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Hans S, Kumar N, Gohil N, Khambhati K, Bhattacharjee G, Deb SS, Maurya R, Kumar V, Reshamwala SMS, Singh V. Rebooting life: engineering non-natural nucleic acids, proteins and metabolites in microorganisms. Microb Cell Fact 2022; 21:100. [PMID: 35643549 PMCID: PMC9148472 DOI: 10.1186/s12934-022-01828-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/15/2022] [Indexed: 12/01/2022] Open
Abstract
The surging demand of value-added products has steered the transition of laboratory microbes to microbial cell factories (MCFs) for facilitating production of large quantities of important native and non-native biomolecules. This shift has been possible through rewiring and optimizing different biosynthetic pathways in microbes by exercising frameworks of metabolic engineering and synthetic biology principles. Advances in genome and metabolic engineering have provided a fillip to create novel biomolecules and produce non-natural molecules with multitude of applications. To this end, numerous MCFs have been developed and employed for production of non-natural nucleic acids, proteins and different metabolites to meet various therapeutic, biotechnological and industrial applications. The present review describes recent advances in production of non-natural amino acids, nucleic acids, biofuel candidates and platform chemicals.
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Asanuma H, Kamiya Y, Kashida H, Murayama K. Xeno nucleic acids (XNAs) having non-ribose scaffolds with unique supramolecular properties. Chem Commun (Camb) 2022; 58:3993-4004. [DOI: 10.1039/d1cc05868a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA and RNA have significance as a genetic materials, therapeutic potential, and supramolecular properties. Advances in nucleic acid chemistry have enabled large-scale synthesis of DNA and RNA oligonucleotides and oligomers...
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Mattelaer CA, Mattelaer HP, Rihon J, Froeyen M, Lescrinier E. Efficient and Accurate Potential Energy Surfaces of Puckering in Sugar-Modified Nucleosides. J Chem Theory Comput 2021; 17:3814-3823. [PMID: 34000809 DOI: 10.1021/acs.jctc.1c00270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Puckering of the sugar unit in nucleosides and nucleotides is an important structural aspect that directly influences the helical structure of nucleic acids. The preference for specific puckering modes in nucleic acids can be analyzed via in silico conformational analysis, but the large amount of conformations and the accuracy of the analysis leads to an extensive amount of computational time. In this paper, we show that the combination of geometry optimizations with the HF-3c method with single point energies at the RI-MP2 level results in accurate results for the puckering potential energy surface (PES) of DNA and RNA nucleosides while significantly reducing the necessary computational time. Applying this method to a series of known xeno nucleic acids (XNAs) allowed us to rapidly explore the puckering PES of each of the respective nucleosides and to explore the puckering PES of six-membered modified XNA (HNA and β-homo-DNA) for the first time.
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Affiliation(s)
- Charles-Alexandre Mattelaer
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Henri-Philippe Mattelaer
- Campus Drie Eiken, Laboratory of Medicinal Chemistry, UAntwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Jérôme Rihon
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Matheus Froeyen
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Eveline Lescrinier
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
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Lambert BP, Gillen AJ, Boghossian AA. Synthetic Biology: A Solution for Tackling Nanomaterial Challenges. J Phys Chem Lett 2020; 11:4791-4802. [PMID: 32441940 DOI: 10.1021/acs.jpclett.0c00929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Bioengineers have mastered practical techniques for tuning a biomaterial's properties with only limited information on the relationship between the material's structure and function. These techniques have been quintessential to engineering proteins, which are most often riddled with ill-defined structure-function relationships. In this Perspective, we review bioengineering approaches aimed at overcoming the elusive protein structure-function relation. We extend these principles to engineering synthetic nanomaterials, specifically applying the underlying theory to optical sensors based on single-stranded DNA-wrapped single-walled carbon nanotubes (ssDNA-SWCNTs). Bioengineering techniques such as directed evolution, computational design, and noncanonical synthesis are reviewed in the broader context of nanomaterials engineering. We further provide an order-of-magnitude analysis of empirical approaches that rely on random or guided searches for designing new nanomaterials. The underlying concepts presented in these approaches can be further extended to a broad range of engineering fields confronted with empirical design strategies, including catalysis, metal-organic frameworks (MOFs), pharmaceutical dosing, and optimization algorithms.
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Affiliation(s)
- Benjamin P Lambert
- École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Alice J Gillen
- École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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Krishna H, Jastrzebska K, Caruthers M. Exploring site-specific activation of bis-N,N'-dialkylaminophosphordiamidites and the synthesis of morpholinophosphoramidate oligonucleotides. FEBS Lett 2019; 593:1459-1467. [PMID: 31206627 DOI: 10.1002/1873-3468.13492] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 11/05/2022]
Abstract
Morpholinos are six-membered rings that may provide higher conformational rigidity when incorporated into an oligonucleotide (ODN) backbone. Phosphorodiamidate morpholinos are chemically modified ODNs containing morpholinos in place of 2'-deoxyribose moieties throughout their backbone and have garnered much interest in recent years due to their ability to function as highly effective steric blockers in exon skipping therapy. To further explore the biophysical and biological properties of ODNs derived from morpholino nucleosides, we have replaced the 2'-deoxyribonucleotides of phosphodiester DNA with morpholinonucleotides to generate phosphoramidate ODNs. Here, we evaluate the mechanistic pathways observed during the solution-phase synthesis of morpholinonucleoside phosphoramidites, solid-phase synthesis of morpholinonucleotide phosphoramidates of mA, mG, mC and mT (prefix 'm' represents morpholino) and our first attempts directed at the solid-phase synthesis of chimeric DNA-phosphoramidate ODNs, as well as fully modified 22-mer phosphoramidate ODNs.
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Whitford CM, Dymek S, Kerkhoff D, März C, Schmidt O, Edich M, Droste J, Pucker B, Rückert C, Kalinowski J. Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications. J Biol Eng 2018; 12:13. [PMID: 30123321 PMCID: PMC6090650 DOI: 10.1186/s13036-018-0105-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/25/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Biosafety is a key aspect in the international Genetically Engineered Machine (iGEM) competition, which offers student teams an amazing opportunity to pursue their own research projects in the field of Synthetic Biology. iGEM projects often involve the creation of genetically engineered bacterial strains. To minimize the risks associated with bacterial release, a variety of biosafety systems were constructed, either to prevent survival of bacteria outside the lab or to hinder horizontal or vertical gene transfer. MAIN BODY Physical containment methods such as bioreactors or microencapsulation are considered the first safety level. Additionally, various systems involving auxotrophies for both natural and synthetic compounds have been utilized by iGEM teams in recent years. Combinatorial systems comprising multiple auxotrophies have been shown to reduced escape frequencies below the detection limit. Furthermore, a number of natural toxin-antitoxin systems can be deployed to kill cells under certain conditions. Additionally, parts of naturally occurring toxin-antitoxin systems can be used for the construction of 'kill switches' controlled by synthetic regulatory modules, allowing control of cell survival. Kill switches prevent cell survival but do not completely degrade nucleic acids. To avoid horizontal gene transfer, multiple mechanisms to cleave nucleic acids can be employed, resulting in 'self-destruction' of cells. Changes in light or temperature conditions are powerful regulators of gene expression and could serve as triggers for kill switches or self-destruction systems. Xenobiology-based containment uses applications of Xeno-DNA, recoded codons and non-canonical amino acids to nullify the genetic information of constructed cells for wild type organisms. A 'minimal genome' approach brings the opportunity to reduce the genome of a cell to only genes necessary for survival under lab conditions. Such cells are unlikely to survive in the natural environment and are thus considered safe hosts. If suitable for the desired application, a shift to cell-free systems based on Xeno-DNA may represent the ultimate biosafety system. CONCLUSION Here we describe different containment approaches in synthetic biology, ranging from auxotrophies to minimal genomes, which can be combined to significantly improve reliability. Since the iGEM competition greatly increases the number of people involved in synthetic biology, we will focus especially on biosafety systems developed and applied in the context of the iGEM competition.
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Affiliation(s)
| | - Saskia Dymek
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Denise Kerkhoff
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Camilla März
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Olga Schmidt
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Maximilian Edich
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Julian Droste
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Boas Pucker
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Present address: Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Christian Rückert
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
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Evéquoz D, Leumann CJ. Probing the Backbone Topology of DNA: Synthesis and Properties of 7',5'-Bicyclo-DNA. Chemistry 2017; 23:7953-7968. [PMID: 28262999 DOI: 10.1002/chem.201700435] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Indexed: 01/18/2023]
Abstract
We describe the synthesis and pairing properties of the novel DNA analogue 7',5'-bicyclo(bc)-DNA. In this analogue, the point of attachment of the connecting phosphodiester group is switched from the 3' to the 7' position of the underlying bicyclic sugar unit and is thus in a topological position that is inaccessible in natural DNA. The corresponding phosphoramidite building blocks carrying all natural nucleobases were synthesized and incorporated into oligonucleotides. From Tm experiments of duplexes with complementary DNA and RNA we find that single modifications are generally well tolerated with some variability as to the nature of the nucleobase. Fully modified oligonucleotides show low affinity for RNA and DNA complements. However, they form antiparallel homo-duplexes with similar thermal stability as DNA. CD spectra of the homo-duplexes show distinct changes in the helix conformation compared to natural DNA. A conformational analysis at the ab initio level of the mononucleosides revealed two minimal energy structures which primarily deviate in the conformation of the cyclopentane ring. Molecular dynamics simulation of a 7',5'-bc-DNA homo-duplex revealed a right-handed structure with a smaller helical rise and a significantly wider minor groove compared to DNA. Interestingly, this duplex is characterized by an atypical, alternating 6'-endo/6'-exo conformational pattern of consecutive nucleotides which seems to be responsible for the poor binding to natural nucleic acids.
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Affiliation(s)
- Damien Evéquoz
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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Robeyns K, Herdewijn P, Van Meervelt L. Direct observation of two cyclohexenyl (CeNA) ring conformations in duplex DNA. ARTIFICIAL DNA, PNA & XNA 2014; 1:2-8. [PMID: 21687521 DOI: 10.4161/adna.1.1.10952] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 12/10/2009] [Accepted: 12/11/2009] [Indexed: 11/19/2022]
Abstract
Cyclohexene Nucleic Acids (CeNA), in which the 2'-deoxyribofuranose ring of the DNA building blocks is substituted by a cyclohexenyl ring, were designed as potential mimics of natural nucleic acids for antisense and, later, for siRNA applications. CeNA units, in contrast to HNA (hexitol nucleic acid) building blocks, show more flexibility at the level of the C2'-C3' bond due to the possibility of the cyclohexenyl moiety to adopt different conformations. In order to analyze the influence of CeNA residues onto the helix conformation and hydration of natural nucleic acid structures and to verify the cyclohexenyl ring conformation, a cyclohexenyl-thymine building block was incorporated into the non-self-complementary sequence d(GCG(xT)GCG)/d(CGCACGC) with (xT) a cyclohexene residue. The crystal structure of this sequence has been determined to a resolution of 1.17 Å and contains two duplexes in the asymmetric unit. The global helices belong to the B-type family and the conformations of the cyclohexenyl rings in both duplexes are different. The cyclohexene ring adopts as well the (2)H(3)-conformation (similar to C2'-endo) as the (3)H(2)-conformation (similar to C3'-endo). The crystal packing is stabilized by cobalt hexamine residues and triplet formation.
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Affiliation(s)
- Koen Robeyns
- Department of Chemistry, Biomolecular Architecture and BioMacS; Katholieke Universiteit Leuven; Leuven, Belgium
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Evmenenko G, Cockroft SL, Dutta P. Effect of solvent polarizability on the assembly and ordering of nanoscale polyhedral oligomeric silsesquioxane films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:196-202. [PMID: 24350622 DOI: 10.1021/la4041425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Understanding the factors that affect molecular self-assembly is crucial to building designed nanoscale structures. We have deposited nanoscale films of polyhedral oligomeric silsesquioxane (POSS) onto polished silicon substrates from a range of organic solvents. We studied these films using synchrotron X-ray reflectivity and found that dip-coating from benzene, toluene, or chloroform results in near-substrate ordering only, but when acetone, hexane, or THF is used, self-assembled layers are formed throughout the entire deposited film. We conclude that solvent polarizability is the factor that determines the alignment of the POSS molecules. We have successfully tested this prediction using additional solvents selected on the basis of their calculated polarizabilities.
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Affiliation(s)
- Guennadi Evmenenko
- Department of Physics and Astronomy, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208-3112, United States
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10
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Zhou J, Abramov M, Liu F, Amrane S, Bourdoncle A, Herdewijn P, Mergny JL. Effects of six-membered carbohydrate rings on structure, stability, and kinetics of G-quadruplexes. Chemistry 2013; 19:14719-25. [PMID: 24027098 DOI: 10.1002/chem.201301743] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/24/2013] [Indexed: 12/13/2022]
Abstract
We have evaluated the conformational, thermal, and kinetic properties of d(TGGGGT) analogues with one or five of the ribose nucleotides replaced with the carbohydrate residues hexitol nucleic acid (HNA), cyclohexenyl nucleic acid (CeNA), or altritol nucleic acid (ANA). All of the modified oligonucleotides formed G-quadruplexes, but substitution with the six-membered rings resulted in a mixture of G-quadruplex structures. UV and CD melting analyses showed that the structure formed by d(TGGGGT) modified with HNA was stabilized whereas that modified with CeNA was destabilized, relative to the structure formed by the unmodified oligonucleotide. Substitution at the fourth base of the G-tract with ANA resulted in a greater stabilization effect than substitution at the first G residue; substitution with five ANA residues resulted in significant stabilization of the G-quadruplex. A single substitution with CeNA at the first base of the G-tract or five substitutions with HNA resulted in striking deceleration or acceleration of G-quadruplex formation, respectively. Our results shed light on the effect of the sugar moiety on the properties of G-quadruplex structures.
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Affiliation(s)
- Jun Zhou
- Univ. Bordeaux, ARNA Laboratory, 33000 Bordeaux (France); INSERM, U869, IECB, 33600 Pessac (France), Fax: (+33) 5-4000-3004
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11
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Liboska R, Snášel J, Barvík I, Buděšínský M, Pohl R, Točík Z, Páv O, Rejman D, Novák P, Rosenberg I. 4'-Alkoxy oligodeoxynucleotides: a novel class of RNA mimics. Org Biomol Chem 2011; 9:8261-7. [PMID: 22051918 DOI: 10.1039/c1ob06148h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
4'-Alkoxy-oligothymidylates were prepared as model compounds to study the influence of a C4'-alkoxy group on hybridisation. The phosphodiester homooligomers (15 units long) containing either a 4'-methoxy or 4'-(2-methoxyethoxy) group were found to display increased hybridisation with both dA(15) and rA(15) complementary counterparts compared to the natural oligothymidylate. In addition, we found their hybridisation behaviour to be similar to that of the regioisomeric 2'-O-methyl-oligothymidylate. The formed complexes (duplexes and triplexes) were studied using UV spectroscopy and polyacrylamide gel electrophoresis (PAGE). Structural background of the hybridization behaviour was examined using NMR and MDS. The favourable hybridisation properties of the 4'-alkoxyoligothymidylates indicated that 4'-alkoxy modified nucleotides are promising compounds for the assembly of chimeric oligonucleotides with tunable properties.
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Affiliation(s)
- Radek Liboska
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v. v. i., Flemingovo 2, 166 10 Prague 6, Czech Republic
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Varada M, Kotikam V, Kumar VA. Robust synthesis of enantiopure cyclohexenyl analogues of 2/3-deoxyribose sugars as carbocyclic nucleoside precursors. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Ovaere M, Herdewijn P, Van Meervelt L. The crystal structure of the CeNA:RNA hybrid ce(GCGTAGCG):r(CGCUACGC). Chemistry 2011; 17:7823-30. [PMID: 21618623 DOI: 10.1002/chem.201003594] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Indexed: 11/11/2022]
Abstract
Cyclohexenyl nucleic acids (CeNA) are characterised by the carbon-carbon double bond replacing the O4'-oxygen atom of the natural D-2'-deoxyribose sugar ring in DNA. CeNAs exhibit a high conformational flexibility, are stable against nuclease activity and their hybridisation is RNA selective. Additionally, CeNA has been shown to induce an enhanced biological activity when incorporated in siRNA. This makes CeNA a good candidate for siRNA and synthetic aptamer applications. The crystal structure of the synthetic CeNA:RNA hybrid ce(GCGTAGCG):r(CGCUACGC) has been solved with a resolution of 2.50 Å. The CeNA:RNA duplex adopts an anti-parallel, right-handed double helix with standard Watson-Crick base pairing. Analyses of the helical parameters revealed the octamer to form an A-like double helix. The cyclohexenyl rings mainly adopt the (3)H(2) conformation, which resembles the C3'-endo conformation of RNA ribose ring. This C3'-endo ring puckering was found in most of the RNA residues and is typical for A-family helices. The crystal structure is stabilised by the presence of hexahydrated magnesium ions. The fact that the CeNA:RNA hybrid adopts an A-type double helical conformation confirms the high potential of CeNAs for the construction of efficient siRNAs which can be used for therapeutical applications.
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Affiliation(s)
- Margriet Ovaere
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F-box 2404, 3001 Leuven, Belgium
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Abstract
Starting from pyranose nucleic acids, several series of modified nucleic acids with a six-membered carbohydrate moiety (mimic) have been synthesized and analyzed over a period of 20 years, and this work is summarized here. The process starts with structural and conformational considerations, followed by synthetic efforts and a structural analysis, and ends up with a biological confirmation of the concept, demonstrating that these modified nucleic acids represent very valuable tools in chemistry and biology.
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Affiliation(s)
- Piet Herdewijn
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven.
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Appella DH. Non-natural nucleic acids for synthetic biology. Curr Opin Chem Biol 2009; 13:687-96. [PMID: 19879178 PMCID: PMC3152792 DOI: 10.1016/j.cbpa.2009.09.030] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2009] [Revised: 09/24/2009] [Accepted: 09/29/2009] [Indexed: 11/29/2022]
Abstract
Genetic manipulation is an important facet of synthetic biology but can be complicated by undesired nuclease degradation. Incorporating non-natural nucleic acids into a gene could convey resistance to nucleases and promote expression. The compatibility of non-natural nucleosides with polymerases is reviewed with a focus on results from the past two years. Details are provided about how the different systems could be useful in synthetic biology.
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Affiliation(s)
- Daniel H Appella
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA.
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16
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Yang S, Busson R, Herdewijn P. Synthesis of N-methyl-d-ribopyranuronamide nucleosides. Tetrahedron 2008; 64:10062-10067. [PMID: 32287418 PMCID: PMC7126205 DOI: 10.1016/j.tet.2008.08.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Revised: 08/05/2008] [Accepted: 08/09/2008] [Indexed: 11/19/2022]
Abstract
The synthesis of N-methyl-d-ribopyranuronamide nucleosides is described. The key route is the rearrangement of a 1,2-O-isopropylidene protected furanose sugar with a carboxamide function in the 4-position to a ribopyranuronamide ring. The Lewis acid catalyzed condensation of adenine and thymine nucleobases with the per-O-acetylated N-methyl-d-ribopyranuronamide sugar is used to give the target nucleosides as a mixture of the α and β anomers. The mixture was separated and the final compounds were obtained by deacetylation in basic conditions.
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Affiliation(s)
- Shiqiong Yang
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Catholic University of Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Roger Busson
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Catholic University of Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Piet Herdewijn
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Catholic University of Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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17
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Robeyns K, Herdewijn P, Van Meervelt L. Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC. J Am Chem Soc 2008; 130:1979-84. [PMID: 18198873 DOI: 10.1021/ja077313f] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CeNA oligonucleotides consist of a phosphorylated backbone where the deoxyribose sugars are replaced by cyclohexene moieties. The X-ray structure determination and analysis of a fully modified octamer sequence GTGTACAC, which is the first crystal structure of a carbocyclic-based nucleic acid, is presented. This particular sequence was built with left-handed building blocks and crystallizes as a left-handed double helix. The helix can be characterized as belonging to the (mirrored) A-type family. Crystallographic data were processed up to 1.53 A, and the octamer sequence crystallizes in the space group R32. The sugar puckering is found to adopt the 3H2 half-chair conformation which mimics the C3'-endo conformation of the ribose sugar. The double helices stack on top of each other to form continuous helices, and static disorder is observed due to this end-to-end stacking.
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Affiliation(s)
- Koen Robeyns
- Katholieke Universiteit Leuven, Department of Chemistry, Biomolecular Architecture and BioMacS, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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18
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19
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Nauwelaerts K, Fisher M, Froeyen M, Lescrinier E, Aerschot AV, Xu D, DeLong R, Kang H, Juliano RL, Herdewijn P. Structural characterization and biological evaluation of small interfering RNAs containing cyclohexenyl nucleosides. J Am Chem Soc 2007; 129:9340-8. [PMID: 17616127 DOI: 10.1021/ja067047q] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CeNA is an oligonucleotide where the (deoxy)ribose sugars have been replaced by cyclohexenyl moieties. We have determined the NMR structure of a CeNA:RNA duplex and have modeled this duplex in the crystal structure of a PIWI protein. An N puckering of the ribose nucleosides, a 2H3 conformation of the cyclohexenyl nucleosides, and an A-like helix conformation of the backbone, which deviates from the standard A-type helix by a larger twist and a smaller slide, are observed. The model of the CeNA:RNA duplex bound to the PIWI protein does not show major differences in the interaction of the guide CeNA with the protein when compared with dsRNA, suggesting that CeNA modified oligonucleotides might be useful as siRNAs. Incorporation of one or two CeNA units in the sense or antisense strands of dsRNA led to similar or enhanced activity compared to unmodified siRNAs. This was tested by targeting inhibition of expression of the MDR1 gene with accompanying changes in P-glycoprotein expression, drug transport, and drug resistance.
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Affiliation(s)
- Koen Nauwelaerts
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven, Belgium
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Herdewijn P, Juliano R. Nucleic acids with a six-membered carbohydrate mimic and RNA interference. Blood Cells Mol Dis 2007; 38:100-1. [PMID: 17208470 DOI: 10.1016/j.bcmd.2006.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 10/24/2006] [Indexed: 11/19/2022]
Abstract
Cyclohexenyl nucleic acids and altritol nucleic acids were evaluated as RNA modifications in an siRNA experiment targeting the P-glycoprotein expression. Both modified oligonucleotides are well accepted as RNA mimics leading to an increase in potency and duration of action of the gene-silencing effect.
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Affiliation(s)
- Piet Herdewijn
- The Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
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Herdewijn P. The interplay between antiviral activity, oligonucleotide hybridisation and nucleic acids incorporation studies. Antiviral Res 2006; 71:317-21. [PMID: 16690140 DOI: 10.1016/j.antiviral.2006.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 04/04/2006] [Accepted: 04/04/2006] [Indexed: 11/22/2022]
Abstract
Nucleoside analogues have been the most successful antiviral compounds. Likewise, they are the most intriguing antiviral compounds, because of their structural relationship to natural nucleosides. This is also the reason why the design process of a potential selective antiviral nucleoside is so difficult. Too many natural processes (from cellular uptake to DNA incorporation) and too many enzymes are involved in their biological effect (activity/toxicity/catabolism/anabolism) to make the design process readily predictable. The relationship between the physicochemical and biochemical properties of nucleoside analogues and their antiviral activity is very complex and could only be understood on a very long term basis. Here we try to explain some of the reasoning that was made during the design process leading to new potent antivirals with a phosphonate functionality.
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Affiliation(s)
- Piet Herdewijn
- Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
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Kempeneers V, Renders M, Froeyen M, Herdewijn P. Investigation of the DNA-dependent cyclohexenyl nucleic acid polymerization and the cyclohexenyl nucleic acid-dependent DNA polymerization. Nucleic Acids Res 2005; 33:3828-36. [PMID: 16027107 PMCID: PMC1175020 DOI: 10.1093/nar/gki695] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Revised: 05/27/2005] [Accepted: 06/17/2005] [Indexed: 11/26/2022] Open
Abstract
DNA polymerases from different evolutionary families [Vent (exo-) DNA polymerase from the B-family polymerases, Taq DNA polymerase from the A-family polymerases and HIV reverse transcriptase from the reverse transcriptase family] were examined for their ability to incorporate the sugar-modified cyclohexenyl nucleoside triphosphates. All enzymes were able to use the cyclohexenyl nucleotides as a substrate. Using Vent (exo-) DNA polymerase and HIV reverse transcriptase, we were even able to incorporate seven consecutive cyclohexenyl nucleotides. Using a cyclohexenyl nucleic acid (CeNA) template, all enzymes tested were also able to synthesize a short DNA fragment. Since the DNA-dependent CeNA polymerization and the CeNA-dependent DNA polymerization is possible to a limited extend, we suggest CeNA as an ideal candidate to use in directed evolution methods for the development of a polymerase capable of replicating CeNA.
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Affiliation(s)
- Veerle Kempeneers
- Laboratory for Medicinal Chemistry, Rega Institute for Medical ResearchMinderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Marleen Renders
- Laboratory for Medicinal Chemistry, Rega Institute for Medical ResearchMinderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Matheus Froeyen
- Laboratory for Medicinal Chemistry, Rega Institute for Medical ResearchMinderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Piet Herdewijn
- Laboratory for Medicinal Chemistry, Rega Institute for Medical ResearchMinderbroedersstraat 10, B-3000 Leuven, Belgium
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