Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9

• -DNA (6’-diF-bc4,3-DNA). The difluorinated thymidine phosphoramidite building block was synthesized starting from an already known gem-difluorinated tricyclic glycal. This tricyclic siloxydifluorocyclopropane was converted into the [4.3.0]bicyclic nucleoside via cyclopropane ring-opening through the

• addition of an electrophilic iodine during the nucleosidation step followed by reduction. The gem-difluorinated bicyclic nucleoside was then converted into the corresponding phosphoramidite building block which was incorporated into oligonucleotides. Thermal denaturation experiments of these

• oligonucleotides hybridized to RNA showed a similar structure than the natural DNA/RNA duplex. Furthermore, since the structural investigation on the nucleoside level by X-ray crystallography and ab initio calculations pointed to a furanose conformation in the southern region, a RNase H cleavage assay was

New standards for collecting and fitting steady state kinetic data

• Kenneth A. Johnson

Beilstein J. Org. Chem. 2019, 15, 16–29, doi:10.3762/bjoc.15.2

• the alternate substrates are well known. Moreover, it is easy to perform single turnover kinetic measurements to examine steps leading up to the chemical reaction by mixing an enzyme DNA complex with only one nucleoside triphosphate. Recent work on DNA polymerase fidelity has shown that the rate of

6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations

• Sibylle Frei,
• Andrei Istrate and
• Christian J. Leumann

Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288

• either by a NIS-mediated or Vorbrüggen nucleosidation yielded in both cases the β-tricyclic nucleoside as major anomer. Subsequent desilylation and cyclopropane ring opening of these tricyclic intermediates afforded the unsaturated 6’F-bc4,3 nucleosides. The successful incorporation of the corresponding

• = −1.5 to −3.7 °C). Molecular dynamics simulation on the nucleoside and oligonucleotide level revealed the preference of the C1’-exo/C2’-endo alignment of the furanose ring. Moreover, the simulation of duplexes with complementary RNA disclosed a DNA/RNA-type duplex structure suggesting that this

• spectra (Supporting Information File 1). The plan for the pyrimidine nucleoside synthesis comprised the use of the meanwhile well-established β-selective N-iodosuccinimide (NIS)-mediated addition of a persilylated nucleobase to a tricyclic glycal [43][45][53][54]. Therefore, the gem-difluorinated

Nucleoside macrocycles formed by intramolecular click reaction: efficient cyclization of pyrimidine nucleosides decorated with 5'-azido residues and 5-octadiynyl side chains

• Jiang Liu,
• Peter Leonard,
• Sebastian L. Müller,
• Constantin Daniliuc and
• Frank Seela

Beilstein J. Org. Chem. 2018, 14, 2404–2410, doi:10.3762/bjoc.14.217

• Organische Chemie, Universität Münster, Corrensstrasse 40, 48149 Münster, Germany 10.3762/bjoc.14.217 Abstract Copper(I)-promoted "click" cyclization in the presence of TBTA afforded nucleoside macrocycles in very high yields (≈70%) without using protecting groups. To this end, dU and dC derivatives

• ’-azido-2’,5’-dideoxycytidine 2. Earlier, the nucleoside precursor 1 was used for DNA cross-linking and labelling [36]. The unprotected nucleoside 1 was treated with equimolar amounts of carbon tetrabromide and triphenylphosphine and a five-fold excess of sodium azide to obtain the azide derivative 2 (37

• reaction the use of the TBTA complex was essential for the cyclization of dC precursor 2 but not for dU precursor 7. Protection of precursor molecules is not required and only four steps are necessary to convert a nucleoside in a nucleoside macrocycle. The single crystal X-ray structure confirmed the click

Synthesis of new p-tert-butylcalix[4]arene-based polyammonium triazolyl amphiphiles and their binding with nucleoside phosphates

• Vladimir A. Burilov,
• Guzaliya A. Fatikhova,
• Mariya N. Dokuchaeva,
• Ramil I. Nugmanov,
• Diana A. Mironova,
• Pavel V. Dorovatovskii,
• Victor N. Khrustalev,
• Svetlana E. Solovieva and
• Igor S. Antipin

Beilstein J. Org. Chem. 2018, 14, 1980–1993, doi:10.3762/bjoc.14.173

Anomeric modification of carbohydrates using the Mitsunobu reaction

• Julia Hain,
• Patrick Rollin,
• Werner Klaffke and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2018, 14, 1619–1636, doi:10.3762/bjoc.14.138

•  15) [63]. Similar reaction conditions were applied by Nie et al. in the total synthesis of the nucleoside antibiotic A201A [64]. Notably, the n-Bu3P-ADDP reagent system led here to the formation of the pure α-glycoside. Likewise, a Mitsunobu glycosylation of complex phenols was successfully

• Mitsunobu methodology, the rebeccamycin analogue 124 was synthesized in high yield and complete β-stereoselectivity by Wang et al. from the glucose derivative 2 and 123 (Scheme 25) [101]. Application of the anomeric Mitsunobu coupling in nucleoside synthesis was pioneered by Szarek et al. [102], who reacted

• glycosylation, Grochowski explored the synthesis of new nucleoside analogues. 1-Hydroxy-benzotriazole, 1-hydroxy-2-cyanobenzimidazole, 1-hydroxyuracil, and 1-hydroxythymine were used to prepare the respective NO-furanosides in the manno- and ribo-series [115][116][117]. Miscellaneous The Mitsunobu reaction was

Glycosylation reactions mediated by hypervalent iodine: application to the synthesis of nucleosides and carbohydrates

• Yuichi Yoshimura,
• Hideaki Wakamatsu,
• Yoshihiro Natori,
• Yukako Saito and
• Noriaki Minakawa

Beilstein J. Org. Chem. 2018, 14, 1595–1618, doi:10.3762/bjoc.14.137

• , Tokushima, 770-8505, Japan 10.3762/bjoc.14.137 Abstract To synthesize nucleoside and oligosaccharide derivatives, we often use a glycosylation reaction to form a glycoside bond. Coupling reactions between a nucleobase and a sugar donor in the former case, and the reaction between an acceptor and a sugar

• ; nucleoside; oligosaccharide; Introduction Nucleic acids and oligosaccharides are both mandatory polymers for the maintenance of life and cell growth. The former exists in nuclei and codes genetic information, which is transformed into proteins through a transcription process known as the “central dogma

• studies by supplying biological tools for the analyses of these polymers, as well as by synthesizing effective drug candidates for the diseases mentioned above [4][8][9][10][11][12][13][14]. To synthesize nucleoside and oligosaccharide derivatives, glycosylation reactions are often used to form a

Oligonucleotide analogues with cationic backbone linkages

• Melissa Meng and
• Christian Ducho

Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111

• ' (Figure 5) [72][73][74]. In principle, the NAA-modification is inspired by 'high-carbon' nucleoside structures (i.e., nucleosides having more than five carbon atoms in the sugar unit) found in naturally occurring nucleoside antibiotics [75][76][77]. In muraymycin- and caprazamycin-type nucleoside

• antibiotics, among others, such 'high-carbon' nucleosides are uridine-derived amino acid structures ('glycyluridine', GlyU) [78][79][80], which are aminoribosylated at the 5'-hydroxy group. As part of our ongoing research program on muraymycin nucleoside antibiotics (e.g., muraymycin A1 (44)) and their

Mechanochemistry of nucleosides, nucleotides and related materials

• Olga Eguaogie,
• Joseph S. Vyle,
• Patrick F. Conlon,
• Manuela A. Gîlea and
• Yipei Liang

Beilstein J. Org. Chem. 2018, 14, 955–970, doi:10.3762/bjoc.14.81

• exploited grinding to facilitate disaggregation of DNA from tightly bound proteins through selective denaturation of the latter. Despite the wide application of ball milling to amino acid chemistry, there have been limited reports of mechanochemical transformations involving nucleoside or nucleotide

• : specifically, solid solutions, cocrystals, polymorph transitions, carbon nanotube dissolution and inclusion complex formation. Keywords: DNA; green chemistry; mechanochemistry; nucleoside; nucleotide; Introduction Several definitions of mechanochemistry have been attempted since Ostwald included it as one of

• vessel (and its shape); the mass of the ball(s); and the hardness of the colliding materials. In order of descending hardness, zirconia, stainless steel, copper and PTFE have all been used to effect mechanochemical transformation of nucleoside or nucleotide substrates. During a study of amide coupling

On the design principles of peptide–drug conjugates for targeted drug delivery to the malignant tumor site

• Eirinaios I. Vrettos,
• Gábor Mező and
• Andreas G. Tzakos

Beilstein J. Org. Chem. 2018, 14, 930–954, doi:10.3762/bjoc.14.80

• diminishing expressed nucleoside receptors responsible for the cell uptake of gemcitabine [6]. Additionally, chemotherapy with anticancer agents is often hampered by their poor aqueous solubility, low oral bioavailability and metabolic instability. These drawbacks are linked to the unfavorable ADME

• loading that is usually preferred, mostly due to poor physicochemical properties. Below we analyze a set of drugs that have been tailored and incorporated in PDCs. Gemcitabine (Gem): Gemcitabine (dFdC) is a nucleoside analog of deoxycytidine in which the hydrogen atoms on the 2' carbon are replaced by

• deactivation through deamination in its inactive metabolite dFdU, the acquired multidrug resistance (MDR) and its high hydrophilicity deterring its prolonged drug release from various vehicles [88], which therefore reduces the effective concentration of gemcitabine. It enters cells through nucleoside

Phosphodiester models for cleavage of nucleic acids

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

• studies with small molecular phosphodiesters. Keywords: Cleavage; DNA; kinetics; mechanism; RNA; Introduction Nucleic acids are polymeric diesters of phosphoric acid that store and transfer biological information. In biological systems, the diester linkages bridging 3´-O of one nucleoside to the 5´-O of

• transphosphorylation by departure of the 5´-linked nucleoside [3]. The half-life at pH 6–7 and 25 °C is around 10 years [4][5], the enzymatic cleavage by RNase A being 3∙1011 times faster [6]. Interestingly, the RNA phosphodiester bonds are additionally subject to cleavage by RNA itself, viz. by RNA sequences known as

• leaving groups that are less basic than EtO−, such as 5´-O− of nucleoside, the lifetime expectedly is shorter. If the leaving group is very good, such as an aryl group, a synchronous concerted mechanism (ANDN) may take over the stepwise mechanism (AN + DN). Model compounds and experimental tools Studies

Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides

• Kartik Temburnikar and
• Katherine L. Seley-Radtke

Beilstein J. Org. Chem. 2018, 14, 772–785, doi:10.3762/bjoc.14.65

• and supramolecular complexes [10][11][12][13][14][15][16][17][18][19][20][21][22]. Nucleic acids are composed of a monomeric nucleoside unit that features an aromatic nitrogenous moiety (a nucleobase) connected to a pentose sugar, which in turn is attached to a phosphate group (Figure 1) [7]. The

• pentose sugar and the nucleobase are connected by a carbon–nitrogen bond that is adjacent to the sugar oxygen resulting in an hemiaminal ether bond, also known as the glycosidic bond. Because of their key role in many biological processes, modifications to the nucleoside structure have been widely

• employed in the design of drugs, most notably in the fields of virology and cancer research [13][14][15]. Variations in the nucleoside scaffold are typically accomplished by the insertion, deletion or transposition of functional groups or atoms [23][24][25][26][27][28][29]. The varied properties of such

AuBr₃-catalyzed azidation of per-O-acetylated and per-O-benzoylated sugars

• Jayashree Rajput,
• Srinivas Hotha and
• Madhuri Vangala

Beilstein J. Org. Chem. 2018, 14, 682–687, doi:10.3762/bjoc.14.56

• purine and pyrimidine nucleoside synthesis using per-O-acyl/per-O-benzoyl furanosyl and pyranosyl o-hexynylbenzoates [23]. Subsequently, Hotha and co-workers utilized propargyl 1,2-orthoesters and alkynyl glycosyl carbonate donors for the synthesis of pyrimidine nucleosides [24][25]. In addition, N

Enzyme-free genetic copying of DNA and RNA sequences

• Marilyne Sosson and
• Clemens Richert

Beilstein J. Org. Chem. 2018, 14, 603–617, doi:10.3762/bjoc.14.47

• oligonucleotide is present, stacking with the base of its 5'-terminal nucleoside further adds to the attractive forces experienced by incoming monomers. This is shown schematically in Figure 5. Because downstream-binding strands favorably affect the rate and selectivity of primer extension, we have dubbed them

Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing

• Françoise Debart,
• Christelle Dupouy and
• Jean-Jacques Vasseur

Beilstein J. Org. Chem. 2018, 14, 436–469, doi:10.3762/bjoc.14.32

Preparation of trinucleotide phosphoramidites as synthons for the synthesis of gene libraries

• Ruth Suchsland,
• Bettina Appel and
• Sabine Müller

Beilstein J. Org. Chem. 2018, 14, 397–406, doi:10.3762/bjoc.14.28

• of two suitably protected monomers to generate a dinucleotide, which then can be extended in either 5'- or 3'-direction (Figure 3). Surprisingly, only one report has made use of this "economy", first coupling a 5'-O-DMTr-protected nucleoside-3'-ortho-chlorophenylphosphotriester to a 3'-O-levulinoyl

• -azidomethylbenzoyl)-protected nucelosides, followed by removal of the 5'-O-DMTr group and extension of the dimer to the trimer by coupling of another N-acyl-3'-O-(o-chlorophenylphosphate)nucleoside. The final removal of the 2-azidomethylbenzoyl group occurred by reduction of the azide with triphenylphosphine in

• , although using phosphite triester chemistry [27]. In this case, the synthesis started with the coupling of an N-acyl-5'-O-DMTr-protected nucleoside-3'-O-phosphoramidite to an N-acyl-3'-O-TBDMS-protected nucleoside, followed by oxidation of the internucleotide phosphorous. Upon cleavage of the 5'-O-DMTr

Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• derivative. 5-Benzothiophene- and 5-benzofuran-modified uracil in aegPNA exhibited a fluorescence that was marginally sensitive to the environment [195]. When incorporated into PNA, benzothiophene-uracil exhibited an increased fluorescence compared to the free nucleoside. The opposite effect was observed

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• sodium methoxide in MeOH, which yielded the free nucleoside 15 in 71%. Standard DMTr protection furnished compound 16 which was then activated for oligonucleotide solid-phase synthesis (SPS) by phosphitylation using CEP-Cl. The total yield of tCnitro deoxyribose phosphoramidite was 0.8% over 6 steps

• nucleoside in 65% yield. Subsequent phosphitylation followed by salt-formation finally furnished compound 35 in 52% over two steps. Since the quadracyclic adenine presented an overall structural similarity with adenine and keeping a very rigid heterocyclic system suggesting few options for the molecule to

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• adequately prepared and characterized. For that reason, a short description of the most important issues in sample preparation is summarized in chapters 2.2 and 2.3. 2.1. Relation between DNA or RNA secondary structure and polarization spectroscopy Nucleobases are achiral but nucleoside and nucleotide

Acid-catalyzed ring-opening reactions of a cyclopropanated 3-aza-2-oxabicyclo[2.2.1]hept-5-ene with alcohols

• Katrina Tait,
• Alysia Horvath,
• Nicolas Blanchard and
• William Tam

Beilstein J. Org. Chem. 2017, 13, 2888–2894, doi:10.3762/bjoc.13.281

• the structure against cleavage by nucleoside phosphorylases or hydrolases [18][19]. The addition of a cyclopropane unit could provide further rigidity that could better stabilize the compound, thereby enhancing its biological activity. Both of these reported ring-openings of cyclopropanated 3-aza-2

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• nucleophiles such as nucleoside mono-, -di- or -triphosphates and are typically reacted in anhydrous DMF in the presence of zinc chloride. The GMP imidazolide (18) is reacted with m7GDP (17) in the presence of ZnCl2 as catalyst to yield m7GpppG (12) [49]. In the past years, variations of this general synthetic

CF₃SO₂X (X = Na, Cl) as reagents for trifluoromethylation, trifluoromethylsulfenyl-, -sulfinyl- and -sulfonylation and chlorination. Part 2: Use of CF₃SO₂Cl

• Hélène Chachignon,
• Hélène Guyon and
• Dominique Cahard

Beilstein J. Org. Chem. 2017, 13, 2800–2818, doi:10.3762/bjoc.13.273

• surprising formation of a 5’-chloro nucleoside, when used in an attempt to prepare the corresponding 5’-OTf nucleoside [54]. Moreover, considering the excellent selectivity of the combination CF3SO2Cl/Et3N towards the chlorination of substrates displaying a hydroxy group, the reaction could be further

Metal-mediated base pairs in parallel-stranded DNA

• Jens Müller

Beilstein J. Org. Chem. 2017, 13, 2671–2681, doi:10.3762/bjoc.13.265

• Nucleic acids are increasingly being applied in areas beyond their original biological context, e.g., as a scaffold for the defined spatial arrangement of functional entities [1][2][3]. This often goes along with the formal substitution of a canonical nucleoside (or any other nucleic acid component) by an

• -mediated pyrrolocytosine:pyrrolocytosine base pairs [62]. These investigations not only included the 2PyrPC and 3PyrPC residues reported above, but also a PhPC nucleoside bearing a phenyl substituent. Accordingly, a possible additional stabilization due to the presence of the (potentially coordinating

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• –nucleoside conjugates that are bound and assembled along the (dA)10 or T10 template are kept soluble in aqueous media. A higher concentrated stock solution of each chromophore–nucleobase conjugate was prepared in DMSO and added as aliquots to an aqueous solution (2.5 μM) of the (dA)10 or T10 template. The

• was prehybridized, so that canonical base pairing of the chromophore–nucleoside conjugates with the template could be excluded. After centrifugation, compound 3 shows no effective self-assembly to single or double-stranded templates in buffer; only in water an assembly occurring to both single

Phosphonic acid: preparation and applications

• Charlotte M. Sevrain,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2017, 13, 2186–2213, doi:10.3762/bjoc.13.219

• commonly used as precursors of phosphonic acids especially for the synthesis of aminophosphonic acids (α [209][210], β [211] or γ [212]) and also for the synthesis of nucleoside analogues [213]. The use of these intermediates is likely explained by the possibility to use chiral diamine that can act as a