-13409. [PMID: 31617362 DOI: 10.1021/acs.joc.9b01576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this report, we present the synthesis of N8-glycosylated 8-aza-2-methylhypoxanthine and 8-aza-6-thiohypoxanthine 2'-deoxynucleosides as well as methylated 2'-deoxynebularine derivatives. In vitro base pairing properties between each modified and canonical nucleobase were studied. As demonstrated by Tm, incorporation of the modified bases in DNA resulted, with few exceptions, in low stability of duplexes. Modified bases studied in this report are preferentially recognized by T (for N8-glycosylated 8-aza-2-methylhypoxanthine and methylated purines) and G (N8-glycosylated 8-aza-2-methylhypoxanthine). The base pair formed between N8-glycosylated 8-aza-6-thiohypoxanthine and N9-glycosylated 2-methyl-6-thiohypoxanthine (X2:X6) showed, to some extent, an orthogonal interaction. Based on Tm studies, the only potential self-pairing system is formed by the N8-glycosylated 8-aza-6-thiohypoxanthine nucleoside (X2) but only in the absence of canonical G and T. This study indicated that the canonical thymine base is the preferential base partner of methylated purine bases.
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Affiliation(s)
- Piotr Leonczak
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Puneet Srivastava
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Omprakash Bande
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Guy Schepers
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Eveline Lescrinier
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research , Medicinal Chemistry , Herestraat 49, Box 1041 , 3000 Leuven , Belgium
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42
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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: 1] [Impact Index Per Article: 0.2] [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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43
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Naskar S, Guha R, Müller J. Metal-Modified Nucleic Acids: Metal-Mediated Base Pairs, Triples, and Tetrads. Angew Chem Int Ed Engl 2019; 59:1397-1406. [PMID: 31259475 DOI: 10.1002/anie.201905913] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 01/02/2023]
Abstract
The incorporation of metal ions into nucleic acids by means of metal-mediated base pairs represents a promising and prominent strategy for the site-specific decoration of these self-assembling supramolecules with metal-based functionality. Over the past 20 years, numerous nucleoside surrogates have been introduced in this respect, broadening the metal scope by providing perfectly tailored metal-binding sites. More recently, artificial nucleosides derived from natural purine or pyrimidine bases have moved into the focus of AgI -mediated base pairing, due to their expected compatibility with regular Watson-Crick base pairs. This minireview summarizes these advances in metal-mediated base pairing but also includes further recent progress in the field. Moreover, it addresses other aspects of metal-modified nucleic acids, highlighting an expansion of the concept to metal-mediated base triples (in triple helices and three-way junctions) and metal-mediated base tetrads (in quadruplexes). For all types of metal-modified nucleic acids, proposed or accomplished applications are briefly mentioned, too.
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Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
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Naskar S, Guha R, Müller J. Metallmodifizierte Nukleinsäuren: Metallvermittelte Basenpaare, ‐tripel und ‐tetraden. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
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Lahiri H, Mishra S, Mukhopadhyay R. Nanoscale Nucleic Acid Recognition at the Solid-Liquid Interface Using Xeno Nucleic Acid Probes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8875-8888. [PMID: 30398876 DOI: 10.1021/acs.langmuir.8b02770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Challenges in reliable nucleic acid detection are manifold. The major ones are related to false positive or negative signals due to a lack of target specificity in detection and to low sensitivity, especially when a plethora of background sequences are present that can mask the specific recognition signal. Utilizing designed synthetic nucleic acids that are commonly called xeno nucleic acids could offer potential routes to meeting such challenges. In this article, we present the general framework of nucleic acid detection, especially for nanoscale applications, and discuss how and why the xeno nucleic acids could be truly an alternative to the DNA probes. Two specific cases, locked nucleic acid (LNA) and peptide nucleic acid (PNA), which are nuclease-resistant and can form thermally stable duplexes with DNA, are addressed. It is shown that the relative ease of the conformationally rigid LNA probe to be oriented upright on the substrate surface and of the nonionic PNA probe to result into high probe density assists in their use in nanoscale nucleic acid recognition. It is anticipated that success with these probes may lead to important developments such as PCR-independent approaches where the major aim is to detect a small number of target sequences present in the analyte medium.
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Affiliation(s)
- Hiya Lahiri
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
| | - Sourav Mishra
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
| | - Rupa Mukhopadhyay
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
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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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New Size‐Expanded Fluorescent Thymine Analogue: Synthesis, Characterization, and Application. Chemistry 2019; 25:9913-9919. [DOI: 10.1002/chem.201900843] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Indexed: 01/25/2023]
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Miao S, Liang Y, Marathe I, Mao J, DeSantis C, Bong D. Duplex Stem Replacement with bPNA+ Triplex Hybrid Stems Enables Reporting on Tertiary Interactions of Internal RNA Domains. J Am Chem Soc 2019; 141:9365-9372. [PMID: 31094510 PMCID: PMC7043357 DOI: 10.1021/jacs.9b03435] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report herein the synthesis and DNA/RNA binding properties of bPNA+, a new variant of bifacial peptide nucleic acid (bPNA) that binds oligo T/U nucleic acids to form triplex hybrids. By virtue of a new bivalent side chain on bPNA+, similar DNA affinity and hybrid thermostability can be obtained with half the molecular footprint of previously reported bPNA. Lysine derivatives bearing two melamine bases (K2M) can be prepared on multigram scale by double reductive alkylation with melamine acetaldehyde, resulting in a tertiary amine side chain that affords both peptide solubility and selective base-triple formation with 4 T/U bases; the Fmoc-K2M derivative can be used directly in solid phase peptide synthesis, rendering bPNA+ conveniently accessible. A compact bPNA+binding site of two U6 domains can be genetically encoded to replace existing 6 bp stem elements at virtually any location within an RNA transcript. We thus replaced internal 6 bp RNA stems that supported loop regions with 6 base-triple hybrid stems using fluorophore-labeled bPNA+. As the loop regions engaged in RNA tertiary interactions, the labeled hybrid stems provided a fluorescent readout; bPNA+ enabled this readout without covalent chemical modification or introduction of new structural elements. This strategy was demonstrated to be effective for reporting on widely observed RNA tertiary interactions such as intermolecular RNA-RNA kissing loop dimerization, RNA-protein binding, and intramolecular RNA tetraloop-tetraloop receptor binding, illustrating the potential general utility of this method. The modest 6 bp stem binding footprint of bPNA+ makes the hybrid stem replacement method practical for noncovalent installation of synthetic probes of RNA interactions. We anticipate that bPNA+ structural probes will be useful for the study of tertiary interactions in long noncoding RNAs.
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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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Sutton MA, Burton AS, Zaikova E, Sutton RE, Brinckerhoff WB, Bevilacqua JG, Weng MM, Mumma MJ, Johnson SS. Radiation Tolerance of Nanopore Sequencing Technology for Life Detection on Mars and Europa. Sci Rep 2019; 9:5370. [PMID: 30926841 PMCID: PMC6441015 DOI: 10.1038/s41598-019-41488-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/28/2019] [Indexed: 12/02/2022] Open
Abstract
The search for life beyond Earth is a key motivator in space exploration. Informational polymers, like DNA and RNA, are key biosignatures for life as we know it. The MinION is a miniature DNA sequencer based on versatile nanopore technology that could be implemented on future planetary missions. A critical unanswered question is whether the MinION and its protein-based nanopores can withstand increased radiation exposure outside Earth's shielding magnetic field. We evaluated the effects of ionizing radiation on the MinION platform - including flow cells, reagents, and hardware - and discovered limited performance loss when exposed to ionizing doses comparable to a mission to Mars. Targets with harsher radiation environments, like Europa, would require improved radiation resistance via additional shielding or design refinements.
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Affiliation(s)
- Mark A Sutton
- Solar System Exploration Division and Goddard Center for Astrobiology, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
- Wichita State University, Wichita, KS, 67260, USA
| | - Aaron S Burton
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX, 77058, USA
| | - Elena Zaikova
- Department of Biology, Georgetown University, Washington, DC, 20057, USA
| | | | - William B Brinckerhoff
- Solar System Exploration Division and Goddard Center for Astrobiology, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Julie G Bevilacqua
- Department of Biology, Georgetown University, Washington, DC, 20057, USA
| | - Margaret M Weng
- Department of Earth and Planetary Science, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Michael J Mumma
- Solar System Exploration Division and Goddard Center for Astrobiology, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Sarah Stewart Johnson
- Department of Biology, Georgetown University, Washington, DC, 20057, USA.
- Science, Technology, and International Affairs Program, Georgetown University, Washington, DC, 20057, USA.
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