Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

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

• ], NAD-capped RNAs [23][24], 3'-dephospho-CoA linked RNA [25] or methylphosphate capping [26][27] we refer to the indicated articles. Review Enzymatic preparation of capped mRNA Enzymatic preparation of capped mRNA is based on in vitro transcription (IVT) of a DNA template. While RNA synthesized via

• -transcriptional capping In post-transcriptional capping, the RNA from IVT is subjected to a dedicated enzymatic capping reaction. The enzymes used in vitro originate from capping apparatuses of different eukaryotic organisms or DNA viruses and can be produced recombinantly in E. coli [28][29]. Enzymatic formation

• responsible guanylyltransferase uses GTP as substrate and forms a covalent enzyme-(lysyl-N)-GMP intermediate, reminiscent of DNA ligase-AMP intermediates [30][31]. Finally, the cap structure is methylated at the N7-position by an RNA(guanine-N7)methyltransferase using S-adenoysl-L-methionine (AdoMet) as a

Binding abilities of polyaminocyclodextrins: polarimetric investigations and biological assays

• Marco Russo,
• Daniele La Corte,
• Annalisa Pisciotta,
• Serena Riela,
• Rosa Alduina and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2751–2763, doi:10.3762/bjoc.13.271

• tests in order to assess their interaction with a model plasmid DNA (pUC19) and to evaluate whether they may influence the internalization of exogenous DNA in bacterial systems, in particular the Gram-negative model microorganism Escherichia coli. Results and Discussion Polarimetric behavior of AmCDs A

• plasmid DNA. For this, each AmCD was mixed with pDNA at various N/P ratios (average number of nitrogen atoms on the cyclodextrin core/number of phosphate groups of pDNA) and the complexation efficiency was evaluated by electrophoretic mobility shift assays (EMSA). When electrophoresis is applied to pDNA

• dissociation occurred at a heparin concentration of 400 µg/mL for CD1 and 500 µg/mL for CD2 and CD3. This indicates that the binding between DNA and AmCDs is quite strong in comparison to similar systems [28][56][57]. Finally, the effect of the three AmCDs on transformation of E. coli competent cells was

Metal-mediated base pairs in parallel-stranded DNA

• Jens Müller

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

• applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the

• glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine–Ag(I)–cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated

• base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes. Keywords: DNA; metal-mediated base pairs; nucleic acids; Introduction

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

• [4], pyrene-modified peptide nucleic acids (PNA) [5], locked nucleic acids (LNA) [6][7], invader LNA [8], and twisted intercalating nucleic acids (TINA) [9]. Furthermore pyrene-modified nucleotides have been used for the construction of DNA-based multichromophore systems [10][11][12][13], as cancer

• detecting markers [14], as fluorescent DNA probes [15], non-covalent binders to canonical oligonucleotide templates [16], and antiviral agents [17][18]. Notably, pyrene excimer formation in DNA template assemblies is much less efficient than in normal pyrene conjugates due to the helical twist between

• chromophores [19][20][21]. This helical twist was evidenced by circular dichroism, in particular a strong bisignate Cotton effect for the DNA-templated pyrene assemblies [19][20]. Figure 1 shows selected examples of pyrene-modified nucleic acids and nucleosides. On the other hand, pyrene–nucleobase conjugates

Herpetopanone, a diterpene from Herpetosiphon aurantiacus discovered by isotope labeling

• Xinli Pan,
• Nicole Domin,
• Sebastian Schieferdecker,
• Hirokazu Kage,
• Martin Roth and
• Markus Nett

Beilstein J. Org. Chem. 2017, 13, 2458–2465, doi:10.3762/bjoc.13.242

• were mainly reported from plants and, to a lesser degree, also from fungi and marine invertebrates. In recent years, however, the discovery of terpenoids from prokaryotes has gained momentum. The ease of DNA sequencing has strongly favored this development, contributing to the identification of

Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models

• Vladimir Kubyshkin and
• Nediljko Budisa

Beilstein J. Org. Chem. 2017, 13, 2442–2457, doi:10.3762/bjoc.13.241

• measurements can be used to study ligand–protein [12] and protein–protein interactions [13]; membrane proteins [14][15][16] and membrane-associated peptides [17][18]; equilibria among conformations of RNA [19], DNA [20], and peptide nucleic acids (PNA) [21]; and many others. Particularly recent is the

Sulfation and amidinohydrolysis in the biosynthesis of giant linear polyenes

• Hui Hong,
• Markiyan Samborskyy,
• Katsiaryna Usachova,
• Katharina Schnatz and
• Peter F. Leadlay

Beilstein J. Org. Chem. 2017, 13, 2408–2415, doi:10.3762/bjoc.13.238

• cluster. Because the S. mediocidicus strain proved highly resistant to introduction of cloned DNA, we were unable to obtain formal proof that this gene is essential for mediomycin biosynthesis by mutating medi4948 and seeing accumulation of 1a and/or 1b. Instead, we introduced the medi4948 gene, cloned in

Solvent-free copper-catalyzed click chemistry for the synthesis of N-heterocyclic hybrids based on quinoline and 1,2,3-triazole

• Martina Tireli,
• Silvija Maračić,
• Stipe Lukin,
• Marina Juribašić Kulcsár,
• Dijana Žilić,
• Mario Cetina,
• Ivan Halasz,
• Silvana Raić-Malić and
• Krunoslav Užarević

Beilstein J. Org. Chem. 2017, 13, 2352–2363, doi:10.3762/bjoc.13.232

• constituent of compounds with diverse applications, some of which display potent cytostatic activity through different mechanisms of action such as DNA intercalation, apoptosis, abrogation of cell migration, inhibition of angiogenesis and disregulation of nuclear receptor signaling [34][35]. Moreover, it was

β-Cyclodextrin- and adamantyl-substituted poly(acrylate) self-assembling aqueous networks designed for controlled complexation and release of small molecules

• Liang Yan,
• Duc-Truc Pham,
• Philip Clements,
• Stephen F. Lincoln,
• Jie Wang,
• Xuhong Guo and
• Christopher J. Easton

Beilstein J. Org. Chem. 2017, 13, 1879–1892, doi:10.3762/bjoc.13.183

• , fluconazole [40] and curcumin [37], along with larger species exemplified by RNA and DNA segments [26][32][33][36][39][47]. Some systems are designed to target specific tissues [26][35]. We are particularly interested in the extent to which small molecule guest complexation and release characteristics may be

The chemistry and biology of mycolactones

• Matthias Gehringer and
• Karl-Heinz Altmann

Beilstein J. Org. Chem. 2017, 13, 1596–1660, doi:10.3762/bjoc.13.159

A novel approach to oxoisoaporphine alkaloids via regioselective metalation of alkoxy isoquinolines

• Benedikt C. Melzer and
• Franz Bracher

Beilstein J. Org. Chem. 2017, 13, 1564–1571, doi:10.3762/bjoc.13.156

• synthetic, oxoisoaporphine-like analogues were found to have strong DNA binding affinity and therefore high cytotoxicity [5] as well as antiplasmodial activity [6]. Besides menisporphine (2), the related oxoisoaporphine alkaloids dauriporphine (3), 6-O-demethylmenisporphine (4), dauriporphinoline (5) and

Grip on complexity in chemical reaction networks

• Albert S. Y. Wong and
• Wilhelm T. S. Huck

Beilstein J. Org. Chem. 2017, 13, 1486–1497, doi:10.3762/bjoc.13.147

• needed that integrates the thorough appreciation of reaction rates in the design of chemical networks. Learning from the design principles applied in synthetic biology Genetic and small DNA-oligonucleotide networks provide an ideal test bed to address the basic principles of designing (bio)chemical

• complex systems [85][86][87]. Figure 4a shows the successful translation of an earlier discussed network motif into a molecular predator (P)–prey (N) network [88][89]. The information concerning the predator and prey growth and degradation is stored in single-stranded DNA (ssDNA). Importantly, the

• reaction scheme and rate equations could be approximated based on the predictability in the thermodynamics of DNA binding. In presence of an excess of the source ssDNA (denoted by G for “Grass”), traveling waves of a predator–prey molecular network (similar to the spatio-temporal patterns in the BZ

A speedy route to sterically encumbered, benzene-fused derivatives of privileged, naturally occurring hexahydropyrrolo[1,2-b]isoquinoline

• Olga Bakulina,
• Alexander Ivanov,
• Vitalii Suslonov,
• Dmitry Dar’in and
• Mikhail Krasavin

Beilstein J. Org. Chem. 2017, 13, 1413–1424, doi:10.3762/bjoc.13.138

• which may facilitate or prevent compounds’ binding to DNA or DNA-topoisomerase complex. Depending on the medicinal chemistry context, compounds 10 can be decarboxylated to deliver sterically encumbered tetracyclic lactams 14 lacking the carboxylic acid group as we showed for exemplary compound 10h. The

Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research

• Ben Shirt-Ediss,
• Sara Murillo-Sánchez and
• Kepa Ruiz-Mirazo

Beilstein J. Org. Chem. 2017, 13, 1388–1395, doi:10.3762/bjoc.13.135

• will defend the view that in order to reconstruct this process a strict ‘bottom-up’ approach should be pursued, starting with chemical precursors of biomolecules, rather than with fully functional biomolecules. Whereas the encapsulation of biopolymers (DNA, RNA, proteins) or cell extracts in self

• macromolecular structures, like proteins or nucleic acids, took control of metabolic dynamics. In fact, although the mainstream way to experimentally investigate protocells and their evolutionary capacity has been to take a ‘semi-synthetic’ approach (encapsulating populations of RNA or DNA polymers inside lipid

• the basis of a ‘genotype–phenotype’ decoupling, with the development of DNA and coding, to enable an open-ended search for new functionalities. The invention of the cell wall and complex protein machinery controlling cell division made reproduction cycles much more coordinated and reliable

Synthesis of oligonucleotides on a soluble support

• Harri Lönnberg

Beilstein J. Org. Chem. 2017, 13, 1368–1387, doi:10.3762/bjoc.13.134

• . Several of protocols developed for the soluble-supported synthesis allow the preparation of both DNA and RNA oligomers of limited length in gram scale without any special equipment, being evidently of interest for research groups that need oligonucleotides in large amounts for research purposes. However

• , none of them has really tested at such a scale that the feasibility of their industrial use could be critically judged. Keywords: DNA; oligonucleotides; RNA; soluble support; synthesis; Introduction The synthesis of oligonucleotides (ONs) consists of linking nucleosides to each other in a specified

Towards open-ended evolution in self-replicating molecular systems

• Herman Duim and
• Sijbren Otto

Beilstein J. Org. Chem. 2017, 13, 1189–1203, doi:10.3762/bjoc.13.118

• below. Mutation involves the emergence of a difference between the parent template and its copies. The accuracy of the replication process of DNA is generally safeguarded by sophisticated enzymes, but systems that lack such machinery are more prone to occasional errors during replication. Mutations

• that of DNA. A DNA molecule consists of two strands of nucleotides that are intertwined to form a double helix. During the replication process of DNA, each of these strands can act as a template for the formation of a complementary strand. In this way an exact copy of the original structure of DNA is

• formed and the DNA has successfully become replicated. The replication of DNA however is a complex process mediated by enzymes such as DNA polymerase and topoisomerase. To better understand the origin of life and as a possible first step in the synthesis of de novo life it would be very interesting

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• the biosynthesis of glycosidic linkage requires the transfer of a sugar residue from a donor to an acceptor [35]. Acceptor substrates are carbohydrates, proteins, lipids, DNA, flavonol, antibiotics and steroids. In contrast, glycosyl donor substrates are mostly sugar nucleotides, such as UDP-GlcNAc

From chemical metabolism to life: the origin of the genetic coding process

• Antoine Danchin

Beilstein J. Org. Chem. 2017, 13, 1119–1135, doi:10.3762/bjoc.13.111

• views of biology, this fiction is based on an animistic vision, which we might call “the animism of DNA”. This is summarised by the astronomer who discovered the extraterrestrial message: "If we are able to use the computer as a control device, and if we can build a chemical reactor that can act from

• its instructions as they appear –in fact, if we can make a DNA synthesizer– then I think we can start building live tissue”. Today, it is not difficult to find statements of this kind in connection with the study of the genome of living organisms, and, naturally in scenarios of the origin of life

• . This opened up the idea that a primitive coding process was at work during replication, with one strand of DNA entirely specifying the complementary strand. However, this first rule does not solve the riddle of the correspondence between the sequence of DNA and that of proteins, which requires a higher

Synthesis and enzymatic ketonization of the 5-(halo)-2-hydroxymuconates and 5-(halo)-2-hydroxy-2,4-pentadienoates

• Tyler M. M. Stack,
• William H. Johnson Jr. and
• Christian P. Whitman

Beilstein J. Org. Chem. 2017, 13, 1022–1031, doi:10.3762/bjoc.13.101

• the actions of pyruvate aldolase and acetaldehyde dehydrogenase would produce 2-chloroacetaldehyde (7b) and 2-chloroacetyl CoA (8b), which are potential alkylating agents of these enzymes as well as other cellular proteins and DNA. This observation and the potential effects of the halogen on other

Glyco-gold nanoparticles: synthesis and applications

• Federica Compostella,
• Olimpia Pitirollo,
• Alessandro Silvestri and
• Laura Polito

Beilstein J. Org. Chem. 2017, 13, 1008–1021, doi:10.3762/bjoc.13.100

• diameter range can be obtained [4]. Moreover, this synthetic procedure allows to introduce different types of carbohydrates and other ligands (i.e., polyethylene chains, lipids, peptides, DNA, RNA or fluorescent dyes) in controlled ratios [4]. A modification of this technique consists in the application of

Interactions between shape-persistent macromolecules as probed by AFM

• Johanna Blass,
• Jessica Brunke,
• Franziska Emmerich,
• Cédric Przybylski,
• Vasil M. Garamus,
• Artem Feoktystov,
• Roland Bennewitz,
• Gerhard Wenz and
• Marcel Albrecht

Beilstein J. Org. Chem. 2017, 13, 938–951, doi:10.3762/bjoc.13.95

• used in low equilibrium concentrations. Since AFM even allows the investigation of single molecules, such as DNA [37][38] or molecular self-assembling based on “Dip-Pen” nanolithography [39], it was chosen as the most reliable technique to probe highly cooperative recognition processes. The

First total synthesis of kipukasin A

• Chuang Li,
• Haixin Ding,
• Zhizhong Ruan,
• Yirong Zhou and
• Qiang Xiao

Beilstein J. Org. Chem. 2017, 13, 855–862, doi:10.3762/bjoc.13.86

• ; Introduction Endogenous nucleosides are involved in DNA and RNA synthesis, cell signalling, enzyme regulation and metabolism etc. [1][2]. Therefore, the synthesis of novel nucleosides to mimic their physiological counterparts has potential therapeutic significance, which has led to the development of a large

Novel β-cyclodextrin–eosin conjugates

• Gábor Benkovics,
• Damien Afonso,
• András Darcsi,
• Szabolcs Béni,
• Sabrina Conoci,
• Éva Fenyvesi,
• Lajos Szente,
• Milo Malanga and
• Salvatore Sortino

Beilstein J. Org. Chem. 2017, 13, 543–551, doi:10.3762/bjoc.13.52

• ]. Singlet oxygen offers important advantages over conventional drugs as it: i) potentially attacks biological substrates of different nature (i.e., lipids, proteins, and DNA), ii) does not suffer from multidrug resistance (MDR) problems, and iii) due to its short half-life (<0.1 ms) and lack of charge, it

Investigation of the action of poly(ADP-ribose)-synthesising enzymes on NAD⁺ analogues

• Sarah Wallrodt,
• Edward L. Simpson and
• Andreas Marx

Beilstein J. Org. Chem. 2017, 13, 495–501, doi:10.3762/bjoc.13.49

• -ribose and may branch every 20 to 50 monomers [8][9][10]. To date, only four ARTD members were found to accomplish the synthesis of PAR, namely the DNA-dependent ARTD1 and ARTD2 as well as the tankyrases ARTD5 and ARTD6 [2][3]. ARTD1 as the founding member is the best investigated enzyme of ARTDs and is

• considered the main source of cellular PAR [11]. ARTD1 and its closest relative ARTD2 comprise DNA-binding domains and their activity is stimulated by binding to different types of DNA breaks [12]. They fulfil functions in DNA repair, genome maintenance, transcription, and metabolic regulation [11][13]. The

• times were elongated to 1 h, 4 h and 2 h, respectively, to achieve noticeable PAR formation. Moreover, no DNA was added to the tankyrase reactions. Of note, ARTD2 was found to be not activated by short, octameric DNA such as applied in case of ARTD1 and thus activated calf thymus DNA was added to enable

Posttranslational isoprenylation of tryptophan in bacteria

• Masahiro Okada,
• Tomotoshi Sugita and
• Ikuro Abe

Beilstein J. Org. Chem. 2017, 13, 338–346, doi:10.3762/bjoc.13.37

• the bacterial population density, or in other words, the concentration of the specific secreted pheromone. The ComX pheromone induces natural genetic competence under the control of quorum sensing in B. subtilis. Specifically, the ComX pheromone induces competent cell formation for DNA transformation