Selective preparation of tetrasubstituted fluoroalkenes by fluorine-directed oxetane ring-opening reactions

• Clément Q. Fontenelle,
• Thibault Thierry,
• Romain Laporte,
• Emmanuel Pfund and
• Thierry Lequeux

Beilstein J. Org. Chem. 2020, 16, 1936–1946, doi:10.3762/bjoc.16.160

• nucleotides such as the antiviral agent FPMPA (IV) [7][8][9]. Other main structural modifications of ACN relied on the introduction of a hydroxy group into the aliphatic chain to improve hydrogen bonding with enzymes [10], or of a carbon–carbon double bond to constrain the aliphatic chain and to limit

Three new O-isocrotonyl-3-hydroxybutyric acid congeners produced by a sea anemone-derived marine bacterium of the genus Vibrio

• Dandan Li,
• Enjuro Harunari,
• Tao Zhou,
• Naoya Oku and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1869–1874, doi:10.3762/bjoc.16.154

• SI9 was isolated from its outer tissue specimen according to the method described previously [19] and identified as a member of the genus Vibrio on the basis of an 98.6% similarity in the 16S rRNA gene sequence (1458 nucleotides; DDBJ accession number LC498627) to Vibrio nereis DSM 19584T (accession

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• -up of lipid-linked galactan precursors. The crude enzymes used in the assay allow for in situ synthesis of the acceptor for galactan polymerization, decaprenyl-P-P-GlcNAc-Rha (GL2), from endogenous decaprenyl phosphate and sugar nucleotides UDP-GlcNAc and TDP-Rha supplied in the reaction mixture

A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA

• Ekaterina A. Bryushkova,
• Erik R. Gandalipov and
• Julia V. Nuzhina

Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100

•  1, Table S1 and Figure S1). Based on the results of the bioinformatics analysis, an RNA sequence of 60 nucleotides (nt) was selected as a target (Table S2, 60-AR_RNA). This sequence was located in the conserved exon 1, position 1–2140 nt. The specificity of 60-AR_RNA for the human androgen receptor

A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium

• Shun Saito,
• Kota Atsumi,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Naoya Oku,
• Md. Rokon Ul Karim,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1100–1110, doi:10.3762/bjoc.16.97

• (Biological Resource Center, National Institute of Technology and Evaluation, Chiba, Japan). The strain was identified as a member of the genus Pseudosporangium on the basis of 99.7% similarity in the 16S rRNA gene sequence (1428 nucleotides; GenBank accession number LC512747) to Pseudosporangium ferrugineum

Two antibacterial and PPARα/γ-agonistic unsaturated keto fatty acids from a coral-associated actinomycete of the genus Micrococcus

• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku,
• Nobuyasu Matsuura,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 297–304, doi:10.3762/bjoc.16.29

• emerged on the plates, which were transferred onto a new agar medium to obtain pure isolates. One of these isolates, coded as C5-9, was identified as a member of the genus Micrococcus on the basis of 99.9% similarity in the 16S rRNA gene sequence (1395 nucleotides; DNA Data Bank of Japan/DDBJ accession

Two new aromatic polyketides from a sponge-derived Fusarium

• Mada Triandala Sibero,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Ocky K. Karna Radjasa,
• Agus Sabdono,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2019, 15, 2941–2947, doi:10.3762/bjoc.15.289

• ][30]. Strain KJMT.FP.4.3 was identified as Fusarium on the basis of the gene sequence analytical data of the ITS domain of partial 18S rRNA gene and 28S rRNA gene. Strain KJMT.FP.4.3 showed 99.7% similarity of ITS domain of partial 18S rRNA gene and 28S rRNA gene (555 nucleotides, GeneBank accession

• number MK393925.1) to Fusarium oxysporum strain NZZCDHL (549 nucleotides, GeneBank accession number KU939031.1) and 99.5% similarity of ITS domain of partial 18S rRNA gene and 28S rRNA gene to Fusarium oxysporum isolate DG-2 (548 nucleotides, GeneBank accession number MK429839.1). Fermentation Strain

Palladium-catalyzed synthesis and nucleotide pyrophosphatase inhibition of benzo[4,5]furo[3,2-b]indoles

• Hoang Huy Do,
• Saif Ullah,
• Alexander Villinger,
• Joanna Lecka,
• Jean Sévigny,
• Peter Ehlers,
• Jamshed Iqbal and
• Peter Langer

Beilstein J. Org. Chem. 2019, 15, 2830–2839, doi:10.3762/bjoc.15.276

• aryl substituent located on the nitrogen atom. Nucleotide pyrophosphatase activity Nucleotide pyrophosphatases belong to the family of ecto-nucleotidases [34][35]. They can hydrolyze nucleotides, dinucleotides, and nucleotide sugars, e.g., ATP, ADP, NAD+, ADP-ribose and diadenosine polyphosphates [36

Isolation and biosynthesis of an unsaturated fatty acid with unusual methylation pattern from a coral-associated bacterium Microbulbifer sp.

• Amit Raj Sharma,
• Enjuro Harunari,
• Tao Zhou,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2019, 15, 2327–2332, doi:10.3762/bjoc.15.225

• rRNA gene sequence (1405 nucleotides; DDBJ accession number LC456787) to Microbulbifer variabilis Ni-2088T (accession number AB167354). Fermentation The producing strain C4-6 was maintained on marine agar 2216 (Difco). A single colony of strain C4-6 was inoculated into a 500 mL K-1 flask containing 100

Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection

• Shahien Shahsavari,
• Dhananjani N. A. M. Eriyagama,
• Bhaskar Halami,
• Vagarshak Begoyan,
• Marina Tanasova,
• Jinsen Chen and
• Shiyue Fang

Beilstein J. Org. Chem. 2019, 15, 1116–1128, doi:10.3762/bjoc.15.108

• -β-cyanoethyl-dT phosphoramidite were used for incorporating dA, dC, dG and dT nucleotides, respectively. The coupling conditions were standard except that in some cases, coupling was increased from two to three times. Capping failure sequences was achieved using the phosphoramidite 25 with 5

Synthesis of acylglycerol derivatives by mechanochemistry

• Karen J. Ardila-Fierro,
• Andrij Pich,
• Marc Spehr,
• José G. Hernández and
• Carsten Bolm

Beilstein J. Org. Chem. 2019, 15, 811–817, doi:10.3762/bjoc.15.78

• Chemosensation, Institute for Biology II, RWTH Aachen University, D-52074 Aachen, Germany 10.3762/bjoc.15.78 Abstract In recent times, many biologically relevant building blocks such as amino acids, peptides, saccharides, nucleotides and nucleosides, etc. have been prepared by mechanochemical synthesis. However

Thermophilic phosphoribosyltransferases Thermus thermophilus HB27 in nucleotide synthesis

• Ilja V. Fateev,
• Ekaterina V. Sinitsina,
• Aiguzel U. Bikanasova,
• Maria A. Kostromina,
• Elena S. Tuzova,
• Larisa V. Esipova,
• Tatiana I. Muravyova,
• Alexei L. Kayushin,
• Irina D. Konstantinova and
• Roman S. Esipov

Beilstein J. Org. Chem. 2018, 14, 3098–3105, doi:10.3762/bjoc.14.289

• parameters for TthHPRT with natural substrates were determined. Two nucleotides were synthesized: 9-(β-D-ribofuranosyl)-2-chloroadenine 5'-monophosphate (2-Сl-AMP) using TthAPRT and 1-(β-D-ribofuranosyl)pyrazolo[3,4-d]pyrimidine-4-one 5'-monophosphate (Allop-MP) using TthНPRT. Keywords: adenine

• phosphoribosyltransferase; catalysis; enzyme; hypoxanthine phosphoribosyltransferase; multi-enzyme cascade; nucleotides; thermophiles; Introduction Bacterial phosphoribosyltransferases are used in multi-enzymatic cascades that perform nucleotide synthesis de novo [1][2]. Recently, we reported on the possibility of cascade

• corresponding nucleotides (Figure 1). The use of thermophilic phosphoribosyltransferases allows carrying out reactions at a higher temperature, so the concentrations of heterocyclic bases can be increased [1][2][3]. There is great interest in the development of multi-enzymatic cascades [4][5][6][7][8][9] for

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

• unsaturated 6’-fluoro[4.3.0]bicyclo nucleotides (6’F-bc4,3-DNA). Two 6’F-bc4,3 phosphoramidite building blocks (T and C) were synthesized starting from a previously described [3.3.0]bicyclic sugar. The conversion of this sugar to a gem-difluorinated tricyclic intermediate via difluorocarbene addition followed

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

• display increased lipophilicity they have the potential to be utilized for the transmembrane delivery of nucleotides and oligonucleotides. More important, all of the macrocyle moieties and the size of the macrocycle can be altered. The system can be regarded as a new lead for further structural and

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

• for nucleotides sensing through a dye replacement procedure. It is unusual that disubstituted macrocycles 10a,b bind more effectively a less charged adenosine 5'-diphosphate (ADP) than adenosine 5'-triphosphate (ATP). A simple colorimetric method based on polydiacetylene vesicles decorated with 10b

• attention to the synthesis of host molecules with high affinity to biologically important anions [1][2][3][4][5]. Among these anions, nucleotide recognition and sensing represents an especially important research area due to the great biological significance of these anions. Adenine-containing nucleotides

• nucleotides must possess selectivity towards these anions. From this point of view, nucleotide receptors based on polyammonium cations are of great demand because the electrostatic interactions of such polyammonium systems and negatively charged phosphates are strong. Hydrogen bonding [8] and π-stacking

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

• cell viability, their biological synthesis, including the synthesis of their monomer units, e.g., nucleotides, is highly regulated. Damage to these vital molecules often results in congenital disease with ultimately fatal consequences [2][3]. Accordingly, the study of polymers and their biosynthesis is

Phosphoramidite building blocks with protected nitroxides for the synthesis of spin-labeled DNA and RNA

• Timo Weinrich,
• Eva A. Jaumann,
• Ute M. Scheffer,
• Thomas F. Prisner and
• Michael W. Göbel

Beilstein J. Org. Chem. 2018, 14, 1563–1569, doi:10.3762/bjoc.14.133

• required to assemble oligonucleotides by phosphoramidite chemistry and to ligate them enzymatically, are known to partially degrade nitroxides. This problem can be reduced by postsynthetic introduction of the spin label [13][14][15][16][17][18][19][20][21][22][23][24]. Starting from convertible nucleotides

• of hemiacetals. After the annealing procedure, mean spin labeling efficiencies of 96% have been found. Samples of similar quality including TEMPO labeled cytidines are also accessible by postsynthetic modification of convertible nucleotides [8][25][26]. However, the analogous reaction forming TEMPO

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• eight Hoogsteen-paired hydrogen bonds to form a tetrad (Figure 1) has further enhanced our understanding of the diversity of DNA shapes and structures. In a parallel tetramolecular quadruplex d(TG4T), the features of nucleotides at each base resemble that of the B-DNA (C2’-endo sugar pucker, anti

• binding affinity using sophisticated molecular dynamics approach with eight different nucleotides having variety of sequences. It has been observed that QUE appears to be a minor groove binder, whereas FLP involves in combined mode of interaction such as minor groove binding and intercalation. A set of

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

• mills [46][47]. Reaction scales up to 40 g were described and the conditions developed enabled exclusive formation of the β-anomer of nicotinamide riboside (NR) in the absence of toxic bromide salts. Preparation and reactions of nucleotides and their analogues Phosphorylation of NR on gram-scales using

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

• ribozymes [7]. The length of these catalytic sequences varies from 70–150 nucleotides of the so-called small ribozymes to hundreds of nucleotides of large ribozymes. Their catalytic efficiency is somewhat more modest than that of protein enzymes. The remarkable catalytic efficiency has made the action of

An uracil-linked hydroxyflavone probe for the recognition of ATP

• Márton Bojtár,
• Péter Zoltán Janzsó-Berend,
• Dávid Mester,
• Dóra Hessz,
• Mihály Kállay,
• Miklós Kubinyi and
• István Bitter

Beilstein J. Org. Chem. 2018, 14, 747–755, doi:10.3762/bjoc.14.63

• and Materials Science, Budapest University of Technology and Economics, 1521 Budapest, Hungary 10.3762/bjoc.14.63 Abstract Background: Nucleotides are essential molecules in living systems due to their paramount importance in various physiological processes. In the past years, numerous attempts were

• made to selectively recognize and detect these analytes, especially ATP using small-molecule fluorescent chemosensors. Despite the various solutions, the selective detection of ATP is still challenging due to the structural similarity of various nucleotides. In this paper, we report the conjugation of

• ; nucleotide recognition; Introduction Nucleotides play essential roles in various physiological processes, such as energy transportation [1], DNA synthesis [2] and cell signaling events [3]. Especially, adenosine-5’-triphosphate (ATP) is vital, since it is the main energy source in living systems [4]. The

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

• . It involves the incorporation of nucleotides at the terminus of a primer and is directed by base pairing. The reaction occurs in aqueous medium and leads to phosphodiester formation after attack of a nucleophilic group of the primer. Two aspects of this reaction will be discussed in this review. One

• suggest that enzyme-free primer extension is a more powerful reaction than previously thought. Keywords: base pairing; DNA; enzyme-free primer extension; nucleotides; oligonucleotides; replication; RNA; Introduction Replication of genetic information is critical for all living systems. In the cell, this

• examples can also be found in the literature of the 1960s [12]. The early monomer-based work on copying RNA focused on oligomerization of nucleotides on homosequences as templates [13][14]. The best results were observed for poly(C) as template, the 2-methylimidazolide of guanosine as activated monomer

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

• strategies include antisense oligonucleotides (AONs), ribozymes, DNAzymes, small interfering RNAs (siRNAs) and micro RNAs (miRNAs) that specifically target the complementary mRNA sequence of the relevant undesired gene before translation. AONs are single-stranded DNA of 15 to 25 nucleotides in length that

• , more potent than AONs or ribozymes for gene knockdown, is centered on the RNA interference (RNAi) mechanism, which uses two natural pathways for gene silencing. One is guided by double-stranded siRNAs of 19–23 nucleotides in length that are fully complementary to the mRNA targets, and the other is

• guided by miRNAs (22 nucleotides in length) that bind incorrectly within the 3’-untranslated region (3’-UTR) of the target mRNAs [7]. miRNAs also represent interesting targets, and inhibition of their function was obtained using anti-miRNA AONs via an antisense approach or via the blocking of the mRNA

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

• possibility to control randomization. The basic principle consists of using chemically synthesized primers of mixed composition for introducing subsets of the 20 canonical amino acids at a defined position of the protein [9]. In the simplest way, a mixture of the four standard nucleotides is used for coupling

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

• derivatives are optically active. The π→π* transitions of the bases (Scheme 1) contribute to the electronic circular dichroism mostly as a result of the chiral perturbation exerted by the sugar moiety. The ECD signals of single nucleosides/nucleotides are, accordingly, quite small. Coupling into