1
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Lamba R, Salam A, Anjum F, Yadav A, Garg R, Kaushik K, Sharma S, Nandi CK. NIR-emissive carbon nanodots as a tool to mark ribosomal RNA and nucleolus components using super-resolution microscopy. NANOSCALE 2024; 16:11739-11748. [PMID: 38864270 DOI: 10.1039/d4nr01569j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Ribosomal RNA (rRNA) plays a key role in protein synthesis and ribosomal biogenesis. The exclusively used commercial dye for RNA staining is SYTO RNASelect, which works in fixed cells only. To overcome this constraint, we synthesized NIR-emissive, highly photostable, and biocompatible carbon nanodots (CNDs) as a fluorescent biomarker for rRNA. The synthesized CNDs could stain rRNA in both live and fixed cells. We were able to visualize rRNA at different sites in eukaryotic cells using super-resolution microscopy (SRM). The CNDs localized rRNA in the dense fibrillar components (DFCs) of the nucleolus, nuclear membrane, and rough endoplasmic reticulum (RER). The super-resolved hollow ring-structured DFC with an FWHM of 140 nm, nuclear membrane with an FWHM of 120 nm, and ER with an FWHM of 115 nm were observed. We further found a marked contrast between the pre-RNA synthesized in cancer cells and normal cells. We believe that these CNDs have great potential in rRNA imaging and comprehending the complex relationships between rRNA dynamics and basic biological processes, disease development, or drug interactions.
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Affiliation(s)
- Rohan Lamba
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P.-175075, India.
| | - Abdul Salam
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P.-175075, India.
| | - Farhan Anjum
- School of Biological Sciences and Bioengineering, Indian Institute of Technology Mandi, H.P.-175075, India
| | - Aditya Yadav
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P.-175075, India.
| | - Richa Garg
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P.-175075, India.
| | - Kush Kaushik
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P.-175075, India.
| | - Shagun Sharma
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P.-175075, India.
| | - Chayan Kanti Nandi
- School of Chemical Sciences, Indian Institute of Technology Mandi, H.P.-175075, India.
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2
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Deng M, Yu J, Blackmond DG. Symmetry breaking and chiral amplification in prebiotic ligation reactions. Nature 2024; 626:1019-1024. [PMID: 38418914 DOI: 10.1038/s41586-024-07059-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/11/2024] [Indexed: 03/02/2024]
Abstract
The single chirality of biological molecules is a signature of life. Yet, rationalizing how single chirality emerged remains a challenging goal1. Research has commonly focused on initial symmetry breaking and subsequent enantioenrichment of monomer building blocks-sugars and amino acids-that compose the genetic polymers RNA and DNA as well as peptides. If these building blocks are only partially enantioenriched, however, stalling of chain growth may occur, whimsically termed in the case of nucleic acids as "the problem of original syn"2. Here, in studying a new prebiotically plausible route to proteinogenic peptides3-5, we discovered that the reaction favours heterochiral ligation (that is, the ligation of L monomers with D monomers). Although this finding seems problematic for the prebiotic emergence of homochiral L-peptides, we demonstrate, paradoxically, that this heterochiral preference provides a mechanism for enantioenrichment in homochiral chains. Symmetry breaking, chiral amplification and chirality transfer processes occur for all reactants and products in multicomponent competitive reactions even when only one of the molecules in the complex mixture exhibits an imbalance in enantiomer concentrations (non-racemic). Solubility considerations rationalize further chemical purification and enhanced chiral amplification. Experimental data and kinetic modelling support this prebiotically plausible mechanism for the emergence of homochiral biological polymers.
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Affiliation(s)
- Min Deng
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Jinhan Yu
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
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3
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Nogal N, Sanz-Sánchez M, Vela-Gallego S, Ruiz-Mirazo K, de la Escosura A. The protometabolic nature of prebiotic chemistry. Chem Soc Rev 2023; 52:7359-7388. [PMID: 37855729 PMCID: PMC10614573 DOI: 10.1039/d3cs00594a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The field of prebiotic chemistry has been dedicated over decades to finding abiotic routes towards the molecular components of life. There is nowadays a handful of prebiotically plausible scenarios that enable the laboratory synthesis of most amino acids, fatty acids, simple sugars, nucleotides and core metabolites of extant living organisms. The major bottleneck then seems to be the self-organization of those building blocks into systems that can self-sustain. The purpose of this tutorial review is having a close look, guided by experimental research, into the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as how recursively changing conditions could help them engage in self-organized and dissipative networks/assemblies (i.e., systems that consume chemical or physical energy from their environment to maintain their internal organization in a dynamic steady state out of equilibrium). In the article we also pay attention to the implications of this view for the emergence of homochirality. The revealed connectivity between those prebiotic routes should constitute the basis for a robust research program towards the bottom-up implementation of protometabolic systems, taken as a central part of the origins-of-life problem. In addition, this approach should foster further exploration of control mechanisms to tame the combinatorial explosion that typically occurs in mixtures of various reactive precursors, thus regulating the functional integration of their respective chemistries into self-sustaining protocellular assemblies.
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Affiliation(s)
- Noemí Nogal
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Marcos Sanz-Sánchez
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Kepa Ruiz-Mirazo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Philosophy, University of the Basque Country, Leioa, Spain
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Campus de Cantoblanco, 28049, Madrid, Spain
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4
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Harrison K, Mackay AS, Kambanis L, Maxwell JWC, Payne RJ. Synthesis and applications of mirror-image proteins. Nat Rev Chem 2023; 7:383-404. [PMID: 37173596 DOI: 10.1038/s41570-023-00493-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2023] [Indexed: 05/15/2023]
Abstract
The homochirality of biomolecules in nature, such as DNA, RNA, peptides and proteins, has played a critical role in establishing and sustaining life on Earth. This chiral bias has also given synthetic chemists the opportunity to generate molecules with inverted chirality, unlocking valuable new properties and applications. Advances in the field of chemical protein synthesis have underpinned the generation of numerous 'mirror-image' proteins (those comprised entirely of D-amino acids instead of canonical L-amino acids), which cannot be accessed using recombinant expression technologies. This Review seeks to highlight recent work on synthetic mirror-image proteins, with a focus on modern synthetic strategies that have been leveraged to access these complex biomolecules as well as their applications in protein crystallography, drug discovery and the creation of mirror-image life.
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Affiliation(s)
- Katriona Harrison
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Angus S Mackay
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Lucas Kambanis
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Joshua W C Maxwell
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia.
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia.
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5
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Kakoti A, Joyce GF. RNA Polymerase Ribozyme That Recognizes the Template-Primer Complex through Tertiary Interactions. Biochemistry 2023. [PMID: 37256719 DOI: 10.1021/acs.biochem.3c00091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
RNA enzymes (ribozymes) often rely on specific base-pairing interactions to engage RNA substrates, which limits the substrate sequence generality of these enzymes. An RNA polymerase ribozyme that was previously optimized by directed evolution to operate in a more efficient and sequence-general manner can now recognize the RNA template, RNA primer, and incoming nucleoside 5'-triphosphate (NTP) entirely through tertiary interactions. As with proteinaceous polymerases, these tertiary interactions are largely agnostic to the sequence of the template, which is an essential property for the unconstrained transmission of genetic information. The polymerase ribozyme exhibits Michaelis-Menten saturation kinetics, with a catalytic rate of 0.1-1 min-1 and a Km of 0.1-1 μM. Earlier forms of the polymerase did not exhibit a saturable substrate binding site, but this property emerged over the course of directed evolution as the ribozyme underwent a structural rearrangement of its catalytic center. The optimized polymerase makes tertiary contacts with both the template and primer, including a critical interaction at the C2' position of the template nucleotide that opposes the 3'-terminal nucleotide of the primer. UV cross-linking studies paint a picture of how several portions of the ribozyme, including regions that were remodeled by directed evolution, come together to position the template, primer, and NTP within the active site for RNA polymerization.
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Affiliation(s)
- Ankana Kakoti
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gerald F Joyce
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
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6
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Distinguishing Biotic vs. Abiotic Origins of ‘Bio’signatures: Clues from Messy Prebiotic Chemistry for Detection of Life in the Universe. Life (Basel) 2023; 13:life13030766. [PMID: 36983921 PMCID: PMC10058490 DOI: 10.3390/life13030766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/04/2023] [Accepted: 03/11/2023] [Indexed: 03/16/2023] Open
Abstract
It is not a stretch to say that the search for extraterrestrial life is possibly the biggest of the cosmic endeavors that humankind has embarked upon. With the continued discovery of several Earth-like exoplanets, the hope of detecting potential biosignatures is multiplying amongst researchers in the astrobiology community. However, to be able to discern these signatures as being truly of biological origin, we also need to consider their probable abiotic origin. The field of prebiotic chemistry, which is aimed at understanding enzyme-free chemical syntheses of biologically relevant molecules, could particularly aid in this regard. Specifically, certain peculiar characteristics of prebiotically pertinent messy chemical reactions, including diverse and racemic product yields and lower synthesis efficiencies, can be utilized in analyzing whether a perceived ‘signature of life’ could possibly have chemical origins. The knowledge gathered from understanding the transition from chemistry to biology during the origin of life could be used for creating a library of abiotically synthesized biologically relevant organic molecules. This can then be employed in designing, standardizing, and testing mission-specific instruments/analysis systems, while also enabling the effective targeting of exoplanets with potentially ‘ongoing’ molecular evolutionary processes for robust detection of life in future explorative endeavors.
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7
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Liu ZF, Ren J, Li P, Niu LY, Liao Q, Zhang S, Yang QZ. Circularly Polarized Laser Emission from Homochiral Superstructures based on Achiral Molecules with Conformal Flexibility. Angew Chem Int Ed Engl 2023; 62:e202214211. [PMID: 36374590 DOI: 10.1002/anie.202214211] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Indexed: 11/16/2022]
Abstract
Without external chiral intervention, it is a challenge to form homochirality from achiral molecules with conformational flexibility. We here report on a rational strategy that uses multivalent noncovalent interactions to clamp the molecular conformations of achiral D-A molecules. These interactions overcome the otherwise dominant dipole-dipole interactions and thus disfavor their symmetric antiparallel stacking. It in turn facilitates parallel packing, leading to spontaneous symmetry breaking during crystallization and thus the formation of homochiral conglomerates. When this emergent homochirality is coupled with optical gain characteristics of the molecules, the homochiral crystals are explored as excellent circularly polarized micro-lasers with low lasing threshold (16.4 μJ cm-2 ) and high dissymmetry factor glum (0.9). This study therefore provides a facile design strategy for supramolecular chiral materials and active laser ones without the necessity of intrinsic chiral element.
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Affiliation(s)
- Zheng-Fei Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Jiahuan Ren
- Beijing Key Laboratory for Optical Materials and Photonic Devices, Department of Chemistry, Capital Normal University, Beijing, 100048, P. R. China
| | - Pan Li
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Li-Ya Niu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Qing Liao
- Beijing Key Laboratory for Optical Materials and Photonic Devices, Department of Chemistry, Capital Normal University, Beijing, 100048, P. R. China
| | - Shaodong Zhang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Qing-Zheng Yang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
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8
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Konstantinov KK, Konstantinova AF. Evolutionary Approach to Biological Homochirality. ORIGINS LIFE EVOL B 2022; 52:205-232. [DOI: 10.1007/s11084-022-09632-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/30/2022] [Indexed: 11/19/2022]
Abstract
AbstractWe study a very simple linear evolutionary model based on distribution of protocells by total enantiomeric excess and without any mutual inhibition and show that such model can produce two species with values of total enantiomeric excess in each of the species approaching $$\pm 1$$
±
1
when there is a global $$L\leftrightarrow D$$
L
↔
D
symmetry. We then consider a scenario when there is a small external global asymmetry factor, like weak interaction, and show that only one of the species remains in such a case, and that is the one, which is more efficient in replication. We perform an estimate of the time necessary to reach homochirality in such a model and show that reasonable assumptions lead to an estimate of around 300 thousand years plus or minus a couple of orders of magnitude. Despite this seemingly large time to reach homochirality, the model is immune to racemization because amino acids in the model follow the lifespan of the protocells rather than the time needed to reach homochirality. We show that not needing mutual inhibition in such evolutionary model is due to the difference in the topology of the spaces in which considered model and many known models of biological homochirality operate. Bifurcation-based models operate in disconnected zero-dimensional space (the space is just two points with enantiomeric excess equal $$-1$$
-
1
and $$1$$
1
), whereas considered evolutionary model (in its continuous representation) operates in one-dimensional connected space, that is the whole interval between $$-1$$
-
1
and $$1$$
1
of total enantiomeric excess. We then proceed with the analysis of the replication process in non-homochiral environment and show that replication errors (the probability to attach an amino acid of wrong chirality) result in a smooth decrease of replication time when total enantiomeric excess of the replicated structure moves away from zero. We show that this decrease in replication time is sufficient for considered model to work.
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9
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Xu Y, Zhu TF. Mirror-image T7 transcription of chirally inverted ribosomal and functional RNAs. Science 2022; 378:405-412. [DOI: 10.1126/science.abm0646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
To synthesize a chirally inverted ribosome with the goal of building mirror-image biology systems requires the preparation of kilobase-long mirror-image ribosomal RNAs that make up the structural and catalytic core and about two-thirds of the molecular mass of the mirror-image ribosome. Here, we chemically synthesized a 100-kilodalton mirror-image T7 RNA polymerase, which enabled efficient and faithful transcription of the full-length mirror-image 5
S
, 16
S
, and 23
S
ribosomal RNAs from enzymatically assembled long mirror-image genes. We further exploited the versatile mirror-image T7 transcription system for practical applications such as biostable mirror-image riboswitch sensor, long-term storage of unprotected kilobase-long
l
-RNA in water, and
l
-ribozyme–catalyzed
l
-RNA polymerization to serve as a model system for basic RNA research.
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Affiliation(s)
- Yuan Xu
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- School of Life Sciences, Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Ting F. Zhu
- School of Life Sciences, Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
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10
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Umar MI, Chan CY, Kwok CK. Development of RNA G-quadruplex (rG4)-targeting L-RNA aptamers by rG4-SELEX. Nat Protoc 2022; 17:1385-1414. [PMID: 35444329 DOI: 10.1038/s41596-022-00679-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 12/15/2021] [Indexed: 11/09/2022]
Abstract
RNA G-quadruplex (rG4)-SELEX is a method that generates L-RNA aptamers to target an rG4 structure of interest, which can be applied to inhibit G-quadruplex-mediated interactions that have important roles in gene regulation and function. Here we present a Protocol Extension substantially modifying an existing SELEX protocol to describe in detail the procedures involved in performing rG4-SELEX to identify rG4-specific binders that can effectively suppress rG4-peptide and rG4-protein associations. This Protocol Extension improves the speed of aptamer discovery and identification, offering a suite of techniques to characterize the aptamer secondary structure and monitor binding affinity and specificity, and demonstrating the utility of the L-RNA aptamer. The previous protocol mainly describes the identification of RNA aptamers against proteins of interest, whereas in this Protocol Extension we present the development of an unnatural RNA aptamer against an RNA structure of interest, with the potential to be applicable to other nucleic acid motifs or biomolecules. rG4-SELEX starts with a random D-RNA library incubated with the L-rG4 target of interest, followed by binding, washing and elution of the library. Enriched D-aptamer candidates are sequenced and structurally characterized. Then, the L-aptamer is synthesized and used for different applications. rG4-SELEX can be carried out by an experienced molecular biologist with a basic understanding of nucleic acids. The development of rG4-targeting L-RNA aptamers expands the current rG4 toolkit to explore innovative rG4-related applications, and opens new doors to discovering novel rG4 biology in the near future. The duration of each selection cycle as outlined in the protocol is ~2 d.
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Affiliation(s)
- Mubarak I Umar
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,RNA Molecular Biology Group, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD, USA
| | - Chun-Yin Chan
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Institut für Chemische Epigenetik München (ICEM), Ludwig-Maximilians-Universtität München, Munich, Germany
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China. .,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
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11
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Sallembien Q, Bouteiller L, Crassous J, Raynal M. Possible chemical and physical scenarios towards biological homochirality. Chem Soc Rev 2022; 51:3436-3476. [PMID: 35377372 DOI: 10.1039/d1cs01179k] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The single chirality of biological molecules in terrestrial biology raises more questions than certitudes about its origin. The emergence of biological homochirality (BH) and its connection with the appearance of life have elicited a large number of theories related to the generation, amplification and preservation of a chiral bias in molecules of life under prebiotically relevant conditions. However, a global scenario is still lacking. Here, the possibility of inducing a significant chiral bias "from scratch", i.e. in the absence of pre-existing enantiomerically-enriched chemical species, will be considered first. It includes phenomena that are inherent to the nature of matter itself, such as the infinitesimal energy difference between enantiomers as a result of violation of parity in certain fundamental interactions, and physicochemical processes related to interactions between chiral organic molecules and physical fields, polarized particles, polarized spins and chiral surfaces. The spontaneous emergence of chirality in the absence of detectable chiral physical and chemical sources has recently undergone significant advances thanks to the deracemization of conglomerates through Viedma ripening and asymmetric auto-catalysis with the Soai reaction. All these phenomena are commonly discussed as plausible sources of asymmetry under prebiotic conditions and are potentially accountable for the primeval chiral bias in molecules of life. Then, several scenarios will be discussed that are aimed to reflect the different debates about the emergence of BH: extra-terrestrial or terrestrial origin (where?), nature of the mechanisms leading to the propagation and enhancement of the primeval chiral bias (how?) and temporal sequence between chemical homochirality, BH and life emergence (when?). Intense and ongoing theories regarding the emergence of optically pure molecules at different moments of the evolution process towards life, i.e. at the levels of building blocks of Life, of the instructed or functional polymers, or even later at the stage of more elaborated chemical systems, will be critically discussed. The underlying principles and the experimental evidence will be commented for each scenario with particular attention on those leading to the induction and enhancement of enantiomeric excesses in proteinogenic amino acids, natural sugars, and their intermediates or derivatives. The aim of this review is to propose an updated and timely synopsis in order to stimulate new efforts in this interdisciplinary field.
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Affiliation(s)
- Quentin Sallembien
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 Place Jussieu, 75005 Paris, France.
| | - Laurent Bouteiller
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 Place Jussieu, 75005 Paris, France.
| | - Jeanne Crassous
- Univ Rennes, CNRS, Institut des Sciences Chimiques de Rennes, ISCR-UMR 6226, F-35000 Rennes, France.
| | - Matthieu Raynal
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 Place Jussieu, 75005 Paris, France.
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12
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Döring A, Ushakova E, Rogach AL. Chiral carbon dots: synthesis, optical properties, and emerging applications. LIGHT, SCIENCE & APPLICATIONS 2022; 11:75. [PMID: 35351850 PMCID: PMC8964749 DOI: 10.1038/s41377-022-00764-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/09/2022] [Accepted: 03/04/2022] [Indexed: 05/05/2023]
Abstract
Carbon dots are luminescent carbonaceous nanoparticles that can be endowed with chiral properties, making them particularly interesting for biomedical applications due to their low cytotoxicity and facile synthesis. In recent years, synthetic efforts leading to chiral carbon dots with other attractive optical properties such as two-photon absorption and circularly polarized light emission have flourished. We start this review by introducing examples of molecular chirality and its origins and providing a summary of chiroptical spectroscopy used for its characterization. Then approaches used to induce chirality in nanomaterials are reviewed. In the main part of this review we focus on chiral carbon dots, introducing their fabrication techniques such as bottom-up and top-down chemical syntheses, their morphology, and optical/chiroptical properties. We then consider emerging applications of chiral carbon dots in sensing, bioimaging, and catalysis, and conclude this review with a summary and future challenges.
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Affiliation(s)
- Aaron Döring
- Department of Materials Science and Engineering, and Centre for Functional Photonics (CFP), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Elena Ushakova
- Center of Information Optical Technologies, ITMO University, Saint Petersburg, 197101, Russia
| | - Andrey L Rogach
- Department of Materials Science and Engineering, and Centre for Functional Photonics (CFP), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, China.
- Shenzhen Research Institute, City University of Hong Kong, 518057, Shenzhen, China.
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13
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Chirality in Organic and Mineral Systems: A Review of Reactivity and Alteration Processes Relevant to Prebiotic Chemistry and Life Detection Missions. Symmetry (Basel) 2022. [DOI: 10.3390/sym14030460] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Chirality is a central feature in the evolution of biological systems, but the reason for biology’s strong preference for specific chiralities of amino acids, sugars, and other molecules remains a controversial and unanswered question in origins of life research. Biological polymers tend toward homochiral systems, which favor the incorporation of a single enantiomer (molecules with a specific chiral configuration) over the other. There have been numerous investigations into the processes that preferentially enrich one enantiomer to understand the evolution of an early, racemic, prebiotic organic world. Chirality can also be a property of minerals; their interaction with chiral organics is important for assessing how post-depositional alteration processes could affect the stereochemical configuration of simple and complex organic molecules. In this paper, we review the properties of organic compounds and minerals as well as the physical, chemical, and geological processes that affect organic and mineral chirality during the preservation and detection of organic compounds. We provide perspectives and discussions on the reactions and analytical techniques that can be performed in the laboratory, and comment on the state of knowledge of flight-capable technologies in current and future planetary missions, with a focus on organics analysis and life detection.
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14
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Bromberg Y, Aptekmann AA, Mahlich Y, Cook L, Senn S, Miller M, Nanda V, Ferreiro DU, Falkowski PG. Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer. SCIENCE ADVANCES 2022; 8:eabj3984. [PMID: 35030025 PMCID: PMC8759750 DOI: 10.1126/sciadv.abj3984] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/22/2021] [Indexed: 06/07/2023]
Abstract
Biological redox reactions drive planetary biogeochemical cycles. Using a novel, structure-guided sequence analysis of proteins, we explored the patterns of evolution of enzymes responsible for these reactions. Our analysis reveals that the folds that bind transition metal–containing ligands have similar structural geometry and amino acid sequences across the full diversity of proteins. Similarity across folds reflects the availability of key transition metals over geological time and strongly suggests that transition metal–ligand binding had a small number of common peptide origins. We observe that structures central to our similarity network come primarily from oxidoreductases, suggesting that ancestral peptides may have also facilitated electron transfer reactions. Last, our results reveal that the earliest biologically functional peptides were likely available before the assembly of fully functional protein domains over 3.8 billion years ago.Thus, life is a special, very complex form of motion of matter, but this form did not always exist, and it is not separated from inorganic nature by an impassable abyss; rather, it arose from inorganic nature as a new property in the process of evolution of the world. We must study the history of this evolution if we want to solve the problem of the origin of life. [A. I. Oparin (1)]
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Affiliation(s)
- Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Ariel A. Aptekmann
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Yannick Mahlich
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Linda Cook
- Program in Applied and Computational Math, Princeton University, Princeton, NJ 08540, USA
| | - Stefan Senn
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Maximillian Miller
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ 08873, USA
| | - Vikas Nanda
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, and Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Diego U. Ferreiro
- Protein Physiology Lab, Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paul G. Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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15
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Chen J, Chen M, Zhu TF. Directed evolution and selection of biostable L-DNA aptamers with a mirror-image DNA polymerase. Nat Biotechnol 2022; 40:1601-1609. [PMID: 35668324 PMCID: PMC9646512 DOI: 10.1038/s41587-022-01337-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/28/2022] [Indexed: 12/30/2022]
Abstract
Mirror-image aptamers made from chirally inverted nucleic acids are nuclease-resistant and exceptionally biostable, opening up opportunities for unique applications. However, the directed evolution and selection of mirror-image aptamers directly from large randomized L-DNA libraries has, to our knowledge, not been demonstrated previously. Here, we developed a 'mirror-image selection' scheme for the directed evolution and selection of biostable L-DNA aptamers with a mirror-image DNA polymerase. We performed iterative rounds of enrichment and mirror-image polymerase chain reaction (PCR) amplification of L-DNA sequences that bind native human thrombin, in conjunction with denaturing gradient gel electrophoresis (DGGE) to isolate individual aptamers and L-DNA sequencing-by-synthesis to determine their sequences. Based on the selected L-DNA aptamers, we designed biostable thrombin sensors and inhibitors, which remained functional in physiologically relevant nuclease-rich environments, even in the presence of human serum that rapidly degraded D-DNA aptamers. Mirror-image selection of biostable L-DNA aptamers directly from large randomized L-DNA libraries greatly expands the range of biomolecules that can be targeted, broadening their applications as biostable sensors, therapeutics and basic research tools.
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Affiliation(s)
- Ji Chen
- grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Mengyin Chen
- grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Ting F. Zhu
- grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China
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16
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Factors in Protobiomonomer Selection for the Origin of the Standard Genetic Code. Acta Biotheor 2021; 69:745-767. [PMID: 34283307 DOI: 10.1007/s10441-021-09420-4] [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: 08/14/2020] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
Natural selection of specific protobiomonomers during abiogenic development of the prototype genetic code is hindered by the diversity of structural, spatial, and rotational isomers that have identical elemental composition and molecular mass (M), but can vary significantly in their physicochemical characteristics, such as the melting temperature Tm, the Tm:M ratio, and the solubility in water, due to different positions of atoms in the molecule. These parameters differ between cis- and trans-isomers of dicarboxylic acids, spatial monosaccharide isomers, and structural isomers of α-, β-, and γ-amino acids. The stable planar heterocyclic molecules of the major nucleobases comprise four (C, H, N, O) or three (C, H, N) elements and contain a single -C=C bond and two nitrogen atoms in each heterocycle involved in C-N and C=N bonds. They exist as isomeric resonance hybrids of single and double bonds and as a mixture of tautomer forms due to the presence of -C=O and/or -NH2 side groups. They are thermostable, insoluble in water, and exhibit solid-state stability, which is of central importance for DNA molecules as carriers of genetic information. In M-Tm diagrams, proteinogenic amino acids and the corresponding codons are distributed fairly regularly relative to the distinct clusters of purine and pyrimidine bases, reflecting the correspondence between codons and amino acids that was established in different periods of genetic code development. The body of data on the evolution of the genetic code system indicates that the elemental composition and molecular structure of protobiomonomers, and their M, Tm, photostability, and aqueous solubility determined their selection in the emergence of the standard genetic code.
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17
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Abstract
Informational macromolecules in biology are composed of subunits of a single handedness, d-nucleotides in nucleic acids and l-amino acids in proteins. Although this chiral uniformity may be expedient, it is not a chemical necessity, as demonstrated by the recent example of an RNA enzyme that catalyzes the RNA-templated polymerization of RNA molecules of the opposite handedness. This reaction, when carried out iteratively, can provide the basis for exponential amplification of RNA molecules and the information they contain. By carrying out thermal cycling, analogous to the polymerase chain reaction, and supplying oligonucleotide building blocks that comprise both the functional strand of RNA and its complement, cross-chiral exponential amplification was achieved. This process was used to amplify the l-RNA form of the hammerhead ribozyme, catalyzed by the d-RNA form of the polymerase. The resulting l-hammerhead exhibits the expected activity in cleaving a corresponding l-RNA substrate. Exponential amplification was also carried out within individual droplets of a water-in-oil emulsion. The ability to amplify enantio-RNAs, both in bulk solution and within compartments, provides a means to evolve cross-chiral RNA polymerases based on the function of the RNAs they produce.
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Affiliation(s)
- Grant A L Bare
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gerald F Joyce
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
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18
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Sevim İ. Design of Subreplicating Systems from an Existing Self-Replicating Diels-Alder Reaction System by Isosteric Replacement. J Org Chem 2021; 86:14964-14973. [PMID: 34633828 DOI: 10.1021/acs.joc.1c01695] [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
The key feature of non-enzymatic self-replicating systems is the formation of catalytically active ternary complexes in which product templates direct precursors into spatial proximity to allow the formation of new covalent bonds. It is possible to create new replicating species by simply evaluating the ternary active complex of an existing replicating system and applying proper isosteric replacements. In this study, we have evaluated the formerly reported self-replicating Diels-Alder reaction having 61 and 33% selectivity for two diastereomeric replicators. An isosteric replacement on the spacer part connecting recognition and reactive sites of the maleimide component was applied by considering the symmetry of catalytically active ternary complexes, and it was shown that self-replication was conserved. Analysis of the new system showed 77 and 21% diastereoselectivity for the two new replicating species. Seeding experiments indicated autocatalytic activity of both replicators. In other words, both replicators compete with each other by catalyzing their own formation from the same reagent source. Another modification was applied by aiming selective blocking of the autocatalytic cycle of the competing diastereomer. The new system showed a diastereoselectivity of about 94% for the favored replicator. The kinetic data of both systems were analyzed by modeling with SimFit simulations.
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Affiliation(s)
- İlhan Sevim
- Lehrstuhl für Organische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, Bochum 44801, Germany
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19
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Dantsu Y, Zhang Y, Zhang W. Synthesis of 2′‐Deoxy‐2′‐fluoro‐
L
‐cytidine and Fluorinated
L
‐Nucleic Acids for Structural Studies. ChemistrySelect 2021. [DOI: 10.1002/slct.202103202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Yuliya Dantsu
- Department of Biochemistry and Molecular Biology Indiana University School of Medicine 635 Barnhill Drive Indianapolis IN 46202 USA
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology Indiana University School of Medicine 635 Barnhill Drive Indianapolis IN 46202 USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology Indiana University School of Medicine 635 Barnhill Drive Indianapolis IN 46202 USA
- Melvin and Bren Simon Cancer Center 535 Barnhill Dr Indianapolis IN 46202 USA
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20
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Yu CH, Kabza AM, Sczepanski JT. Assembly of long L-RNA by native RNA ligation. Chem Commun (Camb) 2021; 57:10508-10511. [PMID: 34550128 DOI: 10.1039/d1cc04296c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to their intrinsic nuclease resistance, L-oligonucleotides are being increasingly utilized in the development of molecular tools and sensors. Yet, it remains challenging to synthesize long L-oligonucleotides, potential limiting future applications. Herein, we report straightforward and versitile approach to assemble long L-RNAs from two or more shorter fragments using T4 RNA ligase 1. We show that this approach is compatible with the assembly of several classes of functional L-RNA, which we highlight by generating a 124 nt L-RNA biosensor that functions in serum.
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Affiliation(s)
- Chen-Hsu Yu
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
| | - Adam M Kabza
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
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21
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Ma Y, Mou Q, Yan P, Yang Z, Xiong Y, Yan D, Zhang C, Zhu X, Lu Y. A highly sensitive and selective fluoride sensor based on a riboswitch-regulated transcription coupled with CRISPR-Cas13a tandem reaction. Chem Sci 2021; 12:11740-11747. [PMID: 34659710 PMCID: PMC8442723 DOI: 10.1039/d1sc03508h] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/20/2021] [Indexed: 12/26/2022] Open
Abstract
Nucleic acid sensors have realized much success in detecting positively charged and neutral molecules, but have rarely been applied for measuring negatively charged molecules, such as fluoride, even though an effective sensor is needed to promote dental health while preventing osteofluorosis and other diseases. To address this issue, we herein report a quantitative fluoride sensor with a portable fluorometer readout based on fluoride riboswitch-regulated transcription coupled with CRISPR-Cas13-based signal amplification. This tandem sensor utilizes the fluoride riboswitch to regulate in vitro transcription and generate full-length transcribed RNA that can be recognized by CRISPR-Cas13a, triggering the collateral cleavage of the fluorophore-quencher labeled RNA probe and generating a fluorescence signal output. This tandem sensor can quantitatively detect fluoride at ambient temperature in aqueous solution with high sensitivity (limit of detection (LOD) ≈ 1.7 μM), high selectivity against other common anions, a wide dynamic range (0-800 μM) and a short sample-to-answer time (30 min). This work expands the application of nucleic acid sensors to negatively charged targets and demonstrates their potential for the on-site and real-time detection of fluoride in environmental monitoring and point-of-care diagnostics.
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Affiliation(s)
- Yuan Ma
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Quanbing Mou
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Peng Yan
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University 710049 Xi'an PR China
| | - Zhenglin Yang
- Department of Biochemistry, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Ying Xiong
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Deyue Yan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
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22
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Through the looking glass: milestones on the road towards mirroring life. Trends Biochem Sci 2021; 46:931-943. [PMID: 34294544 DOI: 10.1016/j.tibs.2021.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/05/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022]
Abstract
Naturally occurring DNA, RNA, and proteins predominantly exist in only one enantiomeric form (homochirality). Advances in biotechnology and chemical synthesis allow the production of the respective alternate enantiomeric form, enabling access to mirror-image versions of these natural biopolymers. Exploiting the unique properties of such mirror molecules has already led to many applications, such as biostable and nonimmunogenic therapeutics or sensors. However, a 'roadblock' for unlocking the mirror world is the lack of biological systems capable of synthesizing critical building blocks including mirror oligonucleotides and oligopeptides to reducing cost and improve purity. Here, we provide an overview of the current progress, applications, and challenges of the molecular mirror world by identifying milestones towards mirroring life.
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23
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Cojocaru R, Unrau PJ. Processive RNA polymerization and promoter recognition in an RNA World. Science 2021; 371:1225-1232. [PMID: 33737482 DOI: 10.1126/science.abd9191] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/04/2021] [Indexed: 12/21/2022]
Abstract
Early life is thought to have required the self-replication of RNA by RNA replicases. However, how such replicases evolved and subsequently enabled gene expression remains largely unexplored. We engineered and selected a holopolymerase ribozyme that uses a sigma factor-like specificity primer to first recognize an RNA promoter sequence and then, in a second step, rearrange to a processive elongation form. Using its own sequence, the polymerase can also program itself to polymerize from certain RNA promoters and not others. This selective promoter-based polymerization could allow an RNA replicase ribozyme to define "self" from "nonself," an important development for the avoidance of replicative parasites. Moreover, the clamp-like mechanism of this polymerase could eventually enable strand invasion, a critical requirement for replication in the early evolution of life.
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Affiliation(s)
- Razvan Cojocaru
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6.
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24
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Abstract
Chirality is a pervasive structural feature of nature and crucial to the organization and function of nearly all biological systems. At the molecular level, the biased availability of enantiomers in nucleic and amino acids forms the basis for asymmetry. However, chirality expression in natural systems remains complex and intriguing across differing length scales. The translation of chirality toward synthetic systems therefore not only is crucial for fundamental understanding but also may address key challenges in biochemistry and pharmacology. From a structural viewpoint, a fascinating class of cavity-containing supramolecular assemblies, homochiral metal-organic complexes (MOCs), provides a good opportunity to study enantioselective processes. Chiral MOCs are constructed by coordination-driven self-assembly, wherein relatively simple molecular precursors are allowed to assemble into structurally well-defined two-dimensional (2D) metallacycles or 3D metallacages spontaneously with complex and varied functions. These aesthetically appealing structures present nanocavities with space-restricted chiral microenvironments capable of interacting distinctly with molecularly asymmetric guests, which is highly beneficial to explore the relay of chiral information from locally chiral molecules to globally chiral supramolecules, which is a significant challenge.In this Account, we specifically discuss our research toward rationally designed, synthetically accessible chiral MOCs over the past 12 years. The globally supramolecular chirality demonstrated by these well-defined MOCs prominently exceeds the constitutive molecular chirality of the components. First, we discuss chirality transfer and amplification in the context of induction and transmission from the constituent organic ligands of self-assembled chiral metallacycles. The creation of subtly chiral microenvironments in the metallacyclic architectures results from a tiny conformational bias of inner hydrophobic groups, subsequently allowing them to interact very specifically with one enantiomer over the other, thus imparting outstanding enantioseparation properties. Second, we have designed a series of chiral metallacycles and helical metallacages that are able to deploy chiral NH groups with available hydrogen bonding capacity, together with hydrophobic/CH-π interactions, bringing about cooperativity for binding of chiral substrates. It turns out that they can be used as artificial chiral receptors capable of exceptionally high enantiorecognition toward a wide range of biologically relevant molecules. Third, we recently developed a group of highly stable chiral metallacages that feature a catalytically confined nanospace with potential as supramolecular asymmetric catalysts. It has been suggested that the use of molecularly nanocaged chiral hosts in solution to substantially increase reactivity and enantioselectivity compared with the unconfined reactions, highlighting the intermetallic synergy, rationalizes the remarkable catalytic performance. Finally, we discuss our personal perspectives on the promises, opportunities, and key issues toward the future development of chiral MOCs. Needless to say that the fundamental understanding of the translation of chirality from molecular to supramolecular to macroscopic scales is crucial to unveil biological mechanisms. We hope the described supramolecular chirality of MOCs could be extendable to develop new and valuable chiral materials in chemistry, medicine, and beyond.
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Affiliation(s)
- Jinqiao Dong
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Cui
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
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25
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Ochoa S, Milam VT. Modified Nucleic Acids: Expanding the Capabilities of Functional Oligonucleotides. Molecules 2020; 25:E4659. [PMID: 33066073 PMCID: PMC7587394 DOI: 10.3390/molecules25204659] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/20/2022] Open
Abstract
In the last three decades, oligonucleotides have been extensively investigated as probes, molecular ligands and even catalysts within therapeutic and diagnostic applications. The narrow chemical repertoire of natural nucleic acids, however, imposes restrictions on the functional scope of oligonucleotides. Initial efforts to overcome this deficiency in chemical diversity included conservative modifications to the sugar-phosphate backbone or the pendant base groups and resulted in enhanced in vivo performance. More importantly, later work involving other modifications led to the realization of new functional characteristics beyond initial intended therapeutic and diagnostic prospects. These results have inspired the exploration of increasingly exotic chemistries highly divergent from the canonical nucleic acid chemical structure that possess unnatural physiochemical properties. In this review, the authors highlight recent developments in modified oligonucleotides and the thrust towards designing novel nucleic acid-based ligands and catalysts with specifically engineered functions inaccessible to natural oligonucleotides.
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Affiliation(s)
- Steven Ochoa
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Valeria T. Milam
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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26
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Konstantinov KK, Konstantinova AF. Chiral Symmetry Breaking in Large Peptide Systems. ORIGINS LIFE EVOL B 2020; 50:99-120. [PMID: 32945989 DOI: 10.1007/s11084-020-09600-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/25/2020] [Indexed: 11/28/2022]
Abstract
Chiral symmetry breaking in far from equilibrium systems with large number of amino acids and peptides, like a prebiotic Earth, was considered. It was shown that if organic catalysts were abundant, then effective averaging of enantioselectivity would prohibit any symmetry breaking in such systems. It was further argued that non-linear (catalytic) reactions must be very scarce (called the abundance parameter) and catalysts should work on small groups of similar reactions (called the similarity parameter) in order to chiral symmetry breaking have a chance to occur. Models with 20 amino acids and peptide lengths up to three were considered. It was shown that there are preferred ranges of abundance and similarity parameters where the symmetry breaking can occur in the models with catalytic synthesis / catalytic destruction / both catalytic synthesis and catalytic destruction. It was further shown that models with catalytic synthesis and catalytic destruction statistically result in a substantially higher percentage of the models where the symmetry breaking can occur in comparison to the models with just catalytic synthesis or catalytic destruction. It was also shown that when chiral symmetry breaking occurs, then concentrations of some amino acids, which collectively have some mutually beneficial properties, go up, whereas the concentrations of the ones, which don't have such properties, go down. An open source code of the whole system was provided to ensure that the results can be checked, repeated, and extended further if needed.
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Affiliation(s)
- Konstantin K Konstantinov
- Shubnikov Institute of Crystallography, Federal Scientific Research Center "Crystallography and Photonics", Russian Academy of Sciences, Leninskii pr. 59, Moscow, 119333, Russia. .,Softellect Systems, Inc., 414-300 Ave des Sommets, Verdun, QC, H3E 2B7, Canada.
| | - Alisa F Konstantinova
- Shubnikov Institute of Crystallography, Federal Scientific Research Center "Crystallography and Photonics", Russian Academy of Sciences, Leninskii pr. 59, Moscow, 119333, Russia
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27
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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28
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Tjhung KF, Sczepanski JT, Murtfeldt ER, Joyce GF. RNA-Catalyzed Cross-Chiral Polymerization of RNA. J Am Chem Soc 2020; 142:15331-15339. [PMID: 32805113 DOI: 10.1021/jacs.0c05635] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Biology relies almost exclusively on homochiral building blocks to drive the processes of life. Yet cross-chiral interactions can occur between macromolecules of the opposite handedness, including a previously described polymerase ribozyme that catalyzes the template-directed synthesis of enantio-RNA. The present study sought to optimize and generalize this activity, employing in vitro evolution to select cross-chiral polymerases that use either mono- or trinucleotide substrates that are activated as the 5'-triphosphate. There was only modest improvement of the former activity, but dramatic improvement of the latter, which enables the trinucleotide polymerase to react 102-103-fold faster than its ancestor and to accept substrates with all possible sequence combinations. The evolved ribozyme can assemble long RNAs from a mixture of trinucleotide building blocks, including a two-fragment form of the ancestral polymerase ribozyme. Further improvement of this activity could enable the generalized cross-chiral replication of RNA, which would establish a new paradigm for the chemical basis of Darwinian evolution.
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Affiliation(s)
- Katrina F Tjhung
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jonathan T Sczepanski
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
| | - Eric R Murtfeldt
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gerald F Joyce
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
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29
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Salditt A, Keil LMR, Horning DP, Mast CB, Joyce GF, Braun D. Thermal Habitat for RNA Amplification and Accumulation. PHYSICAL REVIEW LETTERS 2020; 125:048104. [PMID: 32794805 DOI: 10.1103/physrevlett.125.048104] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 07/02/2020] [Indexed: 05/07/2023]
Abstract
The RNA world scenario posits replication by RNA polymerases. On early Earth, a geophysical setting is required to separate hybridized strands after their replication and to localize them against diffusion. We present a pointed heat source that drives exponential, RNA-catalyzed amplification of short RNA with high efficiency in a confined chamber. While shorter strands were periodically melted by laminar convection, the temperature gradient caused aggregated polymerase molecules to accumulate, protecting them from degradation in hot regions of the chamber. These findings demonstrate a size-selective pathway for autonomous RNA-based replication in natural nonequilibrium conditions.
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Affiliation(s)
- Annalena Salditt
- Systems Biophysics, Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstraße 54, 80799 Munich, Germany
| | - Lorenz M R Keil
- Systems Biophysics, Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstraße 54, 80799 Munich, Germany
| | - David P Horning
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Christof B Mast
- Systems Biophysics, Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstraße 54, 80799 Munich, Germany
| | - Gerald F Joyce
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Dieter Braun
- Systems Biophysics, Physics Department, Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstraße 54, 80799 Munich, Germany
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30
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Robertson CC, Kosikova T, Philp D. Encoding Multiple Reactivity Modes within a Single Synthetic Replicator. J Am Chem Soc 2020; 142:11139-11152. [PMID: 32414236 DOI: 10.1021/jacs.0c03527] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Establishing programmable and self-sustaining replication networks in pools of chemical reagents is a key challenge in systems chemistry. Self-replicating templates are formed from two constituent components with complementary recognition and reactive sites via a slow bimolecular pathway and a fast template-directed pathway. Here, we re-engineer one of the components of a synthetic replicator to encode an additional recognition function, permitting the assembly of a binary complex between the components that mediates replicator formation through a template-independent pathway, which achieves maximum rate acceleration at early time points in the replication process. The complementarity between recognition sites creates a key conformational equilibrium between the catalytically inert product, formed via the template-independent pathway, and the catalytically active replicator that mediates the template-directed pathway. Consequently, the rapid formation of the catalytically inert isomer kick-starts replication through the template-directed pathway. Through kinetic analyses, we demonstrate that the presence of the two recognition-mediated reactivity modes results in enhanced template formation in comparison to that of systems capable of exploiting only a single recognition-mediated pathway. Finally, kinetic simulations reveal that the conformational equilibrium and both the relative and absolute efficiencies of the recognition-mediated pathways affect the extent to which self-replicating systems can benefit from this additional template-independent reactivity mode. These results allow us to formulate the rules that govern the coupling of replication processes to alternative recognition-mediated reactivity modes. The interplay between template-directed and template-independent pathways for replicator formation has significant relevance to ongoing efforts to design programmable and adaptable replicator networks.
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Affiliation(s)
- Craig C Robertson
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom
| | - Tamara Kosikova
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Douglas Philp
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, United Kingdom.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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31
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Kimura M, Akanuma S. Reconstruction and Characterization of Thermally Stable and Catalytically Active Proteins Comprising an Alphabet of ~ 13 Amino Acids. J Mol Evol 2020; 88:372-381. [PMID: 32201904 DOI: 10.1007/s00239-020-09938-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 03/11/2020] [Indexed: 10/24/2022]
Abstract
While extant organisms synthesize proteins using approximately 20 kinds of genetically coded amino acids, the earliest protein synthesis system is likely to have been much simpler, utilizing a reduced set of amino acids. However, which types of building blocks were involved in primordial protein synthesis remains unclear. Herein, we reconstructed three convergent sequences of an ancestral nucleoside diphosphate kinase, each comprising a 10 amino acid "alphabet," and found that two of these variants folded into soluble and stable tertiary structures. Therefore, an alphabet consisting of 10 amino acids contains sufficient information for creating stable proteins. Furthermore, re-incorporation of a few more amino acid types into the active site of the 10 amino acid variants improved the catalytic activity, although the specific activity was not as high as that of extant proteins. Collectively, our results provide experimental support for the idea that robust protein scaffolds can be built with a subset of the current 20 amino acids that might have existed abundantly in the prebiotic environment, while the other amino acids, especially those with functional sidechains, evolved to contribute to efficient enzyme catalysis.
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Affiliation(s)
- Madoka Kimura
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan
| | - Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, Saitama, 359-1192, Japan.
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32
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Walton T, DasGupta S, Duzdevich D, Oh SS, Szostak JW. In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole-activated substrates. Proc Natl Acad Sci U S A 2020; 117:5741-5748. [PMID: 32123094 PMCID: PMC7084097 DOI: 10.1073/pnas.1914367117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The hypothesized central role of RNA in the origin of life suggests that RNA propagation predated the advent of complex protein enzymes. A critical step of RNA replication is the template-directed synthesis of a complementary strand. Two experimental approaches have been extensively explored in the pursuit of demonstrating protein-free RNA synthesis: template-directed nonenzymatic RNA polymerization using intrinsically reactive monomers and ribozyme-catalyzed polymerization using more stable substrates such as biological 5'-triphosphates. Despite significant progress in both approaches in recent years, the assembly and copying of functional RNA sequences under prebiotic conditions remains a challenge. Here, we explore an alternative approach to RNA-templated RNA copying that combines ribozyme catalysis with RNA substrates activated with a prebiotically plausible leaving group, 2-aminoimidazole (2AI). We applied in vitro selection to identify ligase ribozymes that catalyze phosphodiester bond formation between a template-bound primer and a phosphor-imidazolide-activated oligomer. Sequencing revealed the progressive enrichment of 10 abundant sequences from a random sequence pool. Ligase activity was detected in all 10 RNA sequences; all required activation of the ligator with 2AI and generated a 3'-5' phosphodiester bond. We propose that ribozyme catalysis of phosphodiester bond formation using intrinsically reactive RNA substrates, such as imidazolides, could have been an evolutionary step connecting purely nonenzymatic to ribozyme-catalyzed RNA template copying during the origin of life.
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Affiliation(s)
- Travis Walton
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Saurja DasGupta
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Daniel Duzdevich
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology, 37673 Pohang, Gyeongbuk, South Korea
| | - Jack W Szostak
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114;
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114
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33
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Chan C, Kwok CK. Specific Binding of a
d
‐RNA G‐Quadruplex Structure with an
l
‐RNA Aptamer. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Chun‐Yin Chan
- Department of ChemistryCity University of Hong Kong Tat Chee Avenue Kowloon Tong, Hong Kong SAR China
| | - Chun Kit Kwok
- Department of ChemistryCity University of Hong Kong Tat Chee Avenue Kowloon Tong, Hong Kong SAR China
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34
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Chan CY, Kwok CK. Specific Binding of a d-RNA G-Quadruplex Structure with an l-RNA Aptamer. Angew Chem Int Ed Engl 2020; 59:5293-5297. [PMID: 31975549 DOI: 10.1002/anie.201914955] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/06/2020] [Indexed: 01/24/2023]
Abstract
G-quadruplex (G4) structures are of general importance in chemistry and biology, such as in biosensing, gene regulation, and cancers. Although a large repertoire of G4-binding tools has been developed, no aptamer has been developed to interact with G4. Moreover, the G4 selectivity of current toolkits is very limited. Herein, we report the first l-RNA aptamer that targets a d-RNA G-quadruplex (rG4). Using TERRA rG4 as an example, our results reveal that this l-RNA aptamer, Ap3-7, folds into a unique secondary structure, exhibits high G4 selectivity and effectively interferes with TERRA-rG4-RHAU53 binding. Our approach and findings open a new door in further developing G4-specific tools for diverse applications.
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Affiliation(s)
- Chun-Yin Chan
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
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35
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Tjhung KF, Shokhirev MN, Horning DP, Joyce GF. An RNA polymerase ribozyme that synthesizes its own ancestor. Proc Natl Acad Sci U S A 2020; 117:2906-2913. [PMID: 31988127 PMCID: PMC7022166 DOI: 10.1073/pnas.1914282117] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The RNA-based organisms from which modern life is thought to have descended would have depended on an RNA polymerase ribozyme to copy functional RNA molecules, including copying the polymerase itself. Such a polymerase must have been capable of copying structured RNAs with high efficiency and high fidelity to maintain genetic information across successive generations. Here the class I RNA polymerase ribozyme was evolved in vitro for the ability to synthesize functional ribozymes, resulting in the markedly improved ability to synthesize complex RNAs using nucleoside 5'-triphosphate (NTP) substrates. The polymerase is descended from the class I ligase, which contains the same catalytic core as the polymerase. The class I ligase can be synthesized by the improved polymerase as three separate RNA strands that assemble to form a functional ligase. The polymerase also can synthesize the complement of each of these three strands. Despite this remarkable level of activity, only a very small fraction of the assembled ligases retain catalytic activity due to the presence of disabling mutations. Thus, the fidelity of RNA polymerization should be considered a major impediment to the construction of a self-sustained, RNA-based evolving system. The propagation of heritable information requires both efficient and accurate synthesis of genetic molecules, a requirement relevant to both laboratory systems and the early history of life on Earth.
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Affiliation(s)
- Katrina F Tjhung
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute, La Jolla, CA 92037
| | - Maxim N Shokhirev
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute, La Jolla, CA 92037
| | - David P Horning
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute, La Jolla, CA 92037
| | - Gerald F Joyce
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute, La Jolla, CA 92037
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36
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Janzen E, Blanco C, Peng H, Kenchel J, Chen IA. Promiscuous Ribozymes and Their Proposed Role in Prebiotic Evolution. Chem Rev 2020; 120:4879-4897. [PMID: 32011135 PMCID: PMC7291351 DOI: 10.1021/acs.chemrev.9b00620] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
The ability of enzymes,
including ribozymes, to catalyze side reactions
is believed to be essential to the evolution of novel biochemical
activities. It has been speculated that the earliest ribozymes, whose
emergence marked the origin of life, were low in activity but high
in promiscuity, and that these early ribozymes gave rise to specialized
descendants with higher activity and specificity. Here, we review
the concepts related to promiscuity and examine several cases of highly
promiscuous ribozymes. We consider the evidence bearing on the question
of whether de novo ribozymes would be quantitatively
more promiscuous than later evolved ribozymes or protein enzymes.
We suggest that while de novo ribozymes appear to
be promiscuous in general, they are not obviously more promiscuous
than more highly evolved or active sequences. Promiscuity is a trait
whose value would depend on selective pressures, even during prebiotic
evolution.
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Affiliation(s)
- Evan Janzen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States.,Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, Santa Barbara, California 93109, United States
| | - Celia Blanco
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States
| | - Huan Peng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States
| | - Josh Kenchel
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States.,Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, Santa Barbara, California 93109, United States
| | - Irene A Chen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93109, United States.,Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, Santa Barbara, California 93109, United States.,Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
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37
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An J, Choi J, Hwang D, Park J, Pemble CW, Duong THM, Kim KR, Ahn H, Chung HS, Ahn DR. The crystal structure of a natural DNA polymerase complexed with mirror DNA. Chem Commun (Camb) 2020; 56:2186-2189. [PMID: 31971182 DOI: 10.1039/c9cc09351f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The intrinsic l-DNA binding properties of a natural DNA polymerase was discovered. The binding affinity of Dpo4 polymerase for l-DNA was comparable to that for d-DNA. The crystal structure of Dpo4/l-DNA complex revealed a dimer formed by the little finger domain that provides a binding site for l-DNA.
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Affiliation(s)
- Jinsu An
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. and Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Seoul 02792, Republic of Korea
| | - Jaewoo Choi
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - Dohyeon Hwang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - Jihyun Park
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - Charles W Pemble
- Rigaku Americas Corporation, 9009 New Trails Drive, The Woodlands, TX, USA
| | - Thi Hoai Men Duong
- Department of Pharmacy, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi 13024, Republic of Korea
| | - Kyoung-Ran Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - Heechul Ahn
- Department of Pharmacy, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi 13024, Republic of Korea
| | - Hak Suk Chung
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. and Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Seoul 02792, Republic of Korea
| | - Dae-Ro Ahn
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. and Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Seoul 02792, Republic of Korea
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38
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Chen Y, Ma W. The origin of biological homochirality along with the origin of life. PLoS Comput Biol 2020; 16:e1007592. [PMID: 31914131 PMCID: PMC6974302 DOI: 10.1371/journal.pcbi.1007592] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/21/2020] [Accepted: 12/09/2019] [Indexed: 11/18/2022] Open
Abstract
How homochirality concerning biopolymers (DNA/RNA/proteins) could have originally occurred (i.e., arisen from a non-life chemical world, which tended to be chirality-symmetric) is a long-standing scientific puzzle. For many years, people have focused on exploring plausible physic-chemical mechanisms that may have led to prebiotic environments biased to one chiral type of monomers (e.g., D-nucleotides against L-nucleotides; L-amino-acids against D-amino-acids)–which should have then assembled into corresponding polymers with homochirality, but as yet have achieved no convincing advance. Here we show, by computer simulation–with a model based on the RNA world scenario, that the biased-chirality may have been established at polymer level instead, just deriving from a racemic mixture of monomers (i.e., equally with the two chiral types). In other words, the results suggest that the homochirality may have originated along with the advent of biopolymers during the origin of life, rather than somehow at the level of monomers before the origin of life. People have long been curious about the fact that central molecules in the living world (biopolymers), i.e., nucleic acids and proteins, are asymmetric in chirality (handedness), but as the relevant background, the chemical world is symmetric in chirality. Now that life should have originated from a prebiotic non-life background, how could this dissymmetry have occurred? Previous studies in this area focused their efforts on how the chirality-symmetry may have been broken at the monomer level (i.e., nucleotides or amino acids), but have achieved little advance over decades of years. Here we demonstrate, by in silico simulation, that instead, the required chirality-deviation may have been established along with the emergence of biopolymers at the beginning stage in the origin of life–just deriving from a chirality-symmetric monomer pool. The process is actually not only an issue of chemistry but also an issue involving evolution–thus previously difficult to reveal by pure lab work in this area. By modelling the evolutionary process, the present computer simulation study provides significant clues for experiments in future.
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Affiliation(s)
- Yong Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wentao Ma
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
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39
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Hochberg D, Sánchez Torralba A, Morán F. Chaotic oscillations, dissipation and mirror symmetry breaking in a chiral catalytic network. Phys Chem Chem Phys 2020; 22:27214-27223. [DOI: 10.1039/d0cp05109h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The entropy production per unit volume in the chaotic regime of a chiral hypercycle in an open-flow reactor.
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Affiliation(s)
- David Hochberg
- Department of Molecular Evolution
- Centro de Astrobiología (CSIC-INTA)
- Madrid
- Spain
| | - Antonio Sánchez Torralba
- Departamento de Bioquímica y Biología Molecular I
- Facultad de Ciencias Químicas
- Universidad Complutense de Madrid
- 28040 Madrid
- Spain
| | - Federico Morán
- Departamento de Bioquímica y Biología Molecular I
- Facultad de Ciencias Químicas
- Universidad Complutense de Madrid
- 28040 Madrid
- Spain
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40
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Abstract
Viruses are diverse parasites of cells and extremely abundant. They might have arisen during an early phase of the evolution of life on Earth dominated by ribonucleic acid or RNA-like macromolecules, or when a cellular world was already well established. The theories of the origin of life on Earth shed light on the possible origin of primitive viruses or virus-like genetic elements in our biosphere. Some features of present-day viruses, notably error-prone replication, might be a consequence of the selective forces that mediated their ancestral origin. Two views on the role of viruses in our biosphere predominate; viruses considered as opportunistic, selfish elements, and viruses considered as active participants in the construction of the cellular world via the lateral transfer of genes. These two models have a bearing on viruses being considered predominantly as disease agents or predominantly as cooperators in the shaping of differentiated cellular organisms.
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41
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Abstract
The programmability of DNA/RNA-based molecular circuits provides numerous opportunities in the field of synthetic biology. However, the stability of nucleic acids remains a major concern when performing complex computations in biological environments. Our solution to this problem is L-(deoxy)ribose nucleic acids (L-DNA/RNA), which are mirror images (i.e. enantiomers) of natural D-nucleotides. L-oligonucleotides have the same physical and chemical properties as their natural counterparts, yet they are completely invisible to the stereospecific environment of biology. We recently reported a novel strand-displacement methodology for transferring sequence information between oligonucleotide enantiomers (which are incapable of base pairing with each other), enabling bio-orthogonal L-DNA/RNA circuits to be easily interfaced with living systems. In this perspective, we summarize these so-called "heterochiral" circuits, provide a viewpoint on their potential applications in synthetic biology, and discuss key problems that must be solved before achieving the ultimate goal of engineering complex and reliable functionality.
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42
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The Limited Roles of Autocatalysis and Enantiomeric Cross-Inhibition in Achieving Homochirality in Dilute Systems. ORIGINS LIFE EVOL B 2019; 49:49-60. [DOI: 10.1007/s11084-019-09579-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/04/2019] [Indexed: 10/26/2022]
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43
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Young BE, Kundu N, Sczepanski JT. Mirror-Image Oligonucleotides: History and Emerging Applications. Chemistry 2019; 25:7981-7990. [PMID: 30913332 PMCID: PMC6615976 DOI: 10.1002/chem.201900149] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Indexed: 01/13/2023]
Abstract
As chiral molecules, naturally occurring d-oligonucleotides have enantiomers, l-DNA and l-RNA, which are comprised of l-(deoxy)ribose sugars. These mirror-image oligonucleotides have the same physical and chemical properties as that of their native d-counterparts, yet are highly orthogonal to the stereospecific environment of biology. Consequently, l-oligonucleotides are resistant to nuclease degradation and many of the off-target interactions that plague traditional d-oligonucleotide-based technologies; thus making them ideal for biomedical applications. Despite a flurry of interest during the early 1990s, the inability of d- and l-oligonucleotides to form contiguous Watson-Crick base pairs with each other has ultimately led to the perception that l-oligonucleotides have only limited utility. Recently, however, scientists have begun to uncover novel strategies to harness the bio-orthogonality of l-oligonucleotides, while overcoming (and even exploiting) their inability to Watson-Crick base pair with the natural polymer. Herein, a brief history of l-oligonucleotide research is presented and emerging l-oligonucleotide-based technologies, as well as their applications in research and therapy, are presented.
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Affiliation(s)
- Brian E. Young
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Nandini Kundu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jonathan T. Sczepanski
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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44
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Luo X, Chen Z, Li H, Li W, Cui L, Huang J. Exploiting the application of l-aptamer with excellent stability: an efficient sensing platform for malachite green in fish samples. Analyst 2019; 144:4204-4209. [PMID: 31187804 DOI: 10.1039/c9an00332k] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Effective monitoring of the content of malachite green (MG) in aquaculture is of great importance for food safety. Traditional methods for MG assay, such as chromatography and spectroscopy, have been criticized for expensive instrumentation and complicated pretreatments. An MG RNA aptamer (MGA) is a powerful tool for immediate and rapid detection of MG. However, RNA is easily degraded by nucleases and is unstable in the environment, making accurate and reliable detection of MG difficult. In order to address the problems, an innovative levo (l)-MGA with excellent stability is designed to perform the specific recognition function. Interestingly, the gel electrophoresis and fluorescence measurement results indicate that this unnaturally occurring l-aptamer is resistant to nuclease degradation and it can be kept intact in the standard buffer solution under room temperature for quite a long time. A label-free, simple, and efficient method has been developed for sensitive detection of MG in fish tissue, which holds promising potential in food analysis and environmental monitoring.
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Affiliation(s)
- Xiaowei Luo
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China. and Department of Chemistry, University of Washington, Washington 98195, USA
| | - Zhifeng Chen
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Hongfeng Li
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Wenqin Li
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
| | - Liang Cui
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310008, China.
| | - Jiahao Huang
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Guangdong Provincial Key Laboratory of Medical Image Processing, Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
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Taylor AI, Houlihan G, Holliger P. Beyond DNA and RNA: The Expanding Toolbox of Synthetic Genetics. Cold Spring Harb Perspect Biol 2019; 11:11/6/a032490. [PMID: 31160351 DOI: 10.1101/cshperspect.a032490] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The remarkable physicochemical properties of the natural nucleic acids, DNA and RNA, define modern biology at the molecular level and are widely believed to have been central to life's origins. However, their ability to form repositories of information as well as functional structures such as ligands (aptamers) and catalysts (ribozymes/DNAzymes) is not unique. A range of nonnatural alternatives, collectively termed xeno nucleic acids (XNAs), are also capable of supporting genetic information storage and propagation as well as evolution. This gives rise to a new field of "synthetic genetics," which seeks to expand the nucleic acid chemical toolbox for applications in both biotechnology and molecular medicine. In this review, we outline XNA polymerase and reverse transcriptase engineering as a key enabling technology and summarize the application of "synthetic genetics" to the development of aptamers, enzymes, and nanostructures.
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Affiliation(s)
- Alexander I Taylor
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Gillian Houlihan
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Philipp Holliger
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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46
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Horning DP, Bala S, Chaput JC, Joyce GF. RNA-Catalyzed Polymerization of Deoxyribose, Threose, and Arabinose Nucleic Acids. ACS Synth Biol 2019; 8:955-961. [PMID: 31042360 DOI: 10.1021/acssynbio.9b00044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An RNA-dependent RNA polymerase ribozyme that was highly optimized through in vitro evolution for the ability to copy a broad range of template sequences exhibits promiscuity toward other nucleic acids and nucleic acid analogues, including DNA, threose nucleic acid (TNA), and arabinose nucleic acid (ANA). By operating on various RNA templates, the ribozyme catalyzes multiple successive additions of DNA, TNA, or ANA monomers, although with reduced efficiency compared to RNA monomers. The ribozyme can also copy DNA or TNA templates to complementary RNAs, and to a lesser extent it can operate when both the template and product strands are composed of DNA, TNA, or ANA. These results suggest that polymerase ribozymes, which are thought to have replicated RNA genomes during the early history of life, could have transferred RNA-based genetic information to and from DNA, enabling the emergence of DNA genomes prior to the emergence of proteins. In addition, genetic systems based on nucleic acid-like molecules, which have been proposed as precursors or contemporaries of RNA-based life, could have been operated upon by a promiscuous polymerase ribozyme, thus enabling the evolutionary transition between early genetic systems.
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Affiliation(s)
- David P. Horning
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Saikat Bala
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - John C. Chaput
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Gerald F. Joyce
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
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47
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Hieronymus R, Müller S. Engineering of hairpin ribozyme variants for RNA recombination and splicing. Ann N Y Acad Sci 2019; 1447:135-143. [PMID: 30941784 DOI: 10.1111/nyas.14052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/13/2019] [Accepted: 02/20/2019] [Indexed: 11/28/2022]
Abstract
The hairpin ribozyme is a small, naturally occurring RNA that catalyzes the reversible cleavage of RNA substrates. Among the small endonucleolytic ribozymes, the hairpin ribozyme possesses the unique feature of the internal equilibrium between cleavage and ligation being shifted toward ligation. This allows control of the reaction outcome by structural design: fragments that are strongly bound to the ribozyme are preferentially ligated, whereas substrates that easily dissociate upon cleavage, such that they are not available for religation, are preferentially cleaved. We have made use of this characteristic feature in engineering a number of hairpin ribozyme variants by programmed conformational design that carry out cascades of cleavage and ligation reactions, and as a result mediate more complex RNA processing reactions. Here, we review our work on the engineering of hairpin ribozyme variants for RNA recombination and regular and back-splicing, and discuss the relevance of such activities in early life.
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Affiliation(s)
| | - Sabine Müller
- Institut für Biochemie, Universität Greifswald, Greifswald, Germany
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48
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49
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Flamme M, McKenzie LK, Sarac I, Hollenstein M. Chemical methods for the modification of RNA. Methods 2019; 161:64-82. [PMID: 30905751 DOI: 10.1016/j.ymeth.2019.03.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
RNA is often considered as being the vector for the transmission of genetic information from DNA to the protein synthesis machinery. However, besides translation RNA participates in a broad variety of fundamental biological roles such as gene expression and regulation, protein synthesis, and even catalysis of chemical reactions. This variety of function combined with intricate three-dimensional structures and the discovery of over 100 chemical modifications in natural RNAs require chemical methods for the modification of RNAs in order to investigate their mechanism, location, and exact biological roles. In addition, numerous RNA-based tools such as ribozymes, aptamers, or therapeutic oligonucleotides require the presence of additional chemical functionalities to strengthen the nucleosidic backbone against degradation or enhance the desired catalytic or binding properties. Herein, the two main methods for the chemical modification of RNA are presented: solid-phase synthesis using phosphoramidite precursors and the enzymatic polymerization of nucleoside triphosphates. The different synthetic and biochemical steps required for each method are carefully described and recent examples of practical applications based on these two methods are discussed.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Luke K McKenzie
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Ivo Sarac
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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50
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Weidmann J, Schnölzer M, Dawson PE, Hoheisel JD. Copying Life: Synthesis of an Enzymatically Active Mirror-Image DNA-Ligase Made of D-Amino Acids. Cell Chem Biol 2019; 26:645-651.e3. [PMID: 30880154 DOI: 10.1016/j.chembiol.2019.02.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 11/27/2018] [Accepted: 02/07/2019] [Indexed: 11/17/2022]
Abstract
Our objective is the creation of a mirror-image synthetic biology: that is, to mimic, entirely independent of Nature, a biological system and to re-create it from artificial component parts. Utilizing enantiomeric L-nucleotides and D-amino acids rather than the natural components, we use chemical synthesis toward a basic, self-replicating mirror-image biological system. Here, we report the synthesis of a functional DNA-ligase in the D-enantiomeric conformation, which is an exact mirror-image of the natural enzyme, exhibiting DNA ligation activity on chirally inverted nucleic acids in L-conformation, but not acting on natural substrates and with natural co-factors. Starting from the known structure of the Paramecium bursaria chlorella virus 1 DNA-ligase and the homologous but shorter DNA-ligase of Haemophilus influenza, we designed and synthesized chemically peptides, which could then be assembled into a full-length molecule yielding a functional protein. The structure and the activity of the mirror-image ligase were characterized, documenting its enantiospecific functionality.
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Affiliation(s)
- Joachim Weidmann
- Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jörg D Hoheisel
- Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
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