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Zhang Y, Xiang X, Bao Y, Xu G, Luo H, Tian Y, Guo X. Characterization of Parallel-Stranded DNA Duplexes by Surface-Enhanced Raman Spectroscopy and Bromide-Modified Gold Nanoparticles. Anal Chem 2024; 96:4884-4890. [PMID: 38494753 DOI: 10.1021/acs.analchem.3c05356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The parallel double-stranded DNA (dsDNA) demonstrates potential utility in molecular biology, diagnosis, therapy, and molecular assembly. However, techniques for the characterization of parallel dsDNA are limited. Here, we demonstrate that a series of intensive characteristic Raman bands of three parallel dsDNAs, which are stabilized by reverse Hoogsteen A+·A+ base pairs or hemiprotonated C+·C, G·G minor groove edge, Hoogsteen A·A base pairs, or Hoogsteen T·A, C+·G base pairs, have been observed by surface-enhanced Raman spectroscopy (SERS) when the gold nanoparticles modified by bromine and magnesium ions (Au BMNPs) were used as substrates. The featured bands can not only accurately discriminate parallel dsDNA from antiparallel one but also identify the strand orientation within dsDNA. The proposed approach will have a significant impact on DNA analysis, especially in the detection and differentiation of various DNA conformations.
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Affiliation(s)
- Yujing Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Xiaoxuan Xiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Ying Bao
- Key Laboratory of Polymer Ecomaterials, Jilin Biomedical Polymers Engineering Laboratory, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Guantong Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Hong Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, P. R. China
| | - Xinhua Guo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun 130012, P. R. China
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2
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Luo S, Xiong D, Zhao X, Duan L. An Attempt of Seeking Favorable Binding Free Energy Prediction Schemes Considering the Entropic Effect on Fis-DNA Binding. J Phys Chem B 2023; 127:1312-1324. [PMID: 36735878 DOI: 10.1021/acs.jpcb.2c07811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Protein-DNA binding mechanisms in a complex manner are essential for understanding many biological processes. Over the past decades, numerous experiments and calculations have analyzed the specificity of protein-DNA binding. However, the accuracy of binding free energy prediction for multi-base DNA systems still needs to be improved. Fis is a DNA-binding protein that regulates various transcription and recombination reactions. In the present work, we tested several methods of predict binding free energy based on this system to find a favorable prediction scheme and explore the binding mechanism of Fis protein and DNA. Two solvent models (explicit and implicit solvent models) were chosen for the dynamics process, and the predicted binding free energy was more accurate under the explicit solvent model. When different Poisson-Boltzmann/Generalized Born (PB/GB) models were tested for DNA force fields (BSC1 and OL15), it was found that the binding free energy predicted by the selected OL15 force field performed better and the correlation between predicted and experimental values was improved with the increasing interior dielectric constant (Dk). Finally, using Dk = 8, the GBOBC1 model combined with interaction entropy (IE), which was calculated for entropic contribution (GBOBC1_IE_8), was screened out for the binding free energy prediction and analysis of the Fis-DNA system, and the validity of the method was further verified by testing the Cren7-DNA system. By performing conformational analysis of the minor groove, it was found that mutation of the DNA central sequence A/T to C/G and deletion of the guanine 2-amino group would change the minor groove width and thus affect the formation of the major groove, altering the interaction and atomic contact between the protein and the major groove, thus changing the binding affinity of Fis and DNA. Hopefully, the series of tests in this work can shed some light on the related studies of protein and DNA systems.
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Affiliation(s)
- Song Luo
- School of Physics and Electronics, Shandong Normal University, Jinan, Shandong250014, China
| | - Danyang Xiong
- School of Physics and Electronics, Shandong Normal University, Jinan, Shandong250014, China
| | - Xiaoyu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan, Shandong250014, China
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, Shandong250014, China
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3
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Zhang A, Kondhare D, Leonard P, Seela F. DNA Strand Displacement with Base Pair Stabilizers: Purine-2,6-Diamine and 8-Aza-7-Bromo-7-Deazapurine-2,6-Diamine Oligonucleotides Invade Canonical DNA and New Fluorescent Pyrene Click Sensors Monitor the Reaction. Chemistry 2022; 28:e202202412. [PMID: 36178316 PMCID: PMC10100337 DOI: 10.1002/chem.202202412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Indexed: 12/30/2022]
Abstract
Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides (1 and 2) were implemented in isothermal DNA strand displacement reactions. Nucleoside 1 is a weak stabilizer of dA-dT base pairs, nucleoside 2 evokes strong stabilization. Strand displacement reactions used single-stranded invaders with single and multiple incorporations of stabilizers. Displacement is driven by negative enthalpy changes between target and displaced duplex. Toeholds are not required. Two new environmental sensitive fluorescent pyrene sensors were developed to monitor the progress of displacement reactions. Pyrene was connected to the nucleobase in the invader or to a dendritic linker in the output strand. Both new sensors were constructed by click chemistry; phosphoramidites and oligonucleotides were prepared. Sensors show monomer or excimer emission. Fluorescence intensity changes when the displacement reaction progresses. Our work demonstrates that strand displacement with base pair stabilizers is applicable to DNA, RNA and to related biopolymers with applications in chemical biology, nanotechnology and medicinal diagnostics.
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Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Dasharath Kondhare
- 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
| | - 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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4
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Ay E. Synthesis of new 1,2,3-triazolo-nucleoside analogues with 2-propargylamino pyrimidines via click reactions. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 42:191-205. [PMID: 36047982 DOI: 10.1080/15257770.2022.2118317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
In this study, it was reported that twelve nucleoside analogues were synthesized by click reactions. The reactions were carried out between the azide derivatives of D-glucopyranose, D-galactopyranose, D-ribofuranose and 2-propargylamino pyrimidine derivatives (5 and 7) that are synthesized via a different route for the first time. In the first step, N-propargyl guanidine was obtained with the reaction of 1H-pyrazole-1-carboxamidine hydrochloride and propargyl amine, then condensation of N-propargyl guanidine and β-diketone (4 and 6) resulted in 2-propargylamino pyrimidines (5 and 7) for the first time in good yields (85%). Finally, click reactions were performed with azidosugars (8a-8f) and 2-propargylamino pyrimidine derivatives and produced twelve new nucleoside analogues in good yields. (9a-9f, 10a-10f, 65-73% yields). The chemical structures of the new derivatives were elucidated spectroscopic techniques, such as FT-IR, 1H NMR, 19F NMR, 13C NMR and TOF-ESI-MS.
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Affiliation(s)
- Emriye Ay
- Giresun University, Department of Food Technology, Şebinkarahisar School of Applied Sciences, Giresun, Türkiye.,Manisa Celal Bayar University, Department of Tobacco Technology Engineering, Akhisar, Manisa, Türkiye
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5
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Zhang A, Kondhare D, Leonard P, Seela F. Anomeric DNA Strand Displacement with α-D Oligonucleotides as Invaders and Ethidium Bromide as Fluorescence Sensor for Duplexes with α/β-, β/β- and α/α-D Configuration. Chemistry 2022; 28:e202201294. [PMID: 35652726 PMCID: PMC9543212 DOI: 10.1002/chem.202201294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/15/2022]
Abstract
DNA strand displacement is a technique to exchange one strand of a double stranded DNA by another strand (invader). It is an isothermal, enzyme free method driven by single stranded overhangs (toeholds) and is employed in DNA amplification, mismatch detection and nanotechnology. We discovered that anomeric (α/β) DNA can be used for heterochiral strand displacement. Homochiral DNA in β-D configuration was transformed to heterochiral DNA in α-D/β-D configuration and further to homochiral DNA with both strands in α-D configuration. Single stranded α-D DNA acts as invader. Herein, new anomeric displacement systems with and without toeholds were designed. Due to their resistance against enzymatic degradation, the systems are applicable to living cells. The light-up intercalator ethidium bromide is used as fluorescence sensor to follow the progress of displacement. Anomeric DNA displacement shows benefits over canonical DNA in view of toehold free displacement and simple detection by ethidium bromide.
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Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Dasharath Kondhare
- 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
| | - 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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Zhang A, Leonard P, Seela F. Anomeric DNA: Functionalization of α-D Anomers of 7-Deaza-2'-deoxyadenosine and 2'-Deoxyuridine with Clickable Side Chains and Click Adducts in Homochiral and Heterochiral Double Helices. Chemistry 2021; 28:e202103872. [PMID: 34878201 PMCID: PMC9304229 DOI: 10.1002/chem.202103872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Indexed: 11/21/2022]
Abstract
Anomeric base pairs in heterochiral DNA with strands in the α‐d and β‐d configurations and homochiral DNA with both strands in α‐d configuration were functionalized. The α‐d anomers of 2′‐deoxyuridine and 7‐deaza‐2′‐deoxyadenosine were synthesized and functionalized with clickable octadiynyl side chains. Nucleosides were protected and converted to phosphoramidites. Solid‐phase synthesis furnished 12‐mer oligonucleotides, which were hybridized. Pyrene click adducts display fluorescence, a few of them with excimer emission. Tm values and thermodynamic data revealed the following order of duplex stability α/α‐d≫β/β‐d≥α/β‐d. CD spectra disclosed that conformational changes occur during hybridization. Functionalized DNAs were modeled and energy minimized. Clickable side chains and bulky click adducts are well accommodated in the grooves of anomeric DNA. The investigation shows for the first time that anomeric DNAs can be functionalized in the same way as canonical DNA for potential applications in nucleic acid chemistry, chemical biology, and DNA material science.
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Affiliation(s)
- Aigui Zhang
- Center for Nanotechnology, Laboratory of Bioorganic Chemistry and Chemical Biology, GERMANY
| | - Peter Leonard
- Center for Nanotechnology, Laboratory of Bioorganic Chemistry and Chemical Biology, GERMANY
| | - Frank Seela
- Universität Osnabrück, Institut für Chemie neuer Materialien, Barbarastraße 7, 49076, Osnabrück, GERMANY
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7
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Kondhare D, Leonard P, Seela F. Isoguanine (2-Hydroxyadenine) and 2-Aminoadenine Nucleosides with an 8-Aza-7-deazapurine Skeleton: Synthesis, Functionalization with Fluorescent and Clickable Side Chains, and Impact of 7-Substituents on Physical Properties. J Org Chem 2021; 86:14461-14475. [PMID: 34661407 DOI: 10.1021/acs.joc.1c01283] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
7-Functionalized 8-aza-7-deaza-2'-deoxyisoguanine and 8-aza-7-deaza-2-aminoadenine 2'-deoxyribonucleosides decorated with fluorescent pyrene or benzofuran sensor tags or clickable side chains with terminal triple bonds were synthesized. 8-Aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine was used as the central intermediate and was accessible by an improved two-step glycosylation/amination protocol. Functionalization of position-7 was performed either on 8-aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine followed by selective deamination of the 2-amino group or on 7-iodinated 8-aza-7-deaza-2'-deoxyisoguanosine. Sonogashira and Suzuki-Miyaura cross-coupling reactions were employed for this purpose. Octadiynyl side chains were selected as linkers for click reactions with azido pyrenes. KTaut values calculated from H2O/dioxane mixtures revealed that side chains have a significant influence on the tautomeric equilibrium. Photophysical properties (fluorescence, solvatochromism, and quantum yields) of the new 8-aza-7-deazapurine nucleosides with fluorescent side chains were determined. Remarkably, a strong excimer fluorescence in H2O was observed for pyrene dye conjugates of 8-aza-7-deazaisoguanine and 2-aminoadenine nucleosides with a long linker. In other solvents including methanol, excimer fluorescence was negligible. The 2-aminoadenine and isoguanine nucleosides with the 8-aza-7-deazapurine skeleton expand the class of nucleosides applicable to fluorescence detection with respect to diagnostic and therapeutic purposes.
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Affiliation(s)
- Dasharath Kondhare
- 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
| | - 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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Zhang A, Budow‐Busse S, Leonard P, Seela F. Anomeric and Enantiomeric 2'-Deoxycytidines: Base Pair Stability in the Absence and Presence of Silver Ions. Chemistry 2021; 27:10574-10577. [PMID: 34014006 PMCID: PMC8362019 DOI: 10.1002/chem.202101253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Indexed: 12/25/2022]
Abstract
Dodecamer duplex DNA containing anomeric (α/β-d) and enantiomeric (β-l/β-d) 2'-deoxycytidine mismatches was studied with respect to base pair stability in the absence and presence of silver ions. Stable duplexes with silver-mediated cytosine-cytosine pairs were formed by all anomeric and enantiomeric combinations. Stability changes were observed depending on the composition of the mismatches. Most strikingly, the new silver-mediated base pair of anomeric α-d-dC with enantiomeric β-l-dC is superior to the well-noted β-d/β-d-dC pair in terms of stability. CD spectra were used to follow global helical changes of DNA structure.
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Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Simone Budow‐Busse
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Laboratorium für Organische und Bioorganische ChemieInstitut für Chemie neuer MaterialienUniversität OsnabrückBarbarastrasse 749069OsnabrückGermany
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9
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Chai Y, Kondhare D, Zhang A, Leonard P, Seela F. The 2-Amino Group of 8-Aza-7-deaza-7-bromopurine-2,6-diamine and Purine-2,6-diamine as Stabilizer for the Adenine-Thymine Base Pair in Heterochiral DNA with Strands in Anomeric Configuration. Chemistry 2021; 27:2093-2103. [PMID: 33090562 PMCID: PMC7898646 DOI: 10.1002/chem.202004221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Indexed: 02/05/2023]
Abstract
Stabilization of DNA is beneficial for many applications in the fields of DNA therapeutics, diagnostics, and materials science. Now, this phenomenon is studied on heterochiral DNA, an autonomous DNA recognition system with complementary strands in α-D and β-D configuration showing parallel strand orientation. The 12-mer heterochiral duplexes were constructed from anomeric (α/β-D) oligonucleotide single-strands. Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides having the capability to form tridentate base pairs with dT were used to strengthen the stability of the dA-dT base pair. Tm data and thermodynamic values obtained from UV melting profiles indicated that the 8-aza-7-deaza 2'-deoxyribonucleoside decorated with a bromo substituent is so far the most efficient stabilizer for heterochiral DNA. Compared with that, the stabilizing effect of the purine-2,6-diamine 2'-deoxyribonucleoside is low. Global changes of helix structures were identified by circular dichroism (CD) spectra during melting.
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Affiliation(s)
- Yingying Chai
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Department of RespiratoryCritical Care Medicine Targeted Tracer, Research and Development LaboratoryWest China HospitalSichuan610041P. R. China
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical BiologyCenter for NanotechnologyHeisenbergstrasse 1148149MünsterGermany
- Laboratorium für Organische und Bioorganische ChemieInstitut für Chemie neuer MaterialienUniversität OsnabrückBarbarastrasse 749069OsnabrückGermany
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