Article
Chemistry, Multidisciplinary
Samantha A. Kennelly, Ramkumar Moorthy, Ruben Silva Otero, Daniel A. Harki
Summary: In this study, four candidate CRDD monomers that mimic endogenous pyrimidines were synthesized and evaluated. It was found that two of them (2-NI and 2-NP) can function as CRDDs, while the other two (3-NP and 2-NB) undergo decomposition or transformation to higher-ordered structures upon photolysis. Additionally, it was discovered that all four pyrimidine mimics exhibit greater stability when base-paired against a previously reported 7-nitroindole CRDD monomer.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Organic
Kasper M. Beck, Linette Ruder, Tine S. Nicolai, Robert L. Pham, Nikolaj A. Risgaard, Mick Hornum, Poul Nielsen
Summary: Double-headed nucleotides theoretically store twice as much information as native nucleotides, but the two newly developed analogs still need improvement in enhancing base-pairing specificity. Additionally, an improved synthetic strategy is proposed to avoid using doubly protected diaminopurines and complicated deprotections.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Organic
Rion Maeda, Noriko Saito-Tarashima, Hideaki Wakamatsu, Yoshihiro Natori, Noriaki Minakawa, Yuichi Yoshimura
Summary: A new 4'-thio analogue of LNA/BNA monomer was successfully synthesized and incorporated into oligonucleotides, opening up new possibilities for oligonucleotide therapeutics.
Article
Chemistry, Organic
Kasper M. Beck, Robert L. Pham, Rita A. Nanim, Anders Laustsen, Poul Nielsen
Summary: The study introduces three new double-headed nucleotides with non-natural nucleobases, showing improved DNA duplex stability and mismatch discrimination compared to their unmodified predecessors. Among them, U-ClU stands out as the leading bis-uracil double-headed nucleotide analogue.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Kaivin Hadidi, Yitzhak Tor
Summary: Analogues of N,N-dimethyladenine with thieno- and isothiazolo-pyrimidine cores were modified using 3-substituted azetidines to produce fluorescent fluorophores with high emission quantum yields. The substituents on the azetidine ring correlated with the emission quantum yields. Ribosylation of the modified nucleobase resulted in a lower emission quantum yield in water compared to the precursor nucleobase, but the high emission quantum yield was restored in deuterium oxide, indicating the potential impact of the sugar moiety on the photophysical features of fluorescent nucleosides.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Aigui Zhang, Dasharath Kondhare, Peter Leonard, Frank Seela
Summary: The study explores the molecular recognition of complementary purine and pyrimidine bases in the Watson-Crick coding system. Experimental results show that the introduction of specifically modified base pairs can alter the stability and global helical structure of double-stranded DNA. Introducing purine-purine base pairs can lead to novel molecular recognition patterns.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Organic
Juri Eyberg, Daniela Goehringer, Amila Salihovic, Clemens Richert
Summary: Oligonucleotides are important tools in various fields including diagnostics and therapeutics. However, the use of ethynylpyridone C-nucleosides as analogs of thymidine is hindered by low yields of solid-phase syntheses. This study presents the synthesis of an improved building block that enables the high yield and purity synthesis of oligonucleotides containing ethynylmethylpyridone C-nucleoside.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Kaivin Hadidi, Kfir B. Steinbuch, Lara E. Dozier, Gentry N. Patrick, Yitzhak Tor
Summary: Puromycin derivatives modified with azetidine and 3,3-difluoroazetidine exhibit translation inhibition and bactericidal activity similar to natural antibiotic. These analogues can puromycylate nascent peptides, generating emissive products without follow-up chemistry. The 3,3-difluoroazetidine-containing analogue can fluorescently label newly translated peptides and be visualized in live and fixed cells.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Hidenori Okamura, Giang Hoang Trinh, Zhuoxin Dong, Yoshiaki Masaki, Kohji Seio, Fumi Nagatsugi
Summary: Unnatural base pairs (UBPs) with selective pairing properties have been widely used in nucleic acid-based technologies. In this study, we demonstrate a new design concept for achieving exclusive base pairing through the spatial separation of recognition units. By introducing alkynylated purines and pyridazines with pseudo-nucleobases, we successfully achieved stable and exclusive pairing properties in the DNA major groove. This study highlights the potential of separating the recognition interface as a strategy for developing new types of UBPs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Analytical
Youhui Zeng, Ruiying Peng, Yingcai Hu, Pan Luo, Ronghua Yang, Jishan Li, Jing Zheng
Summary: Spherical nucleic acids (SNAs) have been extensively utilized in molecular imaging and tumor therapy due to their adjustable hybridization activity, antinuclease digestion stability, and superior endocytosis. However, the challenge lies in the background signal caused by highly expressed biomarkers in tumors and the inability to precisely release probes at the chosen region. To address this issue, researchers have proposed an endogenous enzyme-activatable functional SNA (Ep-SNA) strategy for spatiotemporally controlled signal amplification molecular imaging and combinational tumor therapy.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Qinqin Yuan, Lidia Chomicz-Manka, Samanta Makurat, Wenjin Cao, Janusz Rak, Xue-Bin Wang
Summary: This study systematically investigates the electronic and geometric structures of four doubly deprotonated DNA building blocks, providing valuable insights into the mechanism of oxidative DNA damage. The results enhance the understanding of the basic building blocks of DNA at the molecular level, completing the depiction of nucleotides in various charge states.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Mateusz Dyguda, Artur Przydacz, Lukasz Albrecht
Summary: This manuscript describes the application of dearomative formal normal-electron-demand aza-Diels-Alder cycloaddition in the synthesis of tetrahydrofuropyridines. The method involves the aminocatalytic activation of 2-alkyl-3-furfurals and proceeds via the formation of dearomatized dienamine intermediate. The obtained cycloadducts can be further transformed into tetrahydrofuropyridines or functionalized cinnamates. The mechanism of the transformation was confirmed through DFT calculations.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Medicinal
Maria De Fenza, Anna Esposito, Giovanni Talarico, Graciela Andrei, Robert Snoeck, Daniele D'Alonzo, Annalisa Guaragna
Summary: In this study, six-membered nucleoside analogues with a piperidine ring as the preorganized (deoxy)ribose bioisostere were synthesized and evaluated for their antiviral activity. The 5-iododeoxyuridine analogue showed activity against all tested DNA viruses. DFT analysis and pH-dependent NMR experiments suggested that the antiviral activity was attributed to the biomimetic character of the piperidine ring, which can mimic the conformation of natural nucleosides when interacting with viral enzymes.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Mateusz Dyguda, Artur Przydacz, Lukasz Albrecht
Summary: This manuscript describes the application of dearomative formal normal-electron-demand aza-Diels-Alder cycloaddition in the synthesis of tetrahydrofuropyridines. The developed approach utilizes aminocatalytic activation of 2-alkyl-3-furfurals that proceeds via formation of the dearomatized dienamine intermediate. The obtained cycloadducts can be further transformed into tetrahydrofuropyridines or functionalized cinnamates.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Organic
Frederik Muggenburg, Alexander Biallas, Megane Debiais, Michael Smietana, Sabine Muller
Summary: The study demonstrates that 2'- or 3'-azido nucleosides immobilized on solid support can be excellent starting materials for the synthesis of oligonucleotides with 3'-terminal azide.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Organic
Fabienne Seyfert, Mathis Mitha, Hans-Achim Wagenknecht
Summary: The study presents a new strong reducing catalyst for the photoredox catalytic addition of alcohols to alkyl olefins, allowing non-activated substrates to undergo Markovnikov addition. This method also demonstrates tolerance towards various functional groups.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Sara Muller, Felix Manger, Lorenz Graf von Reventlow, Alexander Colsmann, Hans-Achim Wagenknecht
Summary: Supramolecular chemistry enables the construction of complex molecular architectures and the design of collective photophysical properties. Using DNA as a template for supramolecular structures offers precise control of chromophore position. Interaction studies between fullerenes and DNA show potential for advancements in optoelectronic applications.
FRONTIERS IN CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
David Rombach, Bernhard Birenheide, Hans-Achim Wagenknecht
Summary: Properly activated sulfur hexafluoride can serve as a valuable pentafluorosulfanylation reagent under photoredox catalysis, enabling the synthesis of oxygen-containing heterocycles in a single step from substituted alkenes. This advanced protocol, supported by theoretical calculations, not only provides insights into the pentafluorosulfanylation process and carbon-carbon bond formation, but also significantly expands the scope of valuable building blocks for medicinal and material chemistry.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Larissa Doll, Jens Lackner, Franziska Ronicke, Gerd Ulrich Nienhaus, Hans-Achim Wagenknecht
Summary: The research involves labeling siRNA strands with different dyes and tracking the delivery and effect of siRNA in HeLa cells through fluorescence lifetime imaging microscopy, demonstrating the potential of siRNA structures.
Review
Biochemistry & Molecular Biology
Hans-Achim Wagenknecht
Summary: Local DNA photodamaging by light is well-studied, while the mechanisms of remote DNA photodamage are only partially understood. Remote photodamage involves pathways to remote oxidatively generated DNA damage and DNA-mediated energy transport, providing an important extension to our understanding of light-induced DNA damage.
Article
Chemistry, Organic
Daniel Sack, Hans-Achim Wagenknecht
Summary: The study synthesized a short tripeptide as a photoredox catalyst and achieved high yields of methoxylation products with remarkably low catalyst loadings through an unconventional photoredox catalytic cycle. The concept of photozymes for photoredox catalysis shows significant potential for other photocatalytic reactions, especially in enantioselective photocatalysis.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2021)
Article
Chemistry, Organic
Fabian Weick, Desiree Steuernagel, Arina Belov, Hans-Achim Wagenknecht
Review
Chemistry, Organic
David Rombach, Hans-Achim Wagenknecht
Summary: This review summarizes recent efforts in the photoactivation of inert sulfur hexafluoride and provides insights into the photochemical mechanisms of switching between fluorination and pentafluoro-sulfanylation reactions of organic substrates.
SYNTHESIS-STUTTGART
(2022)
Article
Biochemical Research Methods
Julian Gebhard, Lara Hirsch, Christian Schwechheimer, Hans-Achim Wagenknecht
Summary: Fluorescent DNA probes were prepared using a modular approach and a click post-synthetic modification strategy. The probes showed high fluorescence light-up effect and brightness. Additionally, electron transfer and energy transfer processes were utilized to further enhance the fluorescence readout.
BIOCONJUGATE CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Desiree Steuernagel, Hans-Achim Wagenknecht
Summary: Acetals and ketals are important protecting groups for carbonyl compounds. A new method for acetalization and ketalization using photoredox catalysis has been developed. The method utilizes a biscyanolated perylene bisimide as an electron-poor photocatalyst and green light (525 nm LED). Silylenolethers derived from aldehydes react efficiently to give acetals with good to excellent yields, and the method shows a broad substrate range and high functional group tolerance. While aldehydes can be directly converted into their respective acetals, ketones must first be converted into silylenolethers before ketalization. The method does not require the use of acids or photoacids, additives or H-atom transfer reagents, expanding the substrate scope and repertoire of photoredox catalysis in carbonyl chemistry.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Philipp Geng, Eileen List, Franziska Ronicke, Hans-Achim Wagenknecht
Summary: Two green fluorescent tetrazine-modified cyanine-styryl dyes were synthesized for bioorthogonal labelling of DNA. The fluorescence of these dyes can be released by their interaction with DNA and through the conjugated tetrazine as quencher moiety. The dyes can penetrate cells at low concentrations and undergo fluorogenic reactions with BCN-modified DNA in living cells. The two-factor fluorescence release significantly improves the signal-to-noise ratio, eliminating the need for washing procedures prior to cell imaging.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Physical
Desiree Steuernagel, David Rombach, Daniel Sack, Martin Koos, Burkhard Luy, Hans-Achim Wagenknecht
Summary: A new method was developed to activate CCl3F using photoredox catalysis and functionalize alkenes with the CCl2F group. N-phenylphenothiazine was used as a highly reducing organophotocatalyst. This approach combines the efficient disposal of ozone depleting substances and greenhouse gases with the synthesis of valuable organic compounds, complements the concept of atom transfer radical addition, and provides direct synthetic access to the CCl2F group as a structural motif. The broad substrate scope and multifunctionalized product class enable various subsequent transformations.
Editorial Material
Chemistry, Multidisciplinary
Desiree Steuernagel, Hans-Achim Wagenknecht
Summary: Desiree Steuernagel and Hans-Achim Wagenknecht from the Karlsruhe Institute of Technology are featured on the cover of this issue. The image showcases a traffic roundabout, symbolizing the photocatalytic cycle for the conversion of aldehydes and silylenolethers into their acetals. Read the full article at 10.1002/chem.202203767.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Hulya Ucar, Hans-Achim Wagenknecht
Summary: Cyanolated distyrylbenzene conjugated to 2'-deoxyuridine is a new building block for supramolecular DNA architectures that combine aggregation-induced emission and sequence-selective binding. Cyanolated distyrylbenzenes occupy a high number of binding sites on the DNA template. Light can be collected and transferred to terminal Atto dyes in this assembly. Mixed DNA architectures with perylene can be programmed by the sequence of the DNA template.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Huelya Ucar, Hans-Achim Wagenknecht
Summary: Two conjugates of tetraphenylethylene with d-2’-deoxyuridine (1d) and l-2’-deoxyuridine (1l) were synthesized for constructing new supramolecular DNA architectures by self-assembly. The chirality of the non-templated assemblies is controlled by the sugar part configuration, while the DNA-templated assemblies are governed by the DNA configuration. The strong aggregation-induced emission and efficient energy transport properties make these DNA-based materials promising candidates for optoelectronic applications.