1
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Eyberg J, Göhringer D, Salihovic A, Richert C. Acid‐Stable Nucleobase Protection for a Strongly Pairing Pyridone C‐Nucleoside Suitable for Solid‐Phase Synthesis of Oligonucleotides. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Amila Salihovic
- University of Stuttgart: Universitat Stuttgart Chemistry GERMANY
| | - Clemens Richert
- Universität Stuttgart Institut für Organische Chemie Pfaffenwaldring 55 70569 Stuttgart GERMANY
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2
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Svehlova K, Lukšan O, Jakubec M, Curtis EA. Supernova: A Deoxyribozyme that Catalyzes a Chemiluminescent Reaction. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202109347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Katerina Svehlova
- Institute of Organic Chemistry and Biochemistry ASCR Prague Czech Republic
- Faculty of Science Charles University in Prague Prague Czech Republic
| | - Ondřej Lukšan
- Institute of Organic Chemistry and Biochemistry ASCR Prague Czech Republic
| | - Martin Jakubec
- Institute of Organic Chemistry and Biochemistry ASCR Prague Czech Republic
- Faculty of Science Charles University in Prague Prague Czech Republic
| | - Edward A. Curtis
- Institute of Organic Chemistry and Biochemistry ASCR Prague Czech Republic
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3
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Fàbrega C, Aviñó A, Eritja R. Chemical Modifications in Nucleic Acids for Therapeutic and Diagnostic Applications. CHEM REC 2021; 22:e202100270. [DOI: 10.1002/tcr.202100270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Carme Fàbrega
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
| | - Anna Aviñó
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
| | - Ramon Eritja
- Department of Surfactants and Nanobiotechnology Institute for Advanced Chemistry of Catalonia (IQAC) Spanish National Research Council (CSIC) Jordi Girona 18–26 E-08034 Barcelona Spain
- Networking Center on Bioengineering Biomaterials and Nanomedicine (CIBER-BBN) E-08034 Barcelona Spain
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4
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Svehlova K, Lukšan O, Jakubec M, Curtis EA. Supernova: A Deoxyribozyme that Catalyzes a Chemiluminescent Reaction. Angew Chem Int Ed Engl 2021; 61:e202109347. [PMID: 34559935 PMCID: PMC9298802 DOI: 10.1002/anie.202109347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/17/2021] [Indexed: 11/10/2022]
Abstract
Functional DNA molecules are useful components in nanotechnology and synthetic biology. To expand the toolkit of functional DNA parts, in this study we used artificial evolution to identify a glowing deoxyribozyme called Supernova. This deoxyribozyme transfers a phosphate from a 1,2-dioxetane substrate to its 5' hydroxyl group, which triggers a chemiluminescent reaction and a flash of blue light. An engineered version of Supernova is only catalytically active in the presence of an oligonucleotide complementary to its 3' end, demonstrating that light production can be coupled to ligand binding. We anticipate that Supernova will be useful in a wide variety of applications, including as a signaling component in allosterically regulated sensors and in logic gates of molecular computers.
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Affiliation(s)
- Katerina Svehlova
- Institute of Organic Chemistry and Biochemistry ASCR, Prague, Czech Republic.,Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Ondřej Lukšan
- Institute of Organic Chemistry and Biochemistry ASCR, Prague, Czech Republic
| | - Martin Jakubec
- Institute of Organic Chemistry and Biochemistry ASCR, Prague, Czech Republic.,Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Edward A Curtis
- Institute of Organic Chemistry and Biochemistry ASCR, Prague, Czech Republic
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5
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Guo X, Leonard P, Ingale SA, Liu J, Mei H, Sieg M, Seela F. 5-Aza-7-deaza-2'-deoxyguanosine and 2'-Deoxycytidine Form Programmable Silver-Mediated Base Pairs with Metal Ions in the Core of the DNA Double Helix. Chemistry 2018; 24:8883-8892. [PMID: 29573347 DOI: 10.1002/chem.201801273] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Indexed: 02/05/2023]
Abstract
5-Aza-7-deaza-2'-deoxyguanosine (dZ) forms a silver-mediated base pair with dC. The metal ion pair represents a mimic of the H-bonded Watson-Crick dG-dC pair. The modified nucleoside displays a similar shape as the parent 2'-deoxyguanosine from which it can be constructed by transposition of nitrogen-7 to the bridgehead position-5. It lacks the major groove binding site as the positional change moves the dG- acceptor position from nitrogen-7 to nitrogen-1. As a shape mimic of dG, it fits nicely in the DNA double helix. The purine-pyrimidine dZ-dC hetero pair shows a relationship to the pyrimidine-pyrimidine dC-dC homo base pair. The dZ-dC pair forms a mismatch in the absence of silver ions and matches after addition of metal ions. Base-pair formation was verified on self-complementary 6-mer duplexes and 12-mer DNA with random composition by UV-dependent Tm measurements. Modified silver-mediated and hydrogen-bonded canonical base pairs can coexist. The dZ-Ag+ -dC base pair is slightly less stable than the dG-dC pair, shows sequence dependence, and consumes one or two silver ions. These properties make the dZ-Ag+ -dC pair suitable for programmable incorporation of silver ions in DNA which cannot be achieved by canonical base pairs. If the silver ion content is higher than the total number of base pairs the duplexes turn into very stable structures in which all base pairs are considered to be in the silver-mediated pairing mode.
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Affiliation(s)
- Xiurong Guo
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Jiang Liu
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,State Key Laboratory of Oral Diseases and National Clinical, Research Center for Oral Diseases and Department of Oral Medicine, of West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Martha Sieg
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
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6
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Ukale DU, Lönnberg T. Triplex Formation by Oligonucleotides Containing Organomercurated Base Moieties. Chembiochem 2018; 19:1096-1101. [PMID: 29575511 DOI: 10.1002/cbic.201800112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Indexed: 12/26/2022]
Abstract
Homothymine oligonucleotides with a single 5-mercuricytosine or 5-mercuriuracil residue at their termini have been synthesized and their capacity to form triplexes has been examined with an extensive array of double-helical targets. UV and circular dichroism (CD) melting experiments revealed the formation and thermal denaturation of pyrimidine⋅purine*pyrimidine-type triple helices with all oligonucleotide combinations studied. Nearly all triplexes were destabilized upon mercuration of the 3'-terminal residue of the triplex-forming oligonucleotide, in all likelihood due to competing intramolecular HgII -mediated base pairing. Two exceptions from this general pattern were, however, observed: 5-mercuricytosine was stabilizing when placed opposite to a T⋅A or A⋅T base pair. The stabilization was further amplified in the presence of 2-mercaptoethanol (but not hexanethiol, thiophenol or cysteine), suggesting a stabilizing interaction other than HgII -mediated base pairing.
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Affiliation(s)
| | - Tuomas Lönnberg
- University of Turku, Department of Chemistry, Vatselankatu 2, 20014, Turku, Finland
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7
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Hagedorn PH, Persson R, Funder ED, Albæk N, Diemer SL, Hansen DJ, Møller MR, Papargyri N, Christiansen H, Hansen BR, Hansen HF, Jensen MA, Koch T. Locked nucleic acid: modality, diversity, and drug discovery. Drug Discov Today 2017; 23:101-114. [PMID: 28988994 DOI: 10.1016/j.drudis.2017.09.018] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/01/2017] [Accepted: 09/27/2017] [Indexed: 01/05/2023]
Abstract
Over the past 20 years, the field of RNA-targeted therapeutics has advanced based on discoveries of modified oligonucleotide chemistries, and an ever-increasing understanding of how to apply cellular assays to identify oligonucleotides with improved pharmacological properties in vivo. Locked nucleic acid (LNA), which exhibits high binding affinity and potency, is widely used for this purpose. Our understanding of RNA biology has also expanded tremendously, resulting in new approaches to engage RNA as a therapeutic target. Recent observations indicate that each oligonucleotide is a unique entity, and small structural differences between oligonucleotides can often lead to substantial differences in their pharmacological properties. Here, we outline new principles for drug discovery exploiting oligonucleotide diversity to identify rare molecules with unique pharmacological properties.
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Affiliation(s)
- Peter H Hagedorn
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Robert Persson
- Pharmaceutical Sciences, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Erik D Funder
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Nanna Albæk
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Sanna L Diemer
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Dennis J Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Marianne R Møller
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Natalia Papargyri
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Helle Christiansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Bo R Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Henrik F Hansen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Mads A Jensen
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Troels Koch
- Therapeutic Modalities, Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark.
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8
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Okamura H, Taniguchi Y, Sasaki S. Aminopyridinyl-Pseudodeoxycytidine Derivatives Selectively Stabilize Antiparallel Triplex DNA with Multiple CG Inversion Sites. Angew Chem Int Ed Engl 2016; 55:12445-9. [DOI: 10.1002/anie.201606136] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/12/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Hidenori Okamura
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
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9
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Okamura H, Taniguchi Y, Sasaki S. Aminopyridinyl-Pseudodeoxycytidine Derivatives Selectively Stabilize Antiparallel Triplex DNA with Multiple CG Inversion Sites. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606136] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Hidenori Okamura
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences; Kyushu University; 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
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10
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Ma DL, Wang W, Mao Z, Kang TS, Han QB, Chan PWH, Leung CH. Utilization of G-Quadruplex-Forming Aptamers for the Construction of Luminescence Sensing Platforms. Chempluschem 2016; 82:8-17. [DOI: 10.1002/cplu.201600036] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/07/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry; Hong Kong Baptist University; 224 Waterloo Road, Kowloon Tong Hong Kong 852 P. R. China
| | - Wanhe Wang
- Department of Chemistry; Hong Kong Baptist University; 224 Waterloo Road, Kowloon Tong Hong Kong 852 P. R. China
| | - Zhifeng Mao
- Department of Chemistry; Hong Kong Baptist University; 224 Waterloo Road, Kowloon Tong Hong Kong 852 P. R. China
| | - Tian-Shu Kang
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences; University of Macau; Macao 999078 P. R. China
| | - Quan-Bin Han
- School of Chinese Medicine; Hong Kong Baptist University; Kowloon Hong Kong 852 P. R. China
| | - Philip Wai Hong Chan
- School of Chemistry; Monash University; Clayton VIC 3800 Australia
- Department of Chemistry; University of Warwick; Coventry CV4 7AL United Kingdom
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine; Institute of Chinese Medical Sciences; University of Macau; Macao 999078 P. R. China
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11
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Wirth-Hamdoune D, Ullrich S, Scheffer U, Radanović T, Dürner G, Göbel MW. A Bis(guanidinium)alcohol Attached to a Hairpin Polyamide: Synthesis, DNA Binding, and Plasmid Cleavage. Chembiochem 2016; 17:506-14. [DOI: 10.1002/cbic.201500566] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 01/20/2023]
Affiliation(s)
- Daniela Wirth-Hamdoune
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Stefan Ullrich
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Ute Scheffer
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Toni Radanović
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Gerd Dürner
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
| | - Michael W. Göbel
- Institut für Organische Chemie und Chemische Biologie; Johann Wolfgang Goethe-Universität Frankfurt; Max-von-Laue-Strasse 7 60438 Frankfurt am Main Germany
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12
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Marušič M, Plavec J. The Effect of DNA Sequence Directionality on G-Quadruplex Folding. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505348] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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13
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Marušič M, Plavec J. The Effect of DNA Sequence Directionality on G‐Quadruplex Folding. Angew Chem Int Ed Engl 2015; 54:11716-9. [DOI: 10.1002/anie.201505348] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/20/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Maja Marušič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana (Slovenia)
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana (Slovenia)
- EN‐FIST Center of Excellence, 1000 Ljubljana (Slovenia)
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana (Slovenia)
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14
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Aiba Y, Honda Y, Komiyama M. Promotion of double-duplex invasion of peptide nucleic acids through conjugation with nuclear localization signal peptide. Chemistry 2015; 21:4021-6. [PMID: 25640012 DOI: 10.1002/chem.201406085] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 11/10/2022]
Abstract
Pseudo-complementary peptide nucleic acid (pcPNA), as one of the most widely used synthetic DNA analogues, invades double-stranded DNA according to Watson-Crick rules to form invasion complexes. This unique mode of DNA recognition induces structural changes at the invasion site and can be used for a range of applications. In this paper, pcPNA is conjugated with a nuclear localization signal (NLS) peptide, and its invading activity is notably promoted both thermodynamically and kinetically. Thus, the double-duplex invasion complex is formed promptly at low pcPNA concentrations under high salt conditions, where the invasion otherwise never occurs. Furthermore, NLS-modified pcPNA is successfully employed for site-selective DNA scission, and the targeted DNA is selectively cleaved under conditions that are not conducive for DNA cutters using unmodified pcPNAs. This strategy of pcPNA modification is expected to be advantageous and promising for a range of in vitro and in vivo applications.
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Affiliation(s)
- Yuichiro Aiba
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8577 (Japan); Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Present address: Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041 (USA)
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15
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Gyssels E, Carrette LLG, Vercruysse E, Stevens K, Madder A. Triplex crosslinking through furan oxidation requires perturbation of the structured triple-helix. Chembiochem 2015; 16:651-8. [PMID: 25630588 DOI: 10.1002/cbic.201402602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Indexed: 01/08/2023]
Abstract
Short oligonucleotides can selectively recognize duplexes by binding in the major groove thereby forming triplexes. Based on the success of our recently developed strategy for furan-based crosslinking in DNA duplexes, we here investigated for the first time the use of the furan-oxidation crosslink methodology for the covalent locking of triplex structures by an interstrand crosslink. It was shown that in a triplex context, although crosslinking yields are surprisingly low (to nonexistent) when targeting fully complementary duplexes, selective crosslinking can be achieved towards mismatched duplex sites at the interface of triplex to duplex structures. We show the promising potential of furan-containing probes for the selective detection of single-stranded regions within nucleic acids containing a variety of structural motifs.
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Affiliation(s)
- Ellen Gyssels
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4, 9000 Gent (Belgium)
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16
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Okamura H, Taniguchi Y, Sasaki S. An Isocytidine Derivative with a 2-Amino-6-methylpyridine Unit for Selective Recognition of the CG Interrupting Site in an Antiparallel Triplex DNA. Chembiochem 2014; 15:2374-8. [DOI: 10.1002/cbic.201402328] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Indexed: 11/11/2022]
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17
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Kröner C, Thunemann M, Vollmer S, Kinzer M, Feil R, Richert C. Endless: a purine-binding RNA motif that can be expressed in cells. Angew Chem Int Ed Engl 2014; 53:9198-202. [PMID: 25045108 DOI: 10.1002/anie.201403579] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 04/29/2014] [Indexed: 01/16/2023]
Abstract
It is becoming increasingly clear that nature uses RNAs extensively for regulating vital functions of the cell, and short sequences are frequently used to suppress gene expression. However, controlling the concentration of small molecules intracellularly through designed RNA sequences that fold into ligand-binding structures is difficult. The development of "endless", a triplex-based folding motif that can be expressed in mammalian cells and binds the second messenger 3',5'-cyclic guanosine monophosphate (cGMP), is described. In vitro, DNA or RNA versions of endless show low micromolar to nanomolar dissociation constants for cGMP. To test its functionality in vivo, four endless RNA motifs arranged in tandem were co-expressed with a fluorescent cGMP sensor protein in murine vascular smooth muscle cells. Nitric oxide induced endogenous cGMP signals were suppressed in endless-expressing cells compared to cells expressing a control motif, which suggests that endless can act as a genetically encoded cGMP sink to modulate signal transduction in cells.
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Affiliation(s)
- Christoph Kröner
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
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18
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Kröner C, Thunemann M, Vollmer S, Kinzer M, Feil R, Richert C. Endless: A Purine-Binding RNA Motif that Can Be Expressed in Cells. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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19
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Vogel P, Stafforst T. Site-Directed RNA Editing with Antagomir Deaminases - A Tool to Study Protein and RNA Function. ChemMedChem 2014; 9:2021-5. [DOI: 10.1002/cmdc.201402139] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Indexed: 12/20/2022]
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20
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Largy E, Liu W, Hasan A, Perrin DM. A Pyrimidopyrimidine Janus-AT Nucleoside with Improved Base-Pairing Properties to both A and T within a DNA Duplex: The Stabilizing Effect of a Second Endocyclic Ring Nitrogen. Chemistry 2014; 20:1495-9. [DOI: 10.1002/chem.201303867] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Indexed: 12/18/2022]
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21
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Kröner C, Göckel A, Liu W, Richert C. Binding cofactors with triplex-based DNA motifs. Chemistry 2013; 19:15879-87. [PMID: 24194407 DOI: 10.1002/chem.201303098] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Indexed: 12/28/2022]
Abstract
Cofactors are pivotal compounds for the cell and many biotechnological processes. It is therefore interesting to ask how well cofactors can be bound by oligonucleotides designed not to convert but to store and release these biomolecules. Here we show that triplex-based DNA binding motifs can be used to bind nucleotides and cofactors, including NADH, FAD, SAM, acetyl CoA, and tetrahydrofolate (THF). Dissociation constants between 0.1 μM for SAM and 35 μM for THF were measured. A two-nucleotide gap still binds NADH. The selectivity for one ligand over the others can be changed by changing the sequence of the binding pocket. For example, a mismatch placed in one of the two triplets adjacent to the base-pairing site changes the selectivity, favoring the binding of FAD over that of ATP. Further, changing one of the two thymines of an A-binding motif to cytosine gives significant affinity for G, whereas changing the other does not. Immobilization of DNA motifs gives beads that store NADH. Exploratory experiments show that the beads release the cofactor upon warming to body temperature.
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Affiliation(s)
- Christoph Kröner
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany), Fax: (+49) 711-685-64321
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22
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Largy E, Liu W, Hasan A, Perrin DM. Base-pairing behavior of a carbocyclic Janus-AT nucleoside analogue capable of recognizing A and T within a DNA duplex. Chembiochem 2013; 14:2199-208. [PMID: 24115365 DOI: 10.1002/cbic.201300250] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Indexed: 01/18/2023]
Abstract
Janus-type nucleosides are heterocycles with two faces, each of which is designed to complement the H-bonding interactions of natural nucleosides comprising a canonical Watson-Crick base pair. By intercepting all of the hydrogen bonds contained within the base pair, oligomeric Janus nucleosides are expected to achieve sequence-specific DNA recognition through the formation of J-loops that will be more stable than D-loops, which simply replaces one base-pair with another. Herein, we report the synthesis of a novel Janus-AT nucleoside analogue, JAT , affixed on a carbocyclic analogue of deoxyribose that was converted to the corresponding phosphoramidite. A single JAT was successfully incorporated into a DNA strand by solid phase for targeting both A and T bases, and characterized through biophysical and computational methods. Experimental UV-melting and circular dichroism data demonstrated that within the context of a standard duplex, JAT associates preferentially with T over A, and much more poorly with C and G. Density functional theory calculations confirm that the JAT structure is well suited to associate only with A and T thereby highlighting the importance of the electronic structure in terms of H-bonding. Finally, molecular dynamics simulations validated the observation that JAT can substitute more effectively as an A-analogue than as a T-analogue without substantial distortion of the B-helix. Overall, this new Janus nucleotide is a promising tool for the targeting of A-T base pairs in DNA, and will lead to the development of oligo-Janus-nucleotide strands for sequence-specific DNA recognition.
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Affiliation(s)
- Eric Largy
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 (Canada)
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23
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Lee SH, Wang S, Kool ET. Templated chemistry for monitoring damage and repair directly in duplex DNA. Chem Commun (Camb) 2012; 48:8069-71. [PMID: 22782065 DOI: 10.1039/c2cc34060g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We report the fluorogenic detection of the product of base excision repair (an abasic site) in a specific sequence of duplex DNA. This is achieved by DNA-templated chemistry, employing triple helix-forming probes that contain unnatural nucleobases designed to selectively recognize the site of a missing base. Light-up signals of up to 36-fold were documented, and probes could be used to monitor enzymatic removal of a damaged base.
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Affiliation(s)
- Seoung Ho Lee
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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24
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Hari Y, Obika S, Imanishi T. Towards the Sequence-Selective Recognition of Double-Stranded DNA Containing Pyrimidine-Purine Interruptions by Triplex-Forming Oligonucleotides. European J Org Chem 2012. [DOI: 10.1002/ejoc.201101821] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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25
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Bahal R, Sahu B, Rapireddy S, Lee CM, Ly DH. Sequence-unrestricted, Watson-Crick recognition of double helical B-DNA by (R)-miniPEG-γPNAs. Chembiochem 2011; 13:56-60. [PMID: 22135012 DOI: 10.1002/cbic.201100646] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Raman Bahal
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, Pittsburgh, PA 15213, USA
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26
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Li X, Wang Y, Guo J, Tang X. Fluorescence Detection of Single-Nucleotide Polymorphism with Single-Strand Triplex-Forming DNA Probes. Chembiochem 2011; 12:2863-70. [DOI: 10.1002/cbic.201100534] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Indexed: 12/31/2022]
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27
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Biner SM, Häner R. A two-color, self-controlled molecular beacon. Chembiochem 2011; 12:2733-6. [PMID: 22076865 DOI: 10.1002/cbic.201100651] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Indexed: 12/22/2022]
Abstract
Control yourself! A two-color molecular beacon with non-nucleosidic chromophores in a triplex stem is presented. Pyrene and PDI fluorophores act as mutual quenchers by formation of a donor-acceptor complex in the closed form. Hybridization with the target results in two independent fluorescence signals. The two-color read-out provides a "self-control" feature, which helps to eliminate false positive signals in imaging and screening applications.
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Affiliation(s)
- Sarah M Biner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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28
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Stafforst T, Hilvert D. Photolyase-artige Reparatur Psoralen-quervernetzter Nucleinsäuren. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103611] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Stafforst T, Hilvert D. Photolyase-like repair of psoralen-crosslinked nucleic acids. Angew Chem Int Ed Engl 2011; 50:9483-6. [PMID: 21948450 DOI: 10.1002/anie.201103611] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Indexed: 11/08/2022]
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30
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Stafforst T, Hilvert D. Modulating PNA/DNA hybridization by light. Angew Chem Int Ed Engl 2011; 49:9998-10001. [PMID: 21089083 DOI: 10.1002/anie.201004548] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Thorsten Stafforst
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg HCI F339, 8093 Zürich, Switzerland.
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31
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Li H, Franzini RM, Bruner C, Kool ET. Templated chemistry for sequence-specific fluorogenic detection of duplex DNA. Chembiochem 2010; 11:2132-7. [PMID: 20859985 PMCID: PMC4418650 DOI: 10.1002/cbic.201000329] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Indexed: 12/25/2022]
Abstract
We describe the development of templated fluorogenic chemistry for detection of specific sequences of duplex DNA in solution. In this approach, two modified homopyrimidine oligodeoxynucleotide probes are designed to bind by triple-helix formation at adjacent positions on a specific purine-rich target sequence of duplex DNA. One fluorescein-labeled probe contains an α-azidoether linker to a fluorescence quencher; the second (trigger) probe carries a triarylphosphine group that is designed to reduce the azide and cleave the linker. The data showed that at pH 5.6 these probes yielded a strong fluorescence signal within minutes on addition to a complementary homopurine duplex DNA target. The signal increased by a factor of about 60, and was completely dependent on the presence of the target DNA. Replacement of cytosine in the probes with pseudoisocytosine allowed the templated chemistry to proceed readily at pH 7. Single nucleotide mismatches in the target oligonucleotide slowed the templated reaction considerably; this demonstrated high sequence selectivity. The use of templated fluorogenic chemistry for detection of duplex DNAs has not been previously reported and could allow detection of double-stranded DNA, at least for homopurine-homopyrimidine target sites, under native and nondenaturing conditions.
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Affiliation(s)
| | | | | | - Eric T. Kool
- Prof. Dr. E. T. Kool, H. Li, R.M. Franzini, C. Bruner, Department of Chemistry, Stanford University, Stanford, CA 94305-5080 (USA), Fax: (+1)650-725-0259,
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33
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Seela F, Jiang D, Budow S. Triplexes with 8-Aza-2'-deoxyisoguanosine replacing protonated dC: probing third strand stability with a fluorescent nucleobase targeting duplex DNA. Chembiochem 2010; 11:1443-50. [PMID: 20544775 DOI: 10.1002/cbic.201000162] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The fluorescent 8-aza-2'-deoxyisoguanosine (4) as well as the parent 2'-deoxyisoguanosine (1) were used as protonated dCH(+) surrogates in the third strand of oligonucleotide triplexes. Stable triplexes were formed by Hoogsteen base pairing. In contrast to dC, triplexes containing nucleoside 1 or 4 in place of dCH(+) are already formed under neutral conditions or even at alkaline pH values. Triplex melting can be monitored separately from duplex dissociation in cases in which the third strand contains the fluorescent nucleoside 4. Third-strand binding of oligonucleotides with 4, opposite to dG, was selective as demonstrated by hybridisation experiments studying mismatch discrimination. Third-strand binding is more efficient when the stability of the DNA duplex is reduced by mismatches, giving third-strand binding more flexibility.
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Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster Germany
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34
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Ben Gaied N, Zhao Z, Gerrard SR, Fox KR, Brown T. Potent triple helix stabilization by 5',3'-modified triplex-forming oligonucleotides. Chembiochem 2009; 10:1839-51. [PMID: 19554592 DOI: 10.1002/cbic.200900232] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Anthraquinone and pyrene analogues attached to the 3' and/or 5' termini of triplex-forming oligonucleotides (TFOs) by various linkers increased the stability of parallel triple helices. The modifications are simple to synthesize and can be introduced during standard solid-phase oligonucleotide synthesis. Potent triplex stability was achieved by using doubly modified TFOs, which in the most favourable cases gave an increase in melting temperature of 30 degrees C over the unmodified counterparts and maintained their selectivity for the correct target duplex. Such TFOs can produce triplexes with melting temperatures of 40 degrees C at pH 7 even though they do not contain any triplex-stabilizing base analogues. These studies have implications for the design of triplex-forming oligonucleotides for use in biology and nanotechnology.
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Affiliation(s)
- Nouha Ben Gaied
- School of Chemistry, University of Southampton, Highfield, SO17 1BJ, Southampton, UK
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35
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36
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Frey JA, Leist R, Müller A, Leutwyler S. Gas-Phase Watson-Crick and Hoogsteen Isomers of the Nucleobase Mimic 9-Methyladenine⋅2-Pyridone. Chemphyschem 2006; 7:1494-9. [PMID: 16755637 DOI: 10.1002/cphc.200500692] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
2-Pyridone (pyridin-2-one) is a mimic of the uracil and thymine nucleobases, with only one N--H and C==O group. It provides a single H-bonding site, compared to three for the canonical pyrimidine nucleobases. Employing the supersonically cooled 9-methyladenine2-pyridone (9MAd x 2PY) complex, which is the simplest base pair to mimic adenine-uracil or adenine-thymine, we show that its gas-phase UV spectrum consists of contributions from two isomers. Based on the H-bonding sites of 9-methyladenine, these are the Watson-Crick and Hoogsteen forms. Combining two-color two-photon ionisation (2C-R2PI), UV-UV depletion and laser-induced fluorescence spectroscopies allows separation of the two band systems, revealing characteristic intermolecular in-plane vibrations of the two isomers. The calculated S(0) and S(1) intermolecular frequencies are in good agreement with the experimental ones. Ab initio calculations predict the Watson-Crick isomer to be slightly more stable (D(0)=-16.0 kcal mol(-1)) than the Hoogsteen isomer (D(0)=-15.0 kcal mol(-1)). The calculated free energies Delta(f)G(0) of the Watson-Crick and Hoogsteen isomers agree qualitatively with the experimental isomer concentration ratio of 3:1.
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Affiliation(s)
- Jann A Frey
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
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37
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Nadal A, Coll A, Aviñó A, Esteve T, Eritja R, Pla M. Efficient Sequence‐Specific Purification of
Listeria innocua
mRNA Species by Triplex Affinity Capture with Parallel Tail‐Clamps. Chembiochem 2006; 7:1039-47. [PMID: 16729343 DOI: 10.1002/cbic.200500519] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Parallel clamps can interact in a sequence-specific manner with homopyrimidine DNA and RNA oligonucleotides to form triplexes. For longer nucleic acids, we have previously demonstrated the inhibitory effect of DNA-target secondary structures on triplex formation. We further designed a modification of these molecules-that is, tail-clamps formed by addition of a tail sequence to the parallel clamp-and proved efficient binding of the molecules with structured single-stranded DNA targets. Here we explore the possible application of the tail-clamp strategy for triplex formation with RNA targets, which are typically found as strongly folded single-stranded molecules. Efficient and specific binding of a tail-clamp designed to form a parallel triplex with Listeria innocua iap mRNA sequences has been verified by UV melting curves and triplex affinity capture techniques. Furthermore, we show for the first time the formation of stable complexes of mRNA with tail-clamps not only under acidic but also under neutral and slightly basic pH conditions. These results signify a further step towards the possible applications of triplexes with mRNA molecules; research, analytical, and therapeutic uses can be envisaged. As an example, our tail-clamp-based triplex affinity capture assay allowed the specific capture and recovery of iap mRNA molecules from an L. innocua total RNA solution with 45 % yield.
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Affiliation(s)
- Anna Nadal
- Institute of Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (Edif. Politècnica 1), Spain
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38
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López de la Osa J, González C, Gargallo R, Rueda M, Cubero E, Orozco M, Aviñó A, Eritja R. Destabilization of Quadruplex DNA by 8-Aminoguanine. Chembiochem 2005; 7:46-8. [PMID: 16292787 DOI: 10.1002/cbic.200500281] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Michel T, Debart F, Heitz F, Vasseur JJ. Highly stable DNA triplexes formed with cationic phosphoramidate pyrimidine alpha-oligonucleotides. Chembiochem 2005; 6:1254-62. [PMID: 15912553 DOI: 10.1002/cbic.200400436] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The ability of cationic phosphoramidate pyrimidine alpha-oligonucleotides (ONs) to form triplexes with DNA duplexes was investigated by UV melting experiments, circular dichroism spectroscopy and gel mobility shift experiments. Replacement of the phosphodiester linkages in alpha-ONs with positively charged phosphoramidate linkages results in more efficient triplex formation, the triplex stability increasing with the number of positive charges. At a neutral pH and in the absence of magnesium ions, it was found that a fully cationic phosphoramidate alpha-TFO (triplex-forming oligonucleotide) forms a highly stable triplex that melts at a higher temperature than the duplex target. No hysteresis between the annealing and melting curves was noticed; this indicates fast association. Moreover, the recognition of a DNA duplex with a cationic alpha-TFO through Hoogsteen base pairing is highly sequence-specific. To the best of our knowledge, this is the first report of stable triplexes in the pyrimidine motif formed by cationic alpha-oligonucleotides and duplex targets.
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Affiliation(s)
- Thibaut Michel
- LCOBS, UMR 5625 CNRS-UMII, CC 008, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
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40
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Nadal A, Eritja R, Esteve T, Pla M. "Parallel" and "antiparallel tail-clamps" increase the efficiency of triplex formation with structured DNA and RNA targets. Chembiochem 2005; 6:1034-42. [PMID: 15880676 DOI: 10.1002/cbic.200400358] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sequence-specific triple-helix structures can be formed by parallel and antiparallel DNA clamps interacting with single-stranded DNA or RNA targets. Single-stranded nucleic acid molecules are known to adopt secondary structures that might interfere with intermolecular interactions. We demonstrate the correlation between a secondary structure involving the target--a stable stem predicted by in silico folding and experimentally confirmed by thermal stability and competition analyses--and an inhibitory effect on triplex formation. We overcame structural impediments by designing a new type of clamp: "tail-clamps". A combination of gel-shift, kinetic analysis, UV thermal melting and thermodynamic techniques was used to demonstrate that tail-clamps efficiently form triple helices with a structured target sequence. The performance of parallel and antiparallel tail-clamps was compared: antiparallel tail-clamps had higher binding efficiencies than parallel tail-clamps both with structured DNA and RNA targets. In addition, the reported triplex-stabilizing property of 8-aminopurine residues was confirmed for tail-clamps. Finally, we discuss the possible use of this improved triplex technology as a new tool for applications in molecular biology.
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Affiliation(s)
- Anna Nadal
- Departament de Genètica Molecular, Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Jordi Girona 18-26, 08034 Barcelona, Spain
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41
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Kurz M, Göbel K, Hartel C, Göbel MW. Acridine-Labeled Primers as Tools for the Study of Nonenzymatic RNA Oligomerization. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19980810528] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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Tarköy M, Leumann C. Synthesis and Pairing Properties of Decanucleotides from (3′S,5′R)-2′-Deoxy-3′, 5′-ethanoβ-D-ribofuranosyladenine and -thymine. ACTA ACUST UNITED AC 2003. [DOI: 10.1002/anie.199314321] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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43
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Pljevaljcic G, Pignot M, Weinhold E. Design of a new fluorescent cofactor for DNA methyltransferases and sequence-specific labeling of DNA. J Am Chem Soc 2003; 125:3486-92. [PMID: 12643710 DOI: 10.1021/ja021106s] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sequence-specific labeling of DNA is of immense interest for analytical and functional studies of DNA. We present a novel approach for sequence-specific labeling of DNA using a newly designed fluorescent cofactor for the DNA methyltransferase from Thermus aquaticus (M.TaqI). Naturally, M.TaqI catalyzes the nucleophilic attack of the exocyclic amino group of adenine within the double-stranded 5'-TCGA-3' DNA sequence onto the methyl group of the cofactor S-adenosyl-L-methionine (AdoMet) leading to methyl group transfer. The design of a new fluorescent cofactor for covalent labeling of DNA was based on three criteria: (1) Replacement of the methionine side chain of the natural cofactor AdoMet by an aziridinyl residue leads to M.TaqI-catalyzed nucleophilic ring opening and coupling of the whole nucleoside to DNA. (2) The adenosyl moiety is the molecular anchor for cofactor binding. (3) Attachment of a fluorophore via a flexible linker to the 8-position of the adenosyl moiety does not block cofactor binding. According to these criteria the new fluorescent cofactor 8-amino[1''-(N''-dansyl)-4''-aminobutyl]-5'-(1-aziridinyl)-5'-deoxyadenosine (3) was synthesized. 3 binds about 4-fold better than the natural cofactor AdoMet to M.TaqI and is coupled with a short duplex oligodeoxynucleotide by M.TaqI. The identity of the expected modified nucleoside was verified by electrospray ionization mass spectrometry after enzymatic fragmentation of the product duplex. In addition, the new cofactor 3 was used to sequence-specifically label plasmid DNA in a M.TaqI-catalyzed reaction.
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Affiliation(s)
- Goran Pljevaljcic
- Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
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44
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Wellenzohn B, Flader W, Winger RH, Hallbrucker A, Mayer E, Liedl KR. Significance of ligand tails for interaction with the minor groove of B-DNA. Biophys J 2001; 81:1588-99. [PMID: 11509372 PMCID: PMC1301637 DOI: 10.1016/s0006-3495(01)75813-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Minor groove binding ligands are of great interest due to their extraordinary importance as transcription controlling drugs. We performed three molecular dynamics simulations of the unbound d(CGCGAATTCGCG)(2) dodecamer and its complexes with Hoechst33258 and Netropsin. The structural behavior of the piperazine tail of Hoechst33258, which has already been shown to be a contributor in sequence-specific recognition, was analyzed. The simulations also reveal that the tails of the ligands are able to influence the width of the minor groove. The groove width is even sensitive for conformational transitions of these tails, indicating a high adaptability of the minor groove. Furthermore, the ligands also exert an influence on the B(I)/B(II) backbone conformational substate behavior. All together these results are important for the understanding of the binding process of sequence-specific ligands.
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Affiliation(s)
- B Wellenzohn
- Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria
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45
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Sigel RK, Thompson SM, Freisinger E, Glahé F, Lippert B. Metal-modified nucleobase sextet: joining four linear metal fragments (trans-a2PtII) and six model nucleobases to an exceedingly stable entity. Chemistry 2001; 7:1968-80. [PMID: 11405476 DOI: 10.1002/1521-3765(20010504)7:9<1968::aid-chem1968>3.0.co;2-b] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Crosslinking of three different model nucleobases (9-ethyladenine, 9-EtA; 9-ethylguanine, 9-EtGH; 1-methyluracil, 1-MeU) by two linear trans-aPtII (a = NH3 or CH3NH2) entities leads to a flat metal-modified base triplet, trans,trans-[(NH3)2Pt(1-MeU-N3)(mu-9-EtA-N7,N1)Pt(CH3NH2)2(9-EtGH-N7)]3+ (4b). Upon hemideprotonation of the 9-ethylguanine base at the N1 position. 4b spontaneously dimerizes to the metalated nucleobase sextet 5, [(4b)(triple bond)(4b-H)]5+. In this dimeric structure a neutral and an anionic guanine ligand, which are complementary to each other, are joined through three H bonds and additionally by two H bonds between guanine and uracil nucleobases. Four additional interbase H bonds maintain the approximate coplanarity of all six bases. The two base triplets form an exceedingly stable entity (KD = 500 +/- 150 M(-1) in DMSO), which is unprecedented in nucleobase chemistry. The precursor of 4b and several related complexes are described and their structures and solution properties are reported.
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Affiliation(s)
- R K Sigel
- Fachbereich Chemie, Universität Dortmund, Germany
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46
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Parel SP, Marfurt J, Leumann CJ. DNA triple-helix formation at pyrimidine-purine inversion sites. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:411-7. [PMID: 11563056 DOI: 10.1081/ncn-100002315] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A systematic investigation of a series of triplex forming oligonucleotides (TFOs) containing alpha-, and beta-thymidine, alpha- and beta-N7-hypoxanthine, and alpha- and beta-N7 and N9 aminopurine nucleosides, designed to bind to T-A inversion sites in DNA target sequences was performed. Data obtained from gel mobility assays indicate that T-A recognition in the antiparallel triple-helical binding motif is possible if the nucleoside alpha N9-aminopurine is used opposite to the inversion site in the TFO.
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Affiliation(s)
- S P Parel
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
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47
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Wamhoff H, Bamberg A, Sohár P. Efficient synthesis of fused isothiazolo C-nucleosides. III. Synthesis of substituted isothiazol. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:229-41. [PMID: 11393399 DOI: 10.1081/ncn-100002083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The Divakar-Reese procedure has been successfully applied for transforming 7-oxo-isothiazolo[4,5-d]pyrimidine C-nucleosides (4a,b, 5a,b, 6a) via 1,2,4-triazol-1-yl intermediates (7a,b, 8a,b) into various 7-substituted C-nucleosides 15a,b, 16a,b, 17a, 18a, 19a,b, 20a,b; their subsequent deprotection provides novel types of unusual C-glycosides 22b, 23a, 24a,b, 25b, 26b. C-Nucleosides, possessing on its heterocyclic base other than naturally occuring oxo- or amino substituents, are important model compounds for biological or medicinal studies (2,3). We want to report on the synthesis of novel 7-substituted isothiazolo = [4,5-d]pyrimidine C-nucleosides. As we could show in previous papers (1,4), there exists a simple approach to the protected C-glycosides 4-6.
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Affiliation(s)
- H Wamhoff
- Kekulé-Institut für Organische Chemie und Biochemie der Universität Bonn, Germany
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Marchand C, Nguyen CH, Ward B, Sun JS, Bisagni E, Garestier T, Hélène C. A New Family of Sequence-Specific DNA-Cleaving Agents Directed by Triple-Helical Structures: Benzopyridoindole-EDTA Conjugates. Chemistry 2000. [DOI: 10.1002/(sici)1521-3765(20000502)6:9<1559::aid-chem1559>3.0.co;2-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Schmidt KS, Filippov DV, Meeuwenoord NJ, van der Marel GA, van Boom JH, Lippert B, Reedijk J. Solid-Phase Synthesis of a Monofunctionaltrans-a2PtII Complex Tethered to a Single-Stranded Oligonucleotide. Angew Chem Int Ed Engl 2000. [DOI: 10.1002/(sici)1521-3757(20000117)112:2<383::aid-ange383>3.0.co;2-f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Winger RH, Liedl KR, Pichler A, Hallbrucker A, Mayer E. Helix morphology changes in B-DNA induced by spontaneous B(I)<==>B(II) substrate interconversion. J Biomol Struct Dyn 1999; 17:223-35. [PMID: 10563572 DOI: 10.1080/07391102.1999.10508355] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Investigations of spontaneous, i.e. not forced, B-DNA's B(I)<==>B(II) substate transitions are carried out on the d(CGCGAATTCGCG)2 EcoRI dodecamer sequence using Molecular Dynamics Simulations. Analysis of the resulting transition processes with respect to the backbone angles reveals concerted changes not only for backbone angles epsilon, zeta, and beta, but also for the 5'-delta and 5'-chi angles. For alpha and delta inside the interconverting base step, a change is seen in short lived B(II) conformers. With respect to base morphology distinct changes are observed for buckle, propeller twist, shift, roll and twist, as well as x-displacement and tip. The base mainly involved in the changes is identified as the base preceding the interconverting phosphate. Altogether single B(I)<==>B(II) interconversions result only in local distortions represented by the larger spread of most parameters. Comparison of the atomic positional fluctuations derived from the simulation with those obtained from the static X-ray structure results in striking similarities.
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Affiliation(s)
- R H Winger
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Austria
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