1
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Funai T, Adachi N, Aotani M, Wada SI, Urata H. Effects of metal ions on thermal stabilities of DNA duplexes containing homo- and heterochiral mismatched base pairs: comparison of internal and terminal substitutions. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:310-321. [PMID: 31514571 DOI: 10.1080/15257770.2019.1658116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The effects of metal ions on the stabilities of duplexes containing a D-homochiral and heterochiral mismatched base pairs were studied. In some duplexes containing an internal mismatched base pair, significant stabilization by HgII and AgI ions was observed. While, in duplexes containing a terminal mismatched base pair, only the duplexes containing T-T and LT-T mispairs were significantly stabilized by HgII ions, and the stabilities of the duplexes containing T-T and LT-T mispairs exceeded those of the corresponding homochiral matched duplex. The results suggest that the formation of homo- and heterochiral T-HgII-T base pairs at duplex termini would be useful for the thermal and enzymatic stabilization of DNA-based nanodevice.
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Affiliation(s)
- Tatsuya Funai
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Nahomi Adachi
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Megumi Aotani
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Shun-Ichi Wada
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
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2
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Gore BS, Lee CC, Lee J, Wang J. Copper‐Catalyzed Synthesis of Substituted 4‐Quinolones using Water as a Benign Reaction Media: Application for the Construction of Oxolinic Acid and BQCA. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900286] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Babasaheb Sopan Gore
- Department of Medicinal and Applied ChemistryKaohsiung Medical University No. 100, Shih-Chuan 1st Rd, Sanmin district Kaohsiung City 807 Taiwan
| | - Chein Chung Lee
- Department of Medicinal and Applied ChemistryKaohsiung Medical University No. 100, Shih-Chuan 1st Rd, Sanmin district Kaohsiung City 807 Taiwan
| | - Jessica Lee
- Department of Medicinal and Applied ChemistryKaohsiung Medical University No. 100, Shih-Chuan 1st Rd, Sanmin district Kaohsiung City 807 Taiwan
| | - Jeh‐Jeng Wang
- Department of Medicinal and Applied ChemistryKaohsiung Medical University No. 100, Shih-Chuan 1st Rd, Sanmin district Kaohsiung City 807 Taiwan
- Department of Medical ResearchKaohsiung Medical University Hospital No. 100, Tzyou 1st Rd, Sanmin District Kaohsiung City 807 Taiwan
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3
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Saladino R, Šponer JE, Šponer J, Di Mauro E. Rewarming the Primordial Soup: Revisitations and Rediscoveries in Prebiotic Chemistry. Chembiochem 2018; 19:22-25. [PMID: 29164768 PMCID: PMC5768021 DOI: 10.1002/cbic.201700534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Indexed: 01/11/2023]
Abstract
A short history of Campbell's primordial soup: In this essay we try to disclose some of the historical connections between the studies that have contributed to our current understanding of the emergence of catalytic RNA molecules and their components from an inanimate matter.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento di Scienze Ecologiche e BiologicheUniversità della TusciaVia San Camillo De Lellis01100ViterboItaly
| | - Judit E. Šponer
- Institute of Biophysics of the Czech Academy of SciencesKrálovopolská 13561265BrnoCzech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of SciencesKrálovopolská 13561265BrnoCzech Republic
| | - Ernesto Di Mauro
- Dipartimento di Scienze Ecologiche e BiologicheUniversità della TusciaVia San Camillo De Lellis01100ViterboItaly
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4
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Muttach F, Muthmann N, Rentmeister A. Synthetic mRNA capping. Beilstein J Org Chem 2017; 13:2819-2832. [PMID: 30018667 PMCID: PMC5753152 DOI: 10.3762/bjoc.13.274] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 12/04/2017] [Indexed: 12/25/2022] Open
Abstract
Eukaryotic mRNA with its 5'-cap is of central importance for the cell. Many studies involving mRNA require reliable preparation and modification of 5'-capped RNAs. Depending on the length of the desired capped RNA, chemical or enzymatic preparation - or a combination of both - can be advantageous. We review state-of-the art methods and give directions for choosing the appropriate approach. We also discuss the preparation and properties of mRNAs with non-natural caps providing novel features such as improved stability or enhanced translational efficiency.
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Affiliation(s)
- Fabian Muttach
- University of Münster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
| | - Nils Muthmann
- University of Münster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
| | - Andrea Rentmeister
- University of Münster, Department of Chemistry, Institute of Biochemistry, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC1003-CiM), University of Münster, Germany
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5
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Costanzo G, Giorgi A, Scipioni A, Timperio AM, Mancone C, Tripodi M, Kapralov M, Krasavin E, Kruse H, Šponer J, Šponer JE, Ranc V, Otyepka M, Pino S, Di Mauro E. Nonenzymatic Oligomerization of 3',5'-Cyclic CMP Induced by Proton and UV Irradiation Hints at a Nonfastidious Origin of RNA. Chembiochem 2017; 18:1535-1543. [PMID: 28471098 DOI: 10.1002/cbic.201700122] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Indexed: 12/25/2022]
Abstract
We report that 3',5'-cyclic CMP undergoes nonenzymatic di- and trimerization at 20 °C under dry conditions upon proton or UV irradiation. The reaction involves stacking of the cyclic monomers and subsequent polymerization through serial transphosphorylations between the stacked monomers. Proton- and UV-induced oligomerization of 3',5'-cyclic CMP demonstrates that pyrimidines-similar to purines-might also have taken part in the spontaneous generation of RNA under plausible prebiotic conditions as well as in an extraterrestrial context. The observed polymerization of naturally occurring 3',5'-cyclic nucleotides supports the possibility that the extant genetic nucleic acids might have originated by way of a straight Occamian path, starting from simple reactions between plausibly preactivated monomers.
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Affiliation(s)
- Giovanna Costanzo
- Istituto di Biologia e Patologia Molecolari, CNR, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Alessandra Giorgi
- Dipartimento di Scienze Biochimiche, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Anita Scipioni
- Dipartimento di Chimica, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Anna Maria Timperio
- Department of Ecology and Biology, "La Tuscia" University, Viale dell'Università snc, 01100, Viterbo, Italy
| | - Carmine Mancone
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Via Regina Elena 324, 00161, Roma, Italy.,National Institute for Infectious Diseases "L. Spallanzani", IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Marco Tripodi
- Department of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Via Regina Elena 324, 00161, Roma, Italy.,National Institute for Infectious Diseases "L. Spallanzani", IRCCS, Via Portuense 292, 00149, Rome, Italy
| | - Michail Kapralov
- Joint Institute for Nuclear Research, Laboratory of Radiation Biology, 141980, Dubna, Russia
| | - Eugene Krasavin
- Joint Institute for Nuclear Research, Laboratory of Radiation Biology, 141980, Dubna, Russia
| | - Holger Kruse
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu, 771 46, Olomouc, Czech Republic
| | - Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Václav Ranc
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu, 771 46, Olomouc, Czech Republic
| | - Samanta Pino
- Department of Biology and Biotechnology, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Ernesto Di Mauro
- Department of Biology and Biotechnology, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
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6
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Non-Enzymatic Oligomerization of 3', 5' Cyclic AMP. PLoS One 2016; 11:e0165723. [PMID: 27802310 PMCID: PMC5089550 DOI: 10.1371/journal.pone.0165723] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/17/2016] [Indexed: 11/19/2022] Open
Abstract
Recent studies illustrate that short oligonucleotide sequences can be easily produced from nucleotide precursors in a template-free non-enzymatic way under dehydrating conditions, i.e. using essentially dry materials. Here we report that 3',5' cyclic AMP may also serve as a substrate of the reaction, which proceeds under moderate conditions yet with a lower efficiency than the previously reported oligomerization of 3',5' cyclic GMP. Optimally the oligomerization requires (i) a temperature of 80°C, (ii) a neutral to alkaline environment and (iii) a time on the order of weeks. Differences in the yield and required reaction conditions of the oligomerizations utilizing 3',5' cGMP and cAMP are discussed in terms of the crystal structures of the compounds. Polymerization of 3',5' cyclic nucleotides, whose paramount relevance in a prebiotic chemistry context has been widely accepted for decades, supports the possibility that the origin of extant genetic materials might have followed a direct uninterrupted path since its very beginning, starting from non-elaborately pre-activated monomer compounds and simple reactions.
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7
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Vollmer S, Richert C. Effect of preorganization on the affinity of synthetic DNA binding motifs for nucleotide ligands. Org Biomol Chem 2015; 13:5734-42. [PMID: 25902412 DOI: 10.1039/c5ob00508f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Triplexes with a gap in the purine strand have been shown to bind adenosine or guanosine derivatives through a combination of Watson-Crick and Hoogsteen base pairing. Rigidifying the binding site should be advantageous for affinity. Here we report that clamps delimiting the binding site have a modest effect on affinity, while bridging the gap of the purine strand can strongly increase affinity for ATP, cAMP, and FAD. The lowest dissociation constants were measured for two-strand triple helical motifs with a propylene bridge or an abasic nucleoside analog, with Kd values as low as 30 nM for cAMP in the latter case. Taken together, our data suggest that improving preorganization through covalent bridges increases the affinity for nucleotide ligands. But, a bulky bridge may also block one of two alternative binding modes for the adenine base. The results may help to design new receptors, switches, or storage motifs for purine-containing ligands.
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Affiliation(s)
- S Vollmer
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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8
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Gerlach C, Claasen B, Richert C. High-fidelity recognition of RNA: solution structure of a DNA:RNA hybrid duplex with a molecular cap. Chembiochem 2014; 15:2584-9. [PMID: 25318665 DOI: 10.1002/cbic.201402409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Indexed: 11/08/2022]
Abstract
Binding RNA targets, such as microRNAs, with high fidelity is challenging, particularly when the nucleobases to be bound are located at the terminus of the duplex between probe and target. Recently, a peptidyl chain terminating in a quinolone, called ogOA, was shown to act as a cap that enhances affinity and fidelity for RNAs, stabilizing duplexes with Watson-Crick pairing at their termini. Here we report the three-dimensional structure of an intramolecular complex between a DNA strand featuring the ogOA cap and an RNA segment, solved by NMR and restrained torsion angle molecular dynamics. The quinolone stacks on the terminal base pair of the hybrid duplex, positioned by the peptidyl chain, whose prolinol residue induces a sharp bend between the 5' terminus of the DNA chain and the glycine linked to the oxolinic acid residue. The structure explains why canonical base pairing is favored over hard-to-suppress mismatched base combinations, such as T:G and A:A, and helps to design improved high-fidelity probes for RNA.
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Affiliation(s)
- Claudia Gerlach
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
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9
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Marzenell P, Hagen H, Blechinger J, Erfle H, Mokhir A. Terminally modified, short phosphorothioate oligonucleotides as inhibitors of gene expression in cells. Bioorg Med Chem Lett 2014; 24:4694-4698. [PMID: 25176331 DOI: 10.1016/j.bmcl.2014.08.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 08/08/2014] [Accepted: 08/09/2014] [Indexed: 11/24/2022]
Abstract
Phosphorothioates are excellent antisense inhibitors, which are active both in cells and in vivo. Since their affinity to complementary ribonucleic acids is rather low, long strands (⩾20-mers) are typically required to achieve the desired biological activity. However, mismatch discrimination of long inhibitors is reduced. In contrast, shorter phosphorothioates exhibit better sequence specificity, but have in most cases too low affinity for practical applications in cells. We screened a range of terminal modifiers of a 14-mer phosphorothioate sequence, which is complementary to mRNA of a representative gene, whose protein product is fluorescent (DsRed2) and easy to monitor in cells. We found that optimal combinations of 5'- and 3'-modifications include 5'-trimethoxystilbene with 3'-uracil(anthraquinone)-cap, 5'-chloic acid derivative with 3'-uracyl(anthraquinone)-cap and 5'-cholic acid derivative with three 3'-LNA moieties. In contrast to the LNA, stabilizing and activity-enhancing effects of other mentioned modifiers for PTO/RNA duplexes have not been previously reported. We observed that the 14-mer inhibitor carrying 5'-cholic acid derivative with three 3'-LNA moieties inhibits expression of DsRed2 in cells stronger than the unmodified 21-mer. Mismatch discrimination of this inhibitor was found to be comparable to that of the unmodified 14-mer.
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Affiliation(s)
- Paul Marzenell
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Organic Chemistry II, Henkestr. 42, 91054 Erlangen, Germany; Ruprecht-Karls University of Heidelberg, Institute of Inorganic Chemistry, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Helen Hagen
- Ruprecht-Karls University of Heidelberg, Institute of Inorganic Chemistry, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Jenny Blechinger
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Organic Chemistry II, Henkestr. 42, 91054 Erlangen, Germany
| | - Holger Erfle
- Ruprecht-Karls University of Heidelberg, BioQuant, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Andriy Mokhir
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Organic Chemistry II, Henkestr. 42, 91054 Erlangen, Germany
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10
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Haug R, Kramer M, Richert C. Three-pronged probes: high-affinity DNA binding with cap, β-alanines and oligopyrrolamides. Chemistry 2014; 19:15822-6. [PMID: 24222391 DOI: 10.1002/chem.201302972] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Rüdiger Haug
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany), Fax: (+49) 711-685-64321
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11
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Blechinger J, Pieper H, Marzenell P, Kovbasyuk L, Serva A, Starkuviene V, Erfle H, Mokhir A. Short, terminally modified 2'-OMe RNAs as inhibitors of microRNA. Chem Commun (Camb) 2014; 49:7397-9. [PMID: 23863995 DOI: 10.1039/c3cc43174f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We applied 14-mer 2'-OMe RNAs as inhibitors of selected micro RNAs. To improve their properties, we introduced a trimethoxystilbene residue at the 5'-terminus and three 2'-fluoro-2'-deoxynucleotides at the 3'-terminus to obtain potent inhibitors, whose mismatch discrimination is substantially better than that of typically applied >18-mers.
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Affiliation(s)
- Jenny Blechinger
- Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nuremberg, Henkestr. 42, 91054 Erlangen, Germany
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12
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Egetenmeyer S, Richert C. Synthesis of oligodeoxynucleotides with 5'-caps binding RNA targets. ACTA ACUST UNITED AC 2013; Chapter 4:Unit4.53. [PMID: 23255203 DOI: 10.1002/0471142700.nc0453s51] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protocols for the synthesis of oligodeoxynucleotides with a short peptidyl substituent linked to the 5'-O-terminus through a phosphodiester bond are presented. The example given is a peptidyl cap consisting of the residues of L-prolinol, glycine, and the acyl residue of oxolinic acid. DNA probes with this cap, also known as ogOA cap, give melting point increases for duplexes with RNA targets and improve mismatch discrimination at the terminus. The cap is either introduced in one step, using a newly developed phosphoramidite reagent, or assembled on the DNA chain. The step-wise assembly of the peptidyl chain is advantageous for combinatorial studies aimed at the optimization of a cap structure. The block coupling method, introducing the preassembled cap in one step, is attractive for routine use of a cap already optimized for a given application. Cap-bearing probes can increase fidelity of hybridization in a genomic context. They can be synthesized by automated DNA synthesis.
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Affiliation(s)
- Simone Egetenmeyer
- Institute for Organic Chemistry, University of Stuttgart, Stuttgart, Germany
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13
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Said H, Schüller VJ, Eber FJ, Wege C, Liedl T, Richert C. M1.3--a small scaffold for DNA origami . NANOSCALE 2013; 5:284-90. [PMID: 23160434 DOI: 10.1039/c2nr32393a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The DNA origami method produces programmable nanoscale objects that form when one long scaffold strand hybridizes to numerous oligonucleotide staple strands. One scaffold strand is dominating the field: M13mp18, a bacteriophage-derived vector 7249 nucleotides in length. The full-length M13 is typically folded by using over 200 staple oligonucleotides. Here we report the convenient preparation of a 704 nt fragment dubbed "M1.3" as a linear or cyclic scaffold and the assembly of small origami structures with just 15-24 staple strands. A typical M1.3 origami is large enough to be visualized by TEM, but small enough to show a cooperativity in its assembly and thermal denaturation that is reminiscent of oligonucleotide duplexes. Due to its medium size, M1.3 origami with globally modified staples is affordable. As a proof of principle, two origami structures with globally 5'-capped staples were prepared and were shown to give higher UV-melting points than the corresponding assembly with unmodified DNA. M1.3 has the size of a gene, not a genome, and may function as a model for gene-based nanostructures. Small origami with M1.3 as a scaffold may serve as a workbench for chemical, physical, and biological experiments.
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Affiliation(s)
- Hassan Said
- Institute for Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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14
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Biophysical and RNA Interference Inhibitory Properties of Oligonucleotides Carrying Tetrathiafulvalene Groups at Terminal Positions. J CHEM-NY 2013. [DOI: 10.1155/2013/650610] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Oligonucleotide conjugates carrying a single functionalized tetrathiafulvalene (TTF) unit linked through a threoninol molecule to the 3′ or 5′ ends were synthesized together with their complementary oligonucleotides carrying a TTF, pyrene, or pentafluorophenyl group. TTF-oligonucleotide conjugates formed duplexes with higher thermal stability than the corresponding unmodified oligonucleotides and pyrene- and pentafluorophenyl-modified oligonucleotides. TTF-modified oligonucleotides are able to bind to citrate-stabilized gold nanoparticles (AuNPs) and produce stable gold AuNPs functionalized with oligonucleotides. Finally, TTF-oligoribonucleotides have been synthesized to produce siRNA duplexes carrying TTF units. The presence of the TTF molecule is compatible with the RNA interference mechanism for gene inhibition.
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15
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Vogel H, Richert C. Labeling Small RNAs through Chemical Ligation at the 5′ Terminus: Enzyme-Free or Combined with Enzymatic 3′-Labeling. Chembiochem 2012; 13:1474-82. [DOI: 10.1002/cbic.201200214] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Indexed: 01/01/2023]
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16
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Sargsyan G, Balaz M. Porphyrin-DNA conjugates: porphyrin induced adenine-guanine homoduplex stabilization and interduplex assemblies. Org Biomol Chem 2012; 10:5533-40. [PMID: 22692698 DOI: 10.1039/c2ob25710f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
DNA has found widespread uses as a nanosized scaffold for assembly of patterned multichomophoric nanostructures. Herein we report the synthesis, self-assembly, stability, and spectroscopic studies of short alternating non-self-complementary DNA sequences 5'-(dGdA)(4) and 5'-(dAdG)(4) with non-charged tetraarylporphyrins covalently linked to the 5' position of deoxyadenosine or deoxyguanosine via a phosphate or amide linker. The linker, the metal in the porphyrin coordination center, and the neighboring nucleobase have very distinct effects on the duplex formation of porphyrin-deoxyguanosine-deoxyadenosine oligodeoxynucleotides. At ionic strength between 5 mM and 40 mM, free base trispyridylphenylporphyrin appended to the 5' termini of 5'-(dAdG)(4) oligonucleotide via short non-polar amide linker served as a hydrophobic molecular cap inducing deoxyadenosine-deoxyguanosine antiparallel homoduplex. At ionic strength of ≥60 mM, the free base porphyrin functioned as a molecular 'glue' and induced the formation of porphyrin-DNA inter-homoduplex assemblies with characteristic tetrasignate CD Cotton effects in the porphyrin Soret band region. When the porphyrin cap was covalently attached to 5' position of deoxyguanosine or deoxyadenosine via charged phosphate linker, no significant deoxyadenosine-deoxyguanosine hybridization was observed even at elevated ionic strengths.
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Affiliation(s)
- Gevorg Sargsyan
- Department of Chemistry, University of Wyoming, 1000 E. University ave., Laramie, WY 82071, USA
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17
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Lucas R, Vengut-Climent E, Gómez-Pinto I, Aviñó A, Eritja R, González C, Morales JC. Apolar carbohydrates as DNA capping agents. Chem Commun (Camb) 2012; 48:2991-3. [PMID: 22314313 DOI: 10.1039/c2cc17093k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mono- and disaccharides have been shown to stack on top of DNA duplexes stabilizing sequences with terminal C-G base pairs. Here we present an apolar version of glucose and cellobiose as new capping agents that stack on DNA increasing considerably its stability with respect to their natural polyhydroxylated mono- and disaccharide DNA conjugates.
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Affiliation(s)
- Ricardo Lucas
- Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla, Americo Vespucio, 49, 41092 Sevilla, Spain
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