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

• and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA 10.3762/bjoc.19.146 Abstract Long oligodeoxynucleotides (ODNs) are segments of DNAs having over one hundred nucleotides (nt). They are typically assembled using enzymatic methods such as PCR and

• . Keywords: automated synthesis; catching-by-polymerization; gene assembly; long oligonucleotide; synthetic biology; Introduction Long oligodeoxynucleotides (ODNs) are segments of DNAs extending beyond one hundred nucleotides (nt). Emerging research areas such as synthetic biology [1][2], protein

• suppliers were not able to provide single-stranded ODNs (ssODNs) with this length. Because double-stranded ODNs (dsODNs) of a few hundred nucleotides in length devoid of difficult structures are relatively easy to access using well-established technologies such as PCR assembly, and they are available from

Synthesis of ether lipids: natural compounds and analogues

• Marco Antônio G. B. Gomes,
• Alicia Bauduin,
• Chloé Le Roux,
• Romain Fouinneteau,
• Wilfried Berthe,
• Mathieu Berchel,
• Hélène Couthon and
• Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96

Navigating and expanding the roadmap of natural product genome mining tools

• Friederike Biermann,
• Sebastian L. Wenski and
• Eric J. N. Helfrich

Beilstein J. Org. Chem. 2022, 18, 1656–1671, doi:10.3762/bjoc.18.178

• nucleotides at a certain position of a protein or DNA sequence, respectively) with pre-determined transition probabilities from one state to the next (e.g., the transition probability in a sequence between one base at a given position to another base at the next position). A sequence of probabilities is

A new route for the synthesis of 1-deazaguanine and 1-deazahypoxanthine

• Raphael Bereiter,
• Marco Oberlechner and
• Ronald Micura

Beilstein J. Org. Chem. 2022, 18, 1617–1624, doi:10.3762/bjoc.18.172

• nitration. A further strength of our route is divergency, additionally enabling the synthesis of 1-deazahypoxanthine (c1I base). Keywords: deazapurine; heterocycles; imidazopyridines; nucleoside; nucleotides; pyrrolopyrimidines; RNA atomic mutagenesis; Introduction Deazapurines (imidazopyridines and

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

• sugar nucleotides To evaluate pyrophosphorylative coupling using the C6-modified mannose 1-phosphates we selected the recombinant GDP-mannose pyrophosphorylase (GDP-Man PP) from Salmonella enterica, previously established to have a broad promiscuity for GDP-Man synthesis [4][6][15]. Glycosyl 1

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

• optimisation of biocatalytic syntheses of nucleotides as well as nucleotide regeneration systems (Figure 3a and 3b). In a regeneration system (exemplarily shown for the hexokinase-catalysed phosphorylation of glucose (Figure 3a) the formed ADP has to be converted back to ATP to maintain a sufficient pool of

• by accounting for molecular repulsion and attraction caused by van-der-Waals forces, hydrogen bonding, and Coulomb forces. The ePC-SAFT parameters of the nucleotides were fitted in previous works to experimental osmotic pressures of pseudo-binary mixtures of nucleotide and water [29][33]. As

• modelling polyP with high chain length is currently not possible with ePC-SAFT, we assumed that only nucleotides were present in water. The consequence of this assumption is that interactions among nucleotides and polyP were considered to be equal to interactions among nucleotides and polyPn−1, and we

The role of chemistry in the success of oligonucleotides as therapeutics

• Pawan Kumar and
• Tom Brown

Beilstein J. Org. Chem. 2022, 18, 197–199, doi:10.3762/bjoc.18.22

• nucleotides; siRNAs; RNA-targeting oligonucleotides (e.g., antisense, siRNA, and anti-miR) are widely explored as fundamental research tools and are gaining increasing promise as therapeutic agents, particularly against diseases of genetic origin. The idea of treating a disease by targeting the molecular

• double-stranded nucleotides, which are called short interfering RNA or “siRNA,” can target mRNA and prevent it from being translated to make proteins [2]. While the mechanism by which antisense oligonucleotides (single stranded oligonucleotide) and siRNA (short RNA duplexes) work are completely different

• forefront of solving these issues, and have introduced many chemically modified nucleotides into oligonucleotides to increase their binding affinity toward RNA targets, and to improve their stability against nucleases to slow down degradation. This strategy has been successful, and most oligonucleotide

Tenacibactins K–M, cytotoxic siderophores from a coral-associated gliding bacterium of the genus Tenacibaculum

• Yasuhiro Igarashi,
• Yiwei Ge,
• Tao Zhou,
• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku and
• Agus Trianto

Beilstein J. Org. Chem. 2022, 18, 110–119, doi:10.3762/bjoc.18.12

• nucleotides; DDBJ accession number LC498626) to Tenacibaculum aiptasiae a4T (accession number EF416572). Fermentation Strain C16-1 cultured on marine agar was inoculated into a 500 mL K-1 flask containing marine broth seed medium consisting of yeast extract (Kyokuto Pharmaceutical Industrial, Co., Ltd.) 0.2

Unsaturated fatty acids and a prenylated tryptophan derivative from a rare actinomycete of the genus Couchioplanes

• Shun Saito,
• Kanji Indo,
• Naoya Oku,
• Hisayuki Komaki,
• Masashi Kawasaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2939–2949, doi:10.3762/bjoc.17.203

• Couchioplanes on the basis of 98.2% similarity in the 16S rRNA gene sequence (1418 nucleotides; DDBJ accession number LC512746) to Couchioplanes caeruleus strain DSM 44103T (accession number NR_026295.1). Fermentation Strain RD010705, grown on half-strength ISP medium 2 consisting of yeast extract 0.2%, malt

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

• with natural nucleotides for incorporation into the growing HIV DNA chain. The result if the triphosphate is taken up is the termination of the chain elongation because the drug lacks the 3’-hydroxy group on the deoxyribose ring that is necessary for the sugar–phosphate linking as shown in Figure 2

Nomimicins B–D, new tetronate-class polyketides from a marine-derived actinomycete of the genus Actinomadura

• Zhiwei Zhang,
• Tao Zhou,
• Taehui Yang,
• Keisuke Fukaya,
• Enjuro Harunari,
• Shun Saito,
• Katsuhisa Yamada,
• Chiaki Imada,
• Daisuke Urabe and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2194–2202, doi:10.3762/bjoc.17.141

• depth of −800 m at the Izu-Akazawa DSW pumping station in Shizuoka, Japan, as previously reported [13]. The isolated strain was identified as a member of the genus Actinomadura on the basis of 100% similarity in the 16S rRNA gene sequence (1397 nucleotides, DDBJ accession number LC498623) with

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

• , and examining the future design for ASOs. Keywords: antisense oligonucleotides; backbone modifications; cations; nucleobase modifications; sugar modifications; Introduction Antisense oligonucleotides (ASOs) are single-stranded (ss) oligomers composed of typically 10–25 nucleotides linked by

• target generally are of the gapmer-design class (Figure 1), where a central segment of at least five DNA nucleotides termed the 'gap' is flanked by modified nucleotides that promote target binding and protection against exonucleolytic degradation [2]. Another class are the steric block ASOs that bind to

• the target with high affinity without inducing RNase H mediated degradation. Such ASOs are usually in part ('mixmers'), or in full, composed of nucleotides that structurally are incompatible with RNase H activity [3]. A limited number of ASOs has been approved by different agencies as medicines for

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

• of deoxyribonucleic acids (DNA) or ribonucleic acids (RNA), which contain either a purine or pyrimidine nucleobase and a furanosyl moiety of pentose sugars, 2′-deoxyribose or ribose [1][2]. Nucleotides are constituted by addition of a phosphate group at the 5′-position of the nucleosides and these

• structure with a hairpin loop and two flanking sequences [30][31]. Moreover, these nucleotides have been found to orient the additional nucleobase towards the core of the duplex to participate in Watson–Crick base pairing [32][33][34]. The incorporation of the double-headed nucleosides into oligonucleotides

• showed a moderate cytostatic activity against human cervix carcinoma HeLa cells [37]. It is pertinent to mention that Sharma et al. [29] have reviewed the double-headed nucleotides in the recent past with a focus on their effects in nucleic acid duplexes and other secondary structures. Herein, we focused

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

• backbone modification occurs in ribosomal RNA (rRNA) of both pro- and eukaryotes [6]. A very common natural modification that concerns the ribose moiety is 2'-O-methylation (2'-OMe). 2'-OMe nucleotides are scattered throughout all types of RNA, including mRNA, tRNA, rRNA, snRNA, snoRNA, miRNA and viral RNA

• study that placed a single AM1 backbone modification between nucleotides 1 and 2 at the 5'-end of the siRNA passenger strand, whereby the off-target effects of that strand were abolished and the activity of the guide strand was restored [83]. Phosphorodithioate The synthesis of phosphorodithioate (PS2

• mRNA with a persistent silencing effect [188]. A 1.55 Å crystal structure of a Dickerson–Drew dodecamer containing fluoroarabinothymine revealed that these modified nucleotides adopt an O4'-endo (east) conformation that is readily accommodated in a B-form duplex [189] (Figure 8A). Fluoroarabinothymine

Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides

• Roslyn M. Ray,
• Anders Højgaard Hansen,
• Maria Taskova,
• Bernhard Jandl,
• Jonas Hansen,
• Citra Soemardy,
• Kevin V. Morris and
• Kira Astakhova

Beilstein J. Org. Chem. 2021, 17, 891–907, doi:10.3762/bjoc.17.75

• of LNPs through the notoriously protective BBB is to use short positively charged peptides or receptor-specific ligands, both of which have shown to be effective at increasing transport of LNPs, nucleotides, and small molecules through the BBB [9][15][16][17]. For example, the short positively

DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies

• Yongdong Su,
• Maitsetseg Bayarjargal,
• Tracy K. Hale and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65

• was less dependent on the ionic strength, which was predicted for zwitterionic nucleotides that can bind to natural DNA at low ionic strength as well or better than natural DNA [57]. Similar results have been reported for ONs with BCNS groups: the Tm of 2’-OMe duplexes was increased with increasing

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities

• Heiko T. Kiesewalter,
• Carlos N. Lozano-Andrade,
• Mikael L. Strube and
• Ákos T. Kovács

Beilstein J. Org. Chem. 2020, 16, 2983–2998, doi:10.3762/bjoc.16.248

• . Amplification of 16S rRNA hypervariable regions V3-V4 The V3-V4 region of the 16S rRNA gene was PCR-amplified from the extracted DNA samples using Fw_V3V4 (5’-CCTACGGGNGGCWGCAG-3’) and Rv_V3V4 (5’-GACTACHVGGGTATCTAATCC-3’) primers that were tagged with short barcodes with a length of eight nucleotides, listed

• sequences were demultiplexed with the QIIME 2 plugin cutadapt [67]. The minimum overlap of partial matches between the read and the barcode sequence was set to 5 nucleotides to reduce random matches. The QIIME 2 implementation DADA2 was used to denoise and merge paired-end reads [68]. In total, 362,475

• the primer pair used for amplification, and the product length was limited to 200–500 nucleotides [69]. The taxonomy was assigned to the sequences in the feature table generated by DADA2 by using the VSEARCH-based consensus taxonomy classifier [70]. A tree for phylogenetic diversity analyses was

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• important biomolecules including nucleotides, DNA, proteins, lipids etc. in aqueous media. Fluorescent peptides have also been used for specific organelles such as lysosomes tracking. In this review, it is summarized Schmuck group’s tremendous effort in developing fluorescent peptide-based probes for

• of the PDA liposomes to about 48% of the initial value (Figure 10B). The calculated binding constant from Stern–Volmer analysis of fluorescence titration is 1.5 × 106 M−1. This system is very selective towards LPS as other analytes, including nucleotides, anionic sugars, and ctDNA did not increase

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

• Rakesh Biswas,
• Surya Ghosh,
• Shubhra Kanti Bhaumik and
• Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

• stacking interactions with the nucleobases which contributes to the stability of the complexes. In many cases, these stacking interactions provide binding selectivity among the nucleotides [53][54][55][56]. Most of the aforementioned receptors were predominantly “molecular” in nature with the binding of

• the nucleotides occurring through multivalent electrostatic interactions in the cavity/cleft created by the spatial orientation of the imidazolium groups. We herein consider a self-assembly based approach in which amphiphilic monomers with bisimidazolium moieties are utilized to create multivalent

• nano-aggregates for binding to the nucleotides. For this purpose, four pyrene tagged bisimidazolium-based receptors PBImN (Figure 1, N = 4, 10, 12 and 14; N denotes the number of carbons in the n-alkyl chain) were synthesized. The longer chain derivatives with N ≥ 10 underwent self-assembly in aqueous

Nocarimidazoles C and D, antimicrobial alkanoylimidazoles from a coral-derived actinomycete Kocuria sp.: application of ¹J_C,H coupling constants for the unequivocal determination of substituted imidazoles and stereochemical diversity of anteisoalkyl chains in microbial metabolites

• Md. Rokon Ul Karim,
• Enjuro Harunari,
• Amit Raj Sharma,
• Naoya Oku,
• Kazuaki Akasaka,
• Daisuke Urabe,
• Mada Triandala Sibero and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 2719–2727, doi:10.3762/bjoc.16.222

• basis of 100.0% similarity in the 16S rRNA gene sequence (1381 nucleotides; DDBJ accession number LC556325) to Kocuria palustris DSM 11925T (accession number Y16263). Fermentation In a similar manner as described in [22], the strain T35-5 was maintained on Marine Agar 2216 (Difco). A loopful of the

Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes

• Lena Reinke,
• Julia Bartl,
• Marcus Koch and
• Stefan Kubik

Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219

• described for analytes ranging from inorganic ions over low-molecular-weight neutral and charged organic compounds, such as carboxylic acids, amino acids, and nucleotides, to larger biomolecules such as peptides and proteins [1][2][3][4][5][6][13]. All of these systems have specific areas of application

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• range of biomolecules: amino acids [8], peptides [9], glycosides [10], nucleosides/nucleotides [11], and lipids [12]. Also, protein-based nano-bio-conjugates [13] have been prepared by ball milling, retaining the native properties of the proteins after mechanochemical synthesis. Boronic acids and their

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