1
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Lukina MV, Zhdanova PV, Koval VV. Structural and Dynamic Features of the Recognition of 8-oxoguanosine Paired with an 8-oxoG-clamp by Human 8-oxoguanine-DNA Glycosylase. Curr Issues Mol Biol 2024; 46:4119-4132. [PMID: 38785521 PMCID: PMC11120029 DOI: 10.3390/cimb46050253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
8-oxoguanine (oxoG) is formed in DNA by the action of reactive oxygen species. As a highly mutagenic and the most common oxidative DNA lesion, it is an important marker of oxidative stress. Human 8-oxoguanine-DNA glycosylase (OGG1) is responsible for its prompt removal in human cells. OGG1 is a bifunctional DNA glycosylase with N-glycosylase and AP lyase activities. Aspects of the detailed mechanism underlying the recognition of 8-oxoguanine among numerous intact bases and its subsequent interaction with the enzyme's active site amino acid residues are still debated. The main objective of our work was to determine the effect (structural and thermodynamic) of introducing an oxoG-clamp in model DNA substrates on the process of 8-oxoG excision by OGG1. Towards that end, we used DNA duplexes modeling OGG1-specific lesions: 8-oxoguanine or an apurinic/apyrimidinic site with either cytidine or the oxoG-clamp in the complementary strand opposite to the lesion. It was revealed that there was neither hydrolysis of the N-glycosidic bond at oxoG nor cleavage of the sugar-phosphate backbone during the reaction between OGG1 and oxoG-clamp-containing duplexes. Possible structural reasons for the absence of OGG1 enzymatic activity were studied via the stopped-flow kinetic approach and molecular dynamics simulations. The base opposite the damage was found to have a critical effect on the formation of the enzyme-substrate complex and the initiation of DNA cleavage. The oxoG-clamp residue prevented the eversion of the oxoG base into the OGG1 active site pocket and impeded the correct convergence of the apurinic/apyrimidinic site of DNA and the attacking nucleophilic group of the enzyme. An obtained three-dimensional model of the OGG1 complex with DNA containing the oxoG-clamp, together with kinetic data, allowed us to clarify the role of the contact of amino acid residues with DNA in the formation of (and rearrangements in) the enzyme-substrate complex.
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Affiliation(s)
- Maria V. Lukina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (ICBFM SB RAS), Novosibirsk 630090, Russia;
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Polina V. Zhdanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (ICBFM SB RAS), Novosibirsk 630090, Russia;
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Vladimir V. Koval
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (ICBFM SB RAS), Novosibirsk 630090, Russia;
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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2
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Kaczmarek R, Twardy DJ, Olson TL, Korczyński D, Andrei G, Snoeck R, Dolot R, Wheeler KA, Dembinski R. Extension of furopyrimidine nucleosides with 5-alkynyl substituent: Synthesis, high fluorescence, and antiviral effect in the absence of free ribose hydroxyl groups. Eur J Med Chem 2020; 209:112884. [PMID: 33039724 PMCID: PMC7521880 DOI: 10.1016/j.ejmech.2020.112884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/15/2020] [Accepted: 09/23/2020] [Indexed: 11/24/2022]
Abstract
A novel methodology to access alkynyl nucleoside analogues is elaborated. Highly fluorescent 5-alkynylfuropyrimidines were synthesized (97-46%) and their antiviral properties investigated in vitro. Regiochemistry of the functionalization was achieved with the aid of 5-endo-dig electrophilic halocyclization of acetyl 5-p-tolyl- or 5-p-pentylphenyl-2'-deoxyuridine. Structure of one of the resulting nucleosides, 6-p-tolyl-5-iodo-2'-deoxyribofuranosyl-furo[2,3-d]pyrimidin-2-one, was confirmed by X-ray crystallography, and its conformation was compared to related nucleosides. Diverse alkynyl substituents were introduced at the heterobicyclic base C-5 position via Sonogashira coupling of 5-iodo-2'-deoxyribofuranosyl-furo[2,3-d]pyrimidin-2-ones. The resulting compounds had fluorescence emissions of 452-481 nm. High quantum yields of 0.53-0.60 were observed for 9-ethynyl-9-fluorenol and propargyl alcohol/methyl ether-modified furopyrimidines. These modified nucleosides, designed in the form of ribose acetyl esters, are potential tools for fluorescent tagging, studying nucleoside metabolism, 2'-deoxyribonucleoside kinase activity, and antiviral activity. Antiviral assays against a broad spectrum of DNA and RNA viruses showed that in human embryonic lung (HEL) cell cultures some of the compounds posess antiviral activity (EC50 1.3-13.2 μM) against varicella-zoster virus (VZV). The alkynyl furopyrimidine with two p-pentylphenyl substituents emerged as the best compound with reasonable and selective anti-VZV activity, confirming p-pentylphenyl potency as a pharmacophore.
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Affiliation(s)
- Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Dylan J Twardy
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI, 48309-4479, USA
| | - Trevor L Olson
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI, 48309-4479, USA
| | - Dariusz Korczyński
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Graciela Andrei
- Rega Institute, Department of Microbiology, Immunology and Transplantation, Herestraat 49, 3000, Leuven, Belgium
| | - Robert Snoeck
- Rega Institute, Department of Microbiology, Immunology and Transplantation, Herestraat 49, 3000, Leuven, Belgium
| | - Rafał Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland
| | - Kraig A Wheeler
- Department of Chemistry, Whitworth University, 300 W. Hawthorne Rd., Spokane, WA, 99251, USA
| | - Roman Dembinski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Łódź, Poland; Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI, 48309-4479, USA.
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3
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Liu Q, Jing S, Liu M, Jin Y, Li B. Parallel [TG(GA) 3] n-homoduplexes/thioflavin T: an intense and stable fluorescent indicator for label-free biosensing. Analyst 2020; 145:286-294. [PMID: 31750449 DOI: 10.1039/c9an01856e] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different from the classical antiparallel DNA double-stranded structure, parallel DNA duplexes possess unique structures and potential biological functions. In this work, we found that the parallel DNA homoduplex from the [TG(GA)3]n sequence ([TG(GA)3]n-dsDNA) can dramatically enhance the fluorescence of thioflavin T (ThT), and the fluorescence enhancement is proportional to the number (n) of TG(GA)3 units in [TG(GA)3]n. Compared with the traditional G-quadruplex/ThT system, [TG(GA)3]n/ThT showed more stable and stronger fluorescence emission. In addition, coupled with an isothermal exponential amplification reaction, [TG(GA)3]3/ThT was used as a label-free fluorescent probe to detect microRNA, and the [TG(GA)3]3/ThT probe exhibited higher sensitivity than the G-quadruplex/ThT probe. This work provides a new paradigm to design label-free fluorescent biosensing/imaging systems.
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Affiliation(s)
- Qiang Liu
- School of Chemistry & Chemical Engineering, Key laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Shaanxi Normal University, Xi'an 710062, China.
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4
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Schönrath I, Tsvetkov VB, Zatsepin TS, Aralov AV, Müller J. Silver(I)-mediated base pairing in parallel-stranded DNA involving the luminescent cytosine analog 1,3-diaza-2-oxophenoxazine. J Biol Inorg Chem 2019; 24:693-702. [DOI: 10.1007/s00775-019-01682-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/18/2019] [Indexed: 01/03/2023]
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5
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Szabat M, Kierzek R. Parallel-stranded DNA and RNA duplexes - structural features and potential applications. FEBS J 2017; 284:3986-3998. [DOI: 10.1111/febs.14187] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/20/2017] [Accepted: 07/26/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Marta Szabat
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznan Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznan Poland
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6
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Varizhuk AM, Zatsepin TS, Golovin AV, Belyaev ES, Kostyukevich YI, Dedkov VG, Shipulin GA, Shpakovski GV, Aralov AV. Synthesis of oligonucleotides containing novel G-clamp analogue with C8-tethered group in phenoxazine ring: Implication to qPCR detection of the low-copy Kemerovo virus dsRNA. Bioorg Med Chem 2017; 25:3597-3605. [PMID: 28396019 DOI: 10.1016/j.bmc.2017.03.062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 01/20/2023]
Abstract
Nowadays modified oligonucleotides are widely used in diagnostics and as novel therapeutics. Introduction of modified or unnatural residues into oligonucleotides allows fine tuning of their binding properties to complementary nucleic acids and leads to improved stability both in vitro and in vivo. Previously it was demonstrated that insertion of phenoxazine nucleotides with various groups in C9-position into oligonucleotides leads to a significant increase of duplex stability with complementary DNA and RNA. Here the synthesis of a novel G-clamp nucleoside analogue (G8AE-clamp) bearing 2-aminoethyl tether at C8-atom is presented. Introduction of such modified residues into oligonucleotides lead to enhanced specificity of duplex formation towards complementary DNA and RNA targets with increased thermal and 3'-exonuclease stability. According to CD-spectroscopy studies G8AE-clamp does not substantially disrupt helix geometry. Primers containing G8AE-clamp demonstrated superior sensitivity in qPCR detection of dsRNA of Kemerovo virus in comparison to native oligonucleotides.
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Affiliation(s)
- Anna M Varizhuk
- Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Department of Structure-Functional Analysis of Biopolymers, Engelhardt Institute of Molecular Biology, Vavilov Str. 32, Moscow 119991, Russia
| | - Timofei S Zatsepin
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia; Skolkovo Institute of Science and Technology, 3 Nobel Street, Skolkovo, Moscow Region 143026, Russia.
| | - Andrey V Golovin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Evgeny S Belyaev
- Institute for Energy Problems of Chemical Physics of RAS, Leninskij pr. 38/2, Moscow 119334, Russia
| | - Yury I Kostyukevich
- Skolkovo Institute of Science and Technology, 3 Nobel Street, Skolkovo, Moscow Region 143026, Russia
| | - Vladimir G Dedkov
- Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia
| | - German A Shipulin
- Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia
| | - George V Shpakovski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia.
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7
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Zhao H, Leonard P, Guo X, Yang H, Seela F. Silver-Mediated Base Pairs in DNA Incorporating Purines, 7-Deazapurines, and 8-Aza-7-deazapurines: Impact of Reduced Nucleobase Binding Sites and an Altered Glycosylation Position. Chemistry 2017; 23:5529-5540. [PMID: 28195414 DOI: 10.1002/chem.201605982] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Indexed: 02/05/2023]
Abstract
Formation of silver-mediated DNA was studied with oligonucleotides incorporating 8-aza-7-deazapurine, 7-deazapurine, and purine nucleosides. The investigation was performed on non-self-complementary duplexes with one or two modifications and self-complementary duplexes with an alternating dA-dT motif. Homo base pairs as well as base pair mismatches of dA analogues with dC and Watson-Crick pairs with dT were studied by stoichiometric silver ion titration and Tm measurements. N8 -Glycosylated 8-aza-7-deazaadenine forms silver-ion-mediated base pairs capturing two silver ions (low silver content) whereas regularly glycosylated 8-aza-7-deazapurine, 7-deazapurine (c7 Ad ), and dA do not form comparable structures. Stable silver-mediated "dA-dC" base pair mismatches were detected for all nucleosides. Two silver ions per base pair are bound by 8-aza-7-deazapurine whereas c7 Ad binds only one silver ion. The situation is different when the equivalents of silver ions were increased to the number of total base pairs. Surprisingly, in 12-mer duplexes as well as in related 25-mer duplexes every base pair consumed one silver ion.
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Affiliation(s)
- Hang Zhao
- 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.,State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Peter Leonard
- 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
| | - Xiurong Guo
- 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
| | - Haozhe Yang
- 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
| | - 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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8
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Kaushik M, Kaushik S, Roy K, Singh A, Mahendru S, Kumar M, Chaudhary S, Ahmed S, Kukreti S. A bouquet of DNA structures: Emerging diversity. Biochem Biophys Rep 2016; 5:388-395. [PMID: 28955846 PMCID: PMC5600441 DOI: 10.1016/j.bbrep.2016.01.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/28/2015] [Accepted: 01/22/2016] [Indexed: 11/29/2022] Open
Abstract
Structural polymorphism of DNA has constantly been evolving from the time of illustration of the double helical model of DNA by Watson and Crick. A variety of non-canonical DNA structures have constantly been documented across the globe. DNA attracted worldwide attention as a carrier of genetic information. In addition to the classical Watson–Crick duplex, DNA can actually adopt diverse structures during its active participation in cellular processes like replication, transcription, recombination and repair. Structures like hairpin, cruciform, triplex, G-triplex, quadruplex, i-motif and other alternative non-canonical DNA structures have been studied at length and have also shown their in vivo occurrence. This review mainly focuses on non-canonical structures adopted by DNA oligonucleotides which have certain prerequisites for their formation in terms of sequence, its length, number and orientation of strands along with varied solution conditions. This conformational polymorphism of DNA might be the basis of different functional properties of a specific set of DNA sequences, further giving some insights for various extremely complicated biological phenomena. Many of these structures have already shown their linkages with diseases like cancer and genetic disorders, hence making them an extremely striking target for structure-specific drug designing and therapeutic applications. DNA can adopt diverse range of structures other than classical Watson–Crick duplex. Discussion of alternate structures like hairpin, cruciform, triplex, quadruplex etc. This review gives some insights for the biological relevance of DNA structures.
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Affiliation(s)
- Mahima Kaushik
- Cluster Innovation Centre, University of Delhi, Delhi, India.,Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Shikha Kaushik
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Kapil Roy
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Anju Singh
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Swati Mahendru
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Mohan Kumar
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Swati Chaudhary
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Saami Ahmed
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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9
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Jana SK, Leonard P, Ingale SA, Seela F. 2′-O-Methyl- and 2′-O-propargyl-5-methylisocytidine: synthesis, properties and impact on the isoCd–dG and the isoCd–isoGd base pairing in nucleic acids with parallel and antiparallel strand orientation. Org Biomol Chem 2016; 14:4927-42. [DOI: 10.1039/c6ob00622a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The impact of 2′-O-alkyl residues on the stability of iCd–dG and iCd–iGd base pairs was studied in DNA with parallel and antiparallel chain orientation.
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Affiliation(s)
- Sunit K. Jana
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
| | - Sachin A. Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
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10
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Wunnicke D, Ding P, Yang H, Seela F, Steinhoff HJ. DNA with Parallel Strand Orientation: A Nanometer Distance Study with Spin Labels in the Watson-Crick and the Reverse Watson-Crick Double Helix. J Phys Chem B 2015; 119:13593-9. [PMID: 26121221 DOI: 10.1021/acs.jpcb.5b02935] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Parallel-stranded (ps) DNA characterized by its sugar-phosphate backbones pointing in the same direction represents an alternative pairing system to antiparallel-stranded (aps) DNA with the potential to inhibit transcription and translation. 25-mer oligonucleotides were selected containing only dA·dT base pairs to compare spin-labeled nucleobase distances over a range of 10 or 15 base pairs in ps DNA with those in aps DNA. By means of the copper(I)-catalyzed Huisgen-Meldal-Sharpless alkyne-azide cycloaddition, the spin label 4-azido-2,2,6,6-tetramethylpiperidine-1-oxyl was clicked to 7-ethynyl-7-deaza-2'-deoxyadenosine or 5-ethynyl-2'-deoxyuridine to yield 25-mer oligonucleotides incorporating two spin labels. The interspin distances between spin labeled residues were determined by pulse EPR spectroscopy. The results reveal that in ps DNA these distances are between 5 and 10% longer than in aps DNA when the labeled DNA segment is located near the center of the double helix. The interspin distance in ps DNA becomes shorter compared with aps DNA when one of the spin labels occupies a position near the end of the double helix.
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Affiliation(s)
| | - Ping Ding
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstrasse 11, 48149 Münster, Germany
| | - Haozhe Yang
- 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
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11
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Yang H, Mei H, Seela F. Pyrrolo-dC Metal-Mediated Base Pairs in the Reverse Watson-Crick Double Helix: Enhanced Stability of Parallel DNA and Impact of 6-Pyridinyl Residues on Fluorescence and Silver-Ion Binding. Chemistry 2015; 21:10207-19. [PMID: 26096946 DOI: 10.1002/chem.201500582] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Indexed: 11/11/2022]
Abstract
Reverse Watson-Crick DNA with parallel-strand orientation (ps DNA) has been constructed. Pyrrolo-dC (PyrdC) nucleosides with phenyl and pyridinyl residues linked to the 6 position of the pyrrolo[2,3-d]pyrimidine base have been incorporated in 12- and 25-mer oligonucleotide duplexes and utilized as silver-ion binding sites. Thermal-stability studies on the parallel DNA strands demonstrated extremely strong silver-ion binding and strongly enhanced duplex stability. Stoichiometric UV and fluorescence titration experiments verified that a single (2py) PyrdC-(2py) PyrdC pair captures two silver ions in ps DNA. A structure for the PyrdC silver-ion base pair that aligns 7-deazapurine bases head-to-tail instead of head-to-head, as suggested for canonical DNA, is proposed. The silver DNA double helix represents the first example of a ps DNA structure built up of bidentate and tridentate reverse Watson-Crick base pairs stabilized by a dinuclear silver-mediated PyrdC pair.
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Affiliation(s)
- Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster (Germany), Fax: (+49) 251-53406857.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück (Germany)
| | - Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster (Germany), Fax: (+49) 251-53406857.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück (Germany)
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster (Germany), Fax: (+49) 251-53406857. .,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück (Germany).
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12
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Mei H, Röhl I, Seela F. Ag+-mediated DNA base pairing: extraordinarily stable pyrrolo-dC-pyrrolo-dC pairs binding two silver ions. J Org Chem 2013; 78:9457-63. [PMID: 23965151 DOI: 10.1021/jo401109w] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
6-Substituted pyrrolo-dC-pyrrolo-dC mismatches selectively capture silver ions to form extraordinarily stable metal-mediated base pairs. One single modification in a 12-mer duplex causes a Tm increase of 36.0 °C relative to the metal-free mismatched duplex. Spectrophotometric titrations as well as ESI mass spectra confirmed the binding of two silver ions per base pair. The Ag(+)-mediated base pairs may permit the construction of metal-responsive DNA with a very high silver loading.
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Affiliation(s)
- Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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13
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Pujari SS, Seela F. Parallel stranded DNA stabilized with internal sugar cross-links: synthesis and click ligation of oligonucleotides containing 2'-propargylated isoguanosine. J Org Chem 2013; 78:8545-61. [PMID: 23915305 DOI: 10.1021/jo4012706] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Internal sugar cross-links were introduced for the first time into oligonucleotides with parallel chain orientation by click ligation. For this, the 2'- or 3'-position of the isoguanosine ribose moiety was functionalized with clickable propargyl residues, and the synthesis of propargylated cytosine building blocks was significantly improved. Phosphoramidites were prepared and employed in solid-phase synthesis. A series of oligo-2'-deoxyribonucleotides with parallel (ps) and antiparallel (aps) strand orientation were constructed containing isoguanine-cytosine, isoguanine-isocytosine, and adenine-thymine base pairs. Complementary oligonucleotides with propargylated sugar residues were ligated in a stepwise manner with a chelating bis-azide under copper catalysis. Cross-links were introduced within a base pair or in positions separated by two base pairs. From T(m) stability studies it is evident that cross-linking stabilizes DNA with parallel strand orientation strongly (ΔT(m) from +16 to +18.5 °C) with a similar increase as for aps DNA.
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Affiliation(s)
- Suresh S Pujari
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
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14
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Tanpure AA, Pawar MG, Srivatsan SG. Fluorescent Nucleoside Analogs: Probes for Investigating Nucleic Acid Structure and Function. Isr J Chem 2013. [DOI: 10.1002/ijch.201300010] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Zhao H, He S, Yang M, Guo X, Xin G, Zhang C, Ye L, Chu L, Xing Z, Huang W, Chen Q, He Y. Micro-flowers changing to nano-bundle aggregates by translocation of the sugar moiety in Janus TA nucleosides. Chem Commun (Camb) 2013; 49:3742-4. [DOI: 10.1039/c3cc41383g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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16
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Mei H, Budow S, Seela F. Construction and assembly of chimeric DNA: oligonucleotide hybrid molecules composed of parallel or antiparallel duplexes and tetrameric i-motifs. Biomacromolecules 2012; 13:4196-204. [PMID: 23121010 DOI: 10.1021/bm301471d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Chimeric DNA containing parallel (ps) and antiparallel (aps) duplex elements as well as poly-dC tracts were designed and synthesized. Oligonucleotide duplexes with ps chain orientation containing reverse Watson-Crick dA-dT base pairs and short d(C)2 tails are stabilized under slightly acidic conditions by hemiprotonated dCH+-dC base pairs ("clamp" effect). Corresponding molecules with aps orientation containing Watson-Crick dA-dT base pairs do not show this phenomenon. Chimeric DNA with ps duplex elements and long d(C)5 tails at one or at both ends assemble to tetrameric i-motif structures. Molecules with two terminal d(C)5 tails form multimeric assemblies which have the potential to form nanoscopic scaffolds. A preorganization of the ps duplex chains stabilizes the i-motif assemblies up to almost neutral conditions as evidenced by thermal melting and gel electrophoresis. Although, ps DNA is generally less stable than aps DNA, the aps duplexes contribute less to the stability of the i-motif than ps DNA.
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Affiliation(s)
- Hui Mei
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
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Efthymiou T, Gong W, Desaulniers JP. Chemical architecture and applications of nucleic acid derivatives containing 1,2,3-triazole functionalities synthesized via click chemistry. Molecules 2012; 17:12665-703. [PMID: 23103533 PMCID: PMC6268694 DOI: 10.3390/molecules171112665] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/19/2012] [Accepted: 10/19/2012] [Indexed: 11/16/2022] Open
Abstract
There is considerable attention directed at chemically modifying nucleic acids with robust functional groups in order to alter their properties. Since the breakthrough of copper-assisted azide-alkyne cycloadditions (CuAAC), there have been several reports describing the synthesis and properties of novel triazole-modified nucleic acid derivatives for potential downstream DNA- and RNA-based applications. This review will focus on highlighting representative novel nucleic acid molecular structures that have been synthesized via the “click” azide-alkyne cycloaddition. Many of these derivatives show compatibility for various applications that involve enzymatic transformation, nucleic acid hybridization, molecular tagging and purification, and gene silencing. The details of these applications are discussed. In conclusion, the future of nucleic acid analogues functionalized with triazoles is promising.
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Affiliation(s)
| | | | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, ON L1H 7K4, Canada
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