Pd(OAc)₂-catalyzed dehydrogenative C–H activation: An expedient synthesis of uracil-annulated β-carbolinones

• Biplab Mondal,
• Somjit Hazra,
• Tarun K. Panda and
• Brindaban Roy

Beilstein J. Org. Chem. 2015, 11, 1360–1366, doi:10.3762/bjoc.11.146

• control agents for receptor research on bioenzyme inhibitors, such as the inhibition of HLE (human leukocyte elastase) [15][16][17][18]. Uracil, on the other hand, is one of the four nucleobases of RNA. It holds immense importance from a pharmaceutical and biological point of view [19]. For example, 5

Is organic chemistry science – and does this question make any sense at all?

• Andreas Kirschning and
• Thomas A. C. Reydon

Beilstein J. Org. Chem. 2015, 11, 893–896, doi:10.3762/bjoc.11.100

• conditions (molecular recognition, self-assembly and dynamic combinatorial chemistry) and how their molecular composition would be; the question why nature developed DNA and RNA that utilize ribose and 2-deoxyribose as central nucleotide building blocks instead of the more abundant and readily available

Peptide–polymer ligands for a tandem WW-domain, an adaptive multivalent protein–protein interaction: lessons on the thermodynamic fitness of flexible ligands

• Katharina Koschek,
• Vedat Durmaz,
• Oxana Krylova,
• Marek Wieczorek,
• Shilpi Gupta,
• Martin Richter,
• Alexander Bujotzek,
• Christina Fischer,
• Rainer Haag,
• Christian Freund,
• Marcus Weber and
• Jörg Rademann

Beilstein J. Org. Chem. 2015, 11, 837–847, doi:10.3762/bjoc.11.93

• adaptive, divalent receptor as a protein target. As a model protein the tandem-WW-domain of the pre-mRNA splicing factor formin binding protein 21 (FBP21) was selected [13][14][15]. Considering the importance of FBP21 in the activation of RNA splicing, successful ligands should be valuable tools to

• architecture connected with a flexible linker the tandem WW-domains of the protein FBP21 were selected. FBP21 is a protein component of the spliceosome, the multiprotein complex in the nucleus of cells responsible for the processing of primary RNA-transcripts. The two WW domains of FBP21 bind to proline-rich

Multivalent dendritic polyglycerolamine with arginine and histidine end groups for efficient siRNA transfection

• Fatemeh Sheikhi Mehrabadi,
• Hanxiang Zeng,
• Mark Johnson,
• Cathleen Schlesener,
• Zhibin Guan and
• Rainer Haag

Beilstein J. Org. Chem. 2015, 11, 763–772, doi:10.3762/bjoc.11.86

• ; Introduction Since the discovery of RNA interference (RNAi) and awareness of its role in posttranscriptional gene silencing, tremendous efforts and capital have been devoted to the development of therapeutics based on this pathway [1]. So far, there are at least 22 RNAi-based drugs in clinical trials and many

Sequence-specific RNA cleavage by PNA conjugates of the metal-free artificial ribonuclease tris(2-aminobenzimidazole)

• Friederike Danneberg,
• Alice Ghidini,
• Plamena Dogandzhiyski,
• Elisabeth Kalden,
• Roger Strömberg and
• Michael W. Göbel

Beilstein J. Org. Chem. 2015, 11, 493–498, doi:10.3762/bjoc.11.55

• and Nutrition, Novum, SE-141 83 Huddinge, Sweden 10.3762/bjoc.11.55 Abstract Tris(2-aminobenzimidazole) conjugates with antisense oligonucleotides are effective site-specific RNA cleavers. Their mechanism of action is independent of metal ions. Here we investigate conjugates with peptide nucleic

• acids (PNA). RNA degradation occurs with similar rates and substrate specificities as in experiments with DNA conjugates we performed earlier. Although aggregation phenomena are observed in some cases, proper substrate recognition is not compromised. While our previous synthesis of 2-aminobenzimidazoles

• the one hand, they can improve our mechanistic understanding of natural ribonucleases and of phosphodiester reactivity in general. On the other hand, a wide range of practical applications is conceivable for such RNA cleavers ranging from tools in molecular biology to chemotherapeutics targeting mRNAs

C-5’-Triazolyl-2’-oxa-3’-aza-4’a-carbanucleosides: Synthesis and biological evaluation

• Roberto Romeo,
• Caterina Carnovale,
• Salvatore V. Giofrè,
• Maria A. Chiacchio,
• Adriana Garozzo,
• Emanuele Amata,
• Giovanni Romeo and
• Ugo Chiacchio

Beilstein J. Org. Chem. 2015, 11, 328–334, doi:10.3762/bjoc.11.38

• inhibit cell proliferation of Vero, BS-C-1, HEp-2, MDCK, and HFF cells by 50% (CC50) at concentrations in the range of 5.0–40.0 μM. No antiviral activity against both RNA and DNA viruses was observed. Results and Discussion Chemistry The synthetic route to 5’-triazolyl-2’-oxa-3’-aza-4’a-carbanucleosides

• RNA viruses was also evaluated, by using the subsequent cell-virus tests: (a) Vero cell for poliovirus 1, human echovirus 9, herpes simplex type 1 (HSV-1); (b) HEp-2 cell for Coxsackievirus B1, adenovirus type 2; (c) human foreskin fibroblast cells (HFF) for cytomegalovirus (CMV); (d) BS-C-1 cell

Synthesis of dinucleoside acylphosphonites by phosphonodiamidite chemistry and investigation of phosphorus epimerization

• William H. Hersh

Beilstein J. Org. Chem. 2015, 11, 184–191, doi:10.3762/bjoc.11.19

• oligonucleotides, which are modified oligonucleotides that bind to mRNA in order to inhibit translation to proteins, have been intensively investigated for decades [1][2]. Modifications of native DNA or RNA are required to permit pharmaceutical use, for example, for conferring nuclease resistance, enhanced binding

• phosphorothioates is reason enough to investigate the synthesis of P-chiral phosphorothioates [13][14][15][16][17][18][19]. However, none of the reported methods seem to allow for routine, high-yield synthesis with high stereocontrol [20][21][22][23]. The extension to phosphorothioate RNA for applications of RNA

Articulated rods – a novel class of molecular rods based on oligospiroketals (OSK)

• Pablo Wessig,
• Roswitha Merkel and
• Peter Müller

Beilstein J. Org. Chem. 2015, 11, 74–84, doi:10.3762/bjoc.11.11

• relatively rigid molecular and supramolecular systems. These systems mainly consist of peptides and proteins (e.g., scleroproteins, globular proteins, and membrane proteins), lipids (e.g., biological membranes), carbohydrates (e.g., cellulose) and nucleic acids (DNA, RNA). The impressive performance of the

NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A–T phosphoramidite building blocks

• Boris Schmidtgall,
• Claudia Höbartner and
• Christian Ducho

Beilstein J. Org. Chem. 2015, 11, 50–60, doi:10.3762/bjoc.11.8

• Oligonucleotides are important agents for a number of biomedical applications [1]. Thus, they are employed to exert antigene [2] or antisense [3] mechanisms as well as to trigger or inhibit RNA interference [4]. The capability of sequence-specific molecular recognition is a striking feature of nucleic acids, but

• ) in order to study the influence of the spatial orientation of the positive charge. Melting temperature measurements showed that NAA-modified DNA oligonucleotides formed stable duplexes with native unmodified DNA or RNA counterstrands, although moderate destabilization in comparison to native duplexes

• was observed (particularly for DNA/RNA duplexes). Further experiments with native counterstrands bearing one nucleobase mismatch were performed, and duplex structures were studied by CD spectroscopy. Overall, we found that NAA-modified DNA oligonucleotides (i) formed stable duplexes with complementary

Three-component synthesis of C₂F₅-substituted pyrazoles from C₂F₅CH₂NH₂·HCl, NaNO₂ and electron-deficient alkynes

• Pavel K. Mykhailiuk

Beilstein J. Org. Chem. 2015, 11, 16–24, doi:10.3762/bjoc.11.3

• physicochemical and biological properties [1][2][3][4][5][6][7][8]. It is not surprising, therefore, that up to 20% of all modern drugs contain at least one fluorine atom [9][10][11]. Fluorinated pyrazoles, for example, do play a role in medicinal chemistry: among them are inhibitors of the measles virus RNA

Effects of RAMEA-complexed polyunsaturated fatty acids on the response of human dendritic cells to inflammatory signals

• Éva Rajnavölgyi,
• Renáta Laczik,
• Viktor Kun,
• Lajos Szente and
• Éva Fenyvesi

Beilstein J. Org. Chem. 2014, 10, 3152–3160, doi:10.3762/bjoc.10.332

• Toll-like receptor 3 (TLR3) specific for double stranded RNA (dsRNA). To avoid the interaction with cholesterol in the DC membrane in our in vitro experiments we used a non-cholesterol interacting CD, i.e., randomly methylated α-CD (RAMEA) for solubilization of n−3 PUFAs. Results and Discussion

• , USA). Fluorescence intensities were measured with FACSCalibur (BD Biosciences). Data analysis was performed with the FlowJo software (Tree Star, Ashland, OR, USA). Determination of GPR120 expression levels GPR120 expression levels were measured by real-time quantitative PCR (Q-PCR). Total RNA was

Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

• Lidija-Marija Tumir,
• Marijana Radić Stojković and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

• - and RNA-fluorescent markers (ethidium bromide), probes for cell viability (propidium iodide), but also “ill-famed” for various toxic (genotoxic) and mutagenic effects. After two decades of low interest, the discovery of phenanthridine alkaloids and new studies of antiparasitic/antitumor properties of

• improved synthetic approaches. Keywords: ds-DNA and ds-RNA binding; intercalation; minor groove binding; nucleic acids; organic synthesis; phenanthridine; phenanthridinium; Introduction The search for therapeutic agents of the phenanthridine type has increased when the outstanding trypanocidal activity

• of some phenanthridinium compounds became apparent [1]. One of the most studied and used phenanthridine derivatives is 3,8-diamino-5-ethyl-6-phenylphenanthridinium known as ethidium bromide (EB), for many decades applied as gold-standard DNA- and RNA-fluorescent marker, and its close analogue

Nucleic acid chemistry

• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2014, 10, 2928–2929, doi:10.3762/bjoc.10.311

• , markers or other biologically active molecules, can be synthetically introduced into DNA (as well as RNA) by preparing the corresponding artificial DNA and RNA building blocks. More recently, the chemistry was further developed for building blocks that are otherwise synthetically not obtainable. In such

• biological functionality, DNA and RNA are considered as increasingly important architectures and scaffolds for two- and three-dimensional objects, networks and materials for nanosciences. In conclusion, nucleic acid chemistry continues to maintain its appeal and affords good reason to focus on in this

Versatile synthesis of amino acid functionalized nucleosides via a domino carboxamidation reaction

• Vicky Gheerardijn,
• Jos Van den Begin and
• Annemieke Madder

Beilstein J. Org. Chem. 2014, 10, 2566–2572, doi:10.3762/bjoc.10.268

• increased attention for incorporation in modified nucleic acid structures both for the design of aptamers with enhanced binding properties as well as the construction of catalytic DNA and RNA. As a shortcut alternative to the incorporation of multiple modified residues, each bearing one extra functional

• predictable and well-investigated structure, the strength of nucleic acids for a series of applications such as DNA and RNA based drugs [7], drug delivery systems [8][9], DNA-biosensors [10][11] and potential catalysts has now firmly been recognized. Rather than using unmodified oligonucleotides, providing

• enabled by techniques such as solid phase synthesis, post synthetic modifications or enzymatic incorporation of modified analogues. Originating from research into aptamers as strong and selective binders [12][13][14], several research groups are investigating the creation and synthesis of new DNA or RNA

Autonomous assembly of synthetic oligonucleotides built from an expanded DNA alphabet. Total synthesis of a gene encoding kanamycin resistance

• Kristen K. Merritt,
• Kevin M. Bradley,
• Daniel Hutter,
• Mariko F. Matsuura,
• Diane J. Rowold and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 2348–2360, doi:10.3762/bjoc.10.245

• synthesis of complete genes, have followed a convergent assembly strategy. This was used for the first time for the total synthesis of genes encoding transfer RNA [5], but convergent synthesis is generally routine for the synthesis of natural products [6]. In the convergent synthesis of L-DNA, subsets of

Solution phase synthesis of short oligoribonucleotides on a precipitative tetrapodal support

• Alejandro Gimenez Molina,
• Amit M. Jabgunde,
• Pasi Virta and
• Harri Lönnberg

Beilstein J. Org. Chem. 2014, 10, 2279–2285, doi:10.3762/bjoc.10.237

• been elaborated. Novel 2'-O-(2-cyanoethyl)-5'-O-(1-methoxy-1-methylethyl) protected ribonucleoside 3'-phosphoramidites have been prepared and their usefulness as building blocks in RNA synthesis on a soluble support has been demonstrated. As a proof of concept, a pentameric oligoribonucleotide, 3

• , dynamics of chain invasion and recognition by small molecular entities [6][7][8][9][10]. The quantities of short RNA sequences required for such studies are often larger than what can easily be obtained by lab-scale solid phase synthesis. In other words, there seems to be a need for a straightforward

• them has so far been applied to the synthesis of RNA. Tetrakis(4-azidomethylphenyl)pentaerythritol has recently been introduced as a practical soluble support for the synthesis of short oligodeoxyribonucleotides [16]. The 3'-terminal nucleoside is attached as a 3'-O-(4-pentynoyl) derivative to the

Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)–adenine derivatives

• Marijana Radić Stojković,
• Marko Škugor,
• Łukasz Dudek,
• Jarosław Grolik,
• Julita Eilmes and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2175–2185, doi:10.3762/bjoc.10.225

• of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland 10.3762/bjoc.10.225 Abstract An investigation of the interactions of two novel and several known DBTAA–adenine conjugates with double-stranded DNA and RNA has revealed the DNA/RNA groove as the dominant binding site, which is

• in contrast to the majority of previously studied DBTAA analogues (DNA/RNA intercalators). Only DBTAA–propyladenine conjugates revealed the molecular recognition of AT-DNA by an ICD band pattern > 300 nm, whereas significant ICD bands did not appear for other ds-DNA/RNA. A structure–activity relation

• recognition; circular dichroism; DBTAA-adenine conjugate; ds-DNA/RNA; minor groove binding; nucleic acids; Introduction The majority of natural and artificial applications involving small molecule-DNA/RNA recognition depend on several non-covalent binding modes. Typical examples are double-stranded (ds) DNA

Synthesis and optical properties of pyrrolidinyl peptide nucleic acid carrying a clicked Nile red label

• Nattawut Yotapan,
• Chayan Charoenpakdee,
• Pawinee Wathanathavorn,
• Boonsong Ditmangklo,
• Hans-Achim Wagenknecht and
• Tirayut Vilaivan

Beilstein J. Org. Chem. 2014, 10, 2166–2174, doi:10.3762/bjoc.10.224

• – has also been incorporated into DNA as a base replacement, again without showing significant structure-induced fluorescence change [22]. Peptide nucleic acid or PNA is an electrostatically neutral analogue of DNA which can form very stable duplexes with DNA and RNA in a highly sequence specific

Second generation silver(I)-mediated imidazole base pairs

• Susanne Hensel,
• Nicole Megger,
• Kristina Schweizer and
• Jens Müller

Beilstein J. Org. Chem. 2014, 10, 2139–2144, doi:10.3762/bjoc.10.221

• + 1] type could be obtained [14][15]. While most examples focus on the use of DNA, other systems such as RNA [16], GNA [17][18] (glycol nucleic acid), PNA [19][20][21], and other nucleic acid derivatives [22] have been modified as well. It is interesting to note that metal-mediated base pairs do not

Pyrrolidine nucleotide analogs with a tunable conformation

• Lenka Poštová Slavětínská,
• Dominik Rejman and
• Radek Pohl

Beilstein J. Org. Chem. 2014, 10, 1967–1980, doi:10.3762/bjoc.10.205

• nucleoside, nucleotide and oligonucleotide spatial structure. The conformation predefines, for example, the stability of DNA:RNA duplexes – complexes between oligodeoxyribonucleotide and a complementary RNA strain [7] or an overall shape of oligonucleotide. It is also well known that the structure of DNA may

Syntheses of ¹⁵N-labeled pre-queuosine nucleobase derivatives

• Jasmin Levic and
• Ronald Micura

Beilstein J. Org. Chem. 2014, 10, 1914–1918, doi:10.3762/bjoc.10.199

• ]-guanidine as cost-affordable 15N sources. Such derivatives are required to explore the binding process of the preQ1 base to RNA targets using advanced NMR spectroscopic methods. PreQ1 base specifically binds to bacterial mRNA domains and thereby regulates genes that are required for queuosine biosynthesis

• ][7][8]. To explore the binding process of preQ1 base to the RNA and to shed light on the dynamics underpinning this process advanced NMR spectroscopic methods exist for which 15N-labeled preQ1 base derivatives would be highly beneficial. Here, we report efficient routes for the synthesis of three

• preQ1 base. The new derivatives carry the potential for modern NMR spectroscopic applications to study the recognition process of these small molecules with RNA aptamer domains from the three preQ1 riboswitch classes known to this date [4][5][18]. Experimental General.Chemical reagents and solvents were

Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme

• Nico Rublack and
• Sabine Müller

Beilstein J. Org. Chem. 2014, 10, 1906–1913, doi:10.3762/bjoc.10.198

• from aptamers for simple binding of defined ligands, also RNAs for catalysis of chemical reactions have been selected. In the latter case, a key step often is the conjugation of one of the two reactants to the library, requiring suitable strategies for terminal or internal RNA functionalization. With

• derivative suitable for conjugation to RNA and linkage of the conjugated library to a streptavidine-coated surface. Successful conjugation of the cytidine derivative to the 3'-terminus of a model RNA is demonstrated. Keywords: cytidine deaminase; modified nucleoside; nucleic acids; ribozyme; RNA world

• ; SELEX; Introduction Since the discovery of the first catalytic RNA in the ciliate Tetrahymena thermophilia in 1982 [1], a number of naturally occurring ribozymes have been described [2]. Whereas all of these natural ribozymes accelerate transesterifications or, as in the case of the ribosome, the

Structure/affinity studies in the bicyclo-DNA series: Synthesis and properties of oligonucleotides containing bc^en-T and iso-tricyclo-T nucleosides

• Branislav Dugovic,
• Michael Wagner and
• Christian J. Leumann

Beilstein J. Org. Chem. 2014, 10, 1840–1847, doi:10.3762/bjoc.10.194

• the gauche orientation with the furanose ring in a near perfect 2’-endo conformation. Both modifications were incorporated into oligodeoxynucleotides and their thermal melting behavior with DNA and RNA as complements was assessed. We found that the iso-tc-T modification was significantly more

• destabilizing in duplex formation compared to the bcen-T modification. In addition, duplexes with complementary RNA were less stable as compared to duplexes with DNA as complement. A structure/affinity analysis, including the already known bc-T and tc-T modifications, does not lead to a clear correlation of the

• orientation of torsion angle γ with DNA or RNA affinity. There is, however, some correlation between furanose conformation (N- or S-type) and affinity in the sense that a preference for a 3’-endo like conformation is associated with a preference for RNA as complement. As a general rule it appears that Tm data

Sacrolide A, a new antimicrobial and cytotoxic oxylipin macrolide from the edible cyanobacterium Aphanothece sacrum

• Naoya Oku,
• Miyako Matsumoto,
• Kohsuke Yonejima,
• Keijiroh Tansei and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2014, 10, 1808–1816, doi:10.3762/bjoc.10.190

• of the cells, 1 is is not expected to target cell cycle-associated events, such as the synthesis of proteins, DNA, or RNA. Despite their structural diversity, many oxylipins induce a common stress response in plants and animal cells, and this activity is attributed to their ability to modify the

Multicomponent reactions in nucleoside chemistry

• Mariola Koszytkowska-Stawińska and
• Włodzimierz Buchowicz

Beilstein J. Org. Chem. 2014, 10, 1706–1732, doi:10.3762/bjoc.10.179

• educts contribute the majority of the novel skeleton of the product” [44]. In this review, we understand educts as compounds that contribute carbon atoms to the MCR product [45]. By the analogy to nucleosides included in the DNA/RNA nucleic acids, this review is limited to MCRs involving furanosyl