Long oligodeoxynucleotides: chemical synthesis, isolation via catching-by-polymerization, verification via sequencing, and gene expression demonstration

• Yipeng Yin,
• Reed Arneson,
• Alexander Apostle,
• Adikari M. D. N. Eriyagama,
• Komal Chillar,
• Emma Burke,
• Martina Jahfetson,
• Yinan Yuan and
• Shiyue Fang

Beilstein J. Org. Chem. 2023, 19, 1957–1965, doi:10.3762/bjoc.19.146

• containing one single-nucleotide (dA) deletion. In the case of the 401 bp sequence, 19 out of 32 colonies contained the expected 401 bp fragment (Figure 3). Three colonies were submitted for Sanger sequencing (step 5', Figure 1). One colony (the one corresponding to lane 10) was found to have the correct

• full-length sequence. The sequences in the other two colonies had errors with one containing one dG-to-dA substitution and the other containing one single-nucleotide (dC) deletion, and one dT-to-dC and one dG-to-dA substitution. Construction of GFP gene and GFP expression in E. coli Gibson assembly was

• Information File 1 for sequence alignments). One of them contained the correct full-length 399 bp ODN. The other two had errors, among which one contained a dG-to-dA substitution, and the other contained a single-nucleotide (dA) deletion. For the 401 nt GFP fragment, ODNs from three colonies were sequenced as

Characterization of a new fusicoccane-type diterpene synthase and an associated P450 enzyme

• Jia-Hua Huang,
• Jian-Ming Lv,
• Liang-Yan Xiao,
• Qian Xu,
• Fu-Long Lin,
• Gao-Qian Wang,
• Guo-Dong Chen,
• Sheng-Ying Qin,
• Dan Hu and
• Hao Gao

Beilstein J. Org. Chem. 2022, 18, 1396–1402, doi:10.3762/bjoc.18.144

• monitored at 254 nm. Biosynthesis of FC-type diterpenoids. A) The biosynthetic pathway of 1, 2 and 4. B) Cyclization mechanisms of 1 and reported FC-type diterpenes. Supporting Information Supporting Information File 328: Experimental methods, nucleotide sequence, tables, and figures. Acknowledgements We

Synthesis of C6-modified mannose 1-phosphates and evaluation of derived sugar nucleotides against GDP-mannose dehydrogenase

• Sanaz Ahmadipour,
• Alice J. C. Wahart,
• Jonathan P. Dolan,
• Laura Beswick,
• Chris S. Hawes,
• Robert A. Field and
• Gavin J. Miller

Beilstein J. Org. Chem. 2022, 18, 1379–1384, doi:10.3762/bjoc.18.142

• pathogen in these cases is mucoid Pseudomonas aeruginosa. Such infections are characterised by overproduction of the exopolysaccharide alginate. We present herein the design and chemoenzymatic synthesis of sugar nucleotide tools to probe a critical enzyme within alginate biosynthesis, GDP-mannose

• evaluation against GMD. Keywords: alginate; chemical probe; enzymatic synthesis; GDP-mannose dehydrogenase; sugar nucleotide; Introduction The opportunistic Gram-negative pathogen, Pseudomonas aeruginosa (PA), becomes the dominant pathogen in patients suffering from cystic fibrosis (CF) and causes a

• interventions that could halt its production would be of significant value. Within the biosynthetic assembly of alginate there is a critical dependence upon the provision of one sugar nucleotide building block, GDP-mannuronic acid (GDP-ManA, 5). This material is sourced from the cytosolic metabolic pool

Make or break: the thermodynamic equilibrium of polyphosphate kinase-catalysed reactions

• Michael Keppler,
• Sandra Moser,
• Henning J. Jessen,
• Christoph Held and
• Jennifer N. Andexer

Beilstein J. Org. Chem. 2022, 18, 1278–1288, doi:10.3762/bjoc.18.134

• Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany 10.3762/bjoc.18.134 Abstract Polyphosphate kinases (PPKs) have become popular biocatalysts for nucleotide 5'-triphosphate (NTP) synthesis and regeneration. Two unrelated families are described: PPK1 and

• , PPK2) was found in Pseudomonas aeruginosa in 2002 [5]. PPK2 were later subdivided into three classes: PPK2-I, PPK2-II, and PPK2-III phosphorylating nucleotide diphosphates (NDPs), nucleotide monophosphates (NMPs), and both, respectively [6]. Nevertheless, these substrate profiles rather seem to be

• reaction where the terminal phosphate dissociates from the polyP chain before being attacked by the nucleotide [18]. Both mechanisms could proceed without a phosphate group transfer onto an amino acid side chain of the enzyme as in PPK1: here, the enzyme structure generates proximity and polarisation of

Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity

• Jamshid Amiri Moghaddam,
• Huijuan Guo,
• Karsten Willing,
• Thomas Wichard and
• Christine Beemelmanns

Beilstein J. Org. Chem. 2022, 18, 722–731, doi:10.3762/bjoc.18.72

• sequence alignments using MAFFT (7.450) [36]. Structure modelling of UbiA-297 was done using the SWISS-MODEL server [32] and visualized using Pymol (2.3.3). Regional alignment of homologous Ptase genes was done using MultiGeneBlast [37]. Nucleotide sequence accession numbers: The ubiA-297 and menA-1335

Sesquiterpenes from the soil-derived fungus Trichoderma citrinoviride PSU-SPSF346

• Wiriya Yaosanit,
• Vatcharin Rukachaisirikul,
• Souwalak Phongpaichit,
• Sita Preedanon and
• Jariya Sakayaroj

Beilstein J. Org. Chem. 2022, 18, 479–485, doi:10.3762/bjoc.18.50

• accession number MH997897) ribosomal RNA gene revealed that the fungus PSU-SPSF346 had close relationships with several strains of Trichoderma citrinoviride with 99% nucleotide identity for both DNA regions. Therefore, this fungus can be identified as Trichoderma citrinoviride. Fermentation, extraction, and

Chemical and chemoenzymatic routes to bridged homoarabinofuranosylpyrimidines: Bicyclic AZT analogues

• Sandeep Kumar,
• Jyotirmoy Maity,
• Banty Kumar,
• Sumit Kumar and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2022, 18, 95–101, doi:10.3762/bjoc.18.10

• acetylation; Introduction In the last few decades, modification of nucleoside/nucleotide analogues has been a field of keen interest to researchers due to their therapeutic properties for treatment of cancer, viral and microbial infections [1][2][3][4][5][6][7][8][9]. The very first cytotoxic

Synthetic strategies toward 1,3-oxathiolane nucleoside analogues

• Umesh P. Aher,
• Dhananjai Srivastava,
• Girij P. Singh and
• Jayashree B. S

Beilstein J. Org. Chem. 2021, 17, 2680–2715, doi:10.3762/bjoc.17.182

• ; separation of racemic nucleosides; stereoselectivity; Introduction Among all the biomolecules in an organism, nucleic acids, namely DNA and RNA, have the unique role of storing the genetic code – the nucleotide sequence that specifies the amino acid sequence of proteins that is essential for life on Earth

• ), which may be responsible for such differences [24]. Initial results point at a conventional mechanism of action. Therein, the investigation of the cellular metabolism predicts triphosphate formation of the compounds by phosphorylation, and the resulting nucleotide is a selective inhibitor of the HIV-1

Progress and challenges in the synthesis of sequence controlled polysaccharides

• Giulio Fittolani,
• Theodore Tyrikos-Ergas,
• Denisa Vargová,
• Manishkumar A. Chaube and
• Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

• (LG, e.g., phosphate, fluoride, nucleotide) are polymerized by the enzyme to form the desired polysaccharide (Figure 1A). Several classes of enzymes are available, including hydrolases, phosphorylases, sucrases, glycosyltransferases, and glycosynthases [19][20][21][22]. An excellent overview of the

Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides

• Mathias B. Danielsen and
• Jesper Wengel

Beilstein J. Org. Chem. 2021, 17, 1828–1848, doi:10.3762/bjoc.17.125

• review, we focus on important monomeric cationic modifications for ASOs, including locked nucleic acid (LNA) monomers, and their synthesis. Such modifications have been achieved either by direct conjugation to the nucleobase, the sugar or the backbone of nucleotide monomers of such ASOs. In addition, a

• electrostatic repulsion. In the following sections, a series of ASO-type oligonucleotides (ONs) which have been chemically modified with positively charged groups will be described, and their properties highlighted. Review ONs containing amine-group conjugates and nucleotide derivatives Many parameters can

• (poly)amine groups via the nucleobase on ASOs, thereby improving the RNA-binding affinity [26]. This strategy can be employed either on the nucleoside level, which requires many different nucleotide building blocks to be synthesized or via the so-called post-synthetic modification strategy of ONs. The

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

Double-headed nucleosides: Synthesis and applications

• Vineet Verma,
• Jyotirmoy Maity,
• Vipin K. Maikhuri,
• Ritika Sharma,
• Himal K. Ganguly and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2021, 17, 1392–1439, doi:10.3762/bjoc.17.98

• terminal carbons only. Double-headed nucleosides are synthetically derived nucleoside scaffolds that are known to impact significantly secondary structures in nucleic acids [29]. Some oligonucleotides containing a particular double-headed nucleotide monomer have been found to form a three-way junction

• participation of both nucleobases of the double-headed nucleotides in Watson–Crick base pairing. The same group also showed that a multiple incorporation of the double-headed nucleotide is also tolerated, but the double-headed nucleotides with the present design were not suitable as triplex-forming

• complementary base pairs was monitored by UV melting curve analysis [33]. Hybridization data revealed that the synthesized double-headed nucleotide recognized itself either through formation of Watson–Crick base pairs with two complementary adenosines or through the formation of T:T (thymine:thymine) base pairs

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• '-aminonucleoside couples to the 5'-H-phosphonate in the presence of a base (Scheme 1) [64]. In comparison with natural phosphodiester oligonucleotides, these modified oligonucleotides display improved nuclease resistance and an enhanced duplex thermal stability of 2.3–2.6 °C per linkage independent of nucleotide

• at the PS2 nucleotide sites of an siRNA duplex sense strand increase the thermal stability of the duplex to levels comparable to the unmodified variant, it also further improved the binding affinity to the Ago2 protein, hypothesized to be in part caused by a superior hydrophobic effect [92]. Glycol

• nucleotide in the gauche conformation and one in the anti conformation. There is also a large backbone-base inclination (46° to −53°) which results in zipperlike interstrand and reduced intrastrand base stacking interactions [103]. The crystal structure of an RNA duplex containing (R)-GNA revealed that this

Simulating the enzymes of ganglioside biosynthesis with Glycologue

• Andrew G. McDonald and
• Gavin P. Davey

Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64

• negative charge. Figure 1 shows the structure of the monosialylated ganglioside GM1a. The biosynthesis of gangliosides occurs in the endoplasmic reticulum and Golgi, where specific glycosyltransferases act, in stepwise fashion, by adding monosaccharides from sugar nucleotide donors, first to ceramide, and

• . The method involves a set of regular-expression-based rules acting on strings of characters that representing the monosaccharide units, x, model the actions of transferases in the general form, Ax + B = A + xB, where Ax is a nucleotide sugar and B is the carbohydrate moiety of the acceptor, be it a

• glycolipid or some other oligosaccharide, the nucleotide A is the product of the donor and xB is the acceptor product. The strings can be seen as a compression of the familiar condensed linear IUPAC notation, using a single-letter notation to represent sugars, with upper-case denoting ᴅ, and lowercase, the ʟ

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

• the latter was not yet synthetized. It is expected that the introduction of fluorine into the carbon–carbon double bond, in a position equivalent to the ring oxygen of the naturally occurring nucleotide, will improve molecular recognition and activity. In addition, the polarity of the nucleotide and

• deacetylation, 28 was readily converted to E-24 (see Scheme 8). These transformations of alkene E-9 illustrated how the geometry can be controlled for the preparation of tetrasubstituted fluoroalkenes. The synthesis of nucleotide mimics from either phosphonate 29 or azide 28 is underway and will be reported in

• acyclonucleotides. Acyclonucleotides as nucleotide surrogates. Olefination approaches and ring-opening of oxetane derivatives. Preparation of fluoroakylidene-oxetanes and their ring-opening reactions. Synthesis of benzyloxy-substituted fluoroethylidene-oxetane derivative 8. Effect of the medium on the selective

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

• receptor mRNA was developed. It consists of several functional modules including two deoxyribozymes 10–23, an RNA-dependent split malachite green aptamer, and an oligonucleotide platform. Deoxyribozymes specifically release a 27-nucleotide RNA fragment that is readily available for the interaction with the

• aptamer module. This solves a problem of secondary structure in hybridization with the target sequence of full-length mRNA. It was shown that within 24 hours the proposed sensor specifically recognized both a synthetic 60-nucleotide RNA fragment (LOD is 1.4 nM of RNA fragment at 37 °C) and a full-sized

• our SDFS on the sequence inside the first exon. Although splice variants of AR-FL (full-size molecule), AR-V7, and AR-V9 [17][18] are the most important ones from a clinical point of view, we analyzed all nucleotide sequences of the translated AR mRNAs from open databases (Supporting Information File

Opening up connectivity between documents, structures and bioactivity

• Christopher Southan

Beilstein J. Org. Chem. 2020, 16, 596–606, doi:10.3762/bjoc.16.54

• International Nucleotide Sequence Database Collaboration (INSDC) [32]. While compliance is not 100%, extensive literature and data set connections are now captured by both PubMed, PMC and EPMC. The paradox is that no open equivalent ever emerged in the chemistry domain, in part due to the dominance of SciFinder

Synthesis of C-glycosyl phosphonate derivatives of 4-amino-4-deoxy-α-ʟ-arabinose

• Lukáš Kerner and
• Paul Kosma

Beilstein J. Org. Chem. 2020, 16, 9–14, doi:10.3762/bjoc.16.2

• ; lipopolysaccharide; Introduction Glycosyltransferases are important enzymes that accomplish the transfer of activated sugar phosphates onto their respective acceptor molecules [1]. In most cases, nucleotide diphosphate sugars serve as the reactive species, but lipid-linked diphosphate derivatives are equally

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

• for the synthesis of pharmaceutically relevant benzo[4,5]furo[3,2-b]indoles in moderate to very good yield. The synthesized compounds have been analyzed with regard to their inhibitory activity (IC50) of nucleotide pyrophosphatases h-NPP1 and h-NPP3. The activity lies in the nanomolar range. The

• first time, a study related to the activity of the products as nucleotide pyrophosphatase inhibitors. In this context, we also studied the biological activity of previously synthesized diindolofurans and the results are compared with those of benzofuroindoles. Results and Discussion Following a

• 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

Installation of -SO₂F groups onto primary amides

• Jing Liu,
• Shi-Meng Wang,
• Njud S. Alharbi and
• Hua-Li Qin

Beilstein J. Org. Chem. 2019, 15, 1907–1912, doi:10.3762/bjoc.15.186

• liver [23]. The nucleotide-derived probe 5’-(para-fluorosulfonylbenzoyl)adenosine (5’-FSBA) was used for labelling the second nucleotide binding site, the adenine nucleotide regulatory site [24]. In addition, aryl fluorosulfates have also been widely applied as sustainable alternative to aryl halides in

Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries

• Xiao Xie,
• Michela Zuffo,
• Marie-Paule Teulade-Fichou and
• Anton Granzhan

Beilstein J. Org. Chem. 2019, 15, 1872–1889, doi:10.3762/bjoc.15.183

• fluorescence intensity in the presence of one or another G4-DNA or RNA structure, while no dye displayed preferential response to double-stranded DNA or single-stranded RNA analytes employed at equivalent nucleotide concentration. Thus, preferential fluorimetric response towards G4 structures appears to be a

• were made to take into account the peculiarities of some of the samples. In particular, 46AG was tested at 2.5 µM, to account for its dimeric G4 nature, and ct DNA and cl RNA were tested at 110 µM nucleotide concentration, which is equivalent to the total nucleotide concentration in a 5 µM sample of a

• ) Variation of the Het+ core. Heat map of the relative emission intensity enhancement (I/I0) of styryl dyes and thioflavin T (ThT) (c = 2.5 µM in K-100 buffer) in the presence of 2 molar equiv of G4-DNA (46AG: 1 molar equivalent), G4-RNA, or ct DNA and cl RNA controls used at equivalent nucleotide

Design, synthesis and biological evaluation of immunostimulating mannosylated desmuramyl peptides

• Rosana Ribić,
• Ranko Stojković,
• Lidija Milković,
• Mariastefania Antica,
• Marko Cigler and
• Srđanka Tomić

Beilstein J. Org. Chem. 2019, 15, 1805–1814, doi:10.3762/bjoc.15.174

• replacing the whole Mycobacterium in complete Freund’s adjuvant. MDP triggers an immune response by activating the mammalian NOD-like receptor, nucleotide binding oligomerization domain-containing protein 2 (NOD2). NOD2 is an intracellular protein that signals via the NF-κB pathway to proximally activate

Phylogenomic analyses and distribution of terpene synthases among Streptomyces

• Lara Martín-Sánchez,
• Kumar Saurabh Singh,
• Mariana Avalos,
• Gilles P. van Wezel,
• Jeroen S. Dickschat and
• Paolina Garbeva

Beilstein J. Org. Chem. 2019, 15, 1181–1193, doi:10.3762/bjoc.15.115

• redundant information. It may also reflect the mechanism of integration of the incoming genetic information into the chromosome of the target organism by homologous recombination within identical or highly similar nucleotide sequences. In this study, we searched for the minimal number of events that are

• filter and download the nucleotide and protein sequences of all complete genomes including an annotation file in GFF format. The 93 selected sequences and their accession numbers are listed in Table S2 (Supporting Information File 1). Construction of orthologous gene families Sequence data of the

• pipeline. Phylogenetic analyses Phylogenetic analyses on three different terpene synthases (geosmin synthases, 2-MIB synthases and epi-isozizaene synthases) were performed. Protein and nucleotide sequences were extracted from the Streptomyces genomes based on their distribution. Phylogenetic trees were

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

• -(ethylthio)-1H-tetrazole as activator instead of the typically used acetic anhydride. Oxidation was performed under standard conditions. The last nucleotide at the 5'-end of ODN was incorporated with a 5'-trityl nucleoside phosphoramidite instead of a 5'-DMTr counterpart. At the end of the synthesis, the 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

• relevant building blocks with mechanochemistry has further been shown by the recent mechanochemical protocols to transform nucleoside and nucleotide substrates (Figure 1) [18][19]. On the other hand, reports on mechanochemical protocols for the synthesis or derivatization of lipids are scarce [20][21