A new building block for DNA network formation by self-assembly and polymerase chain reaction

• Holger Bußkamp,
• Sascha Keller,
• Marta Robotta,
• Malte Drescher and
• Andreas Marx

Beilstein J. Org. Chem. 2014, 10, 1037–1046, doi:10.3762/bjoc.10.104

• oligonucleotide synthesis was performed at 0.2 µmol scale (trityl-on mode) employing the standard phosphoramidites and 6 which was diluted in a mixture containing 10% CH2Cl2 in CH3CN to a final concentration of 0.12 M. 3000 Å LCAA-CPG support was used, derivatized with the respective 3'-nucleotide of the

• terminal thymidine that is covalently connected to the benzene core via a rigid ethylene bridge is amenable to contribute to duplex stability. This was evidenced by an increase in Tm, when ODN I was hybridized to 10 in comparison to the one nucleotide shorter 9. Next, bDNA constructs were characterized by

• natural dNTPs. We obtained spectra showing that the spin-labeled nucleotide was indeed incorporated into the DNA (Figure 5B,C). All spectra were quantitatively analyzed by spectral line shape simulations. Thereby, the dynamics of the nitroxide spin-labels are reflected in rotational correlation times τc

Synthesis of nucleotide–amino acid conjugates designed for photo-CIDNP experiments by a phosphotriester approach

• Tatyana V. Abramova,
• Olga B. Morozova,
• Vladimir N. Silnikov and
• Alexandra V. Yurkovskaya

Beilstein J. Org. Chem. 2013, 9, 2898–2909, doi:10.3762/bjoc.9.326

• phosphotriester block liquid phase synthesis. The phosphotriester approach to the oligonucleotide synthesis was shown to be a versatile and economic strategy for preparing the required amount of high quality samples of nucleotide–amino acid conjugates. Keywords: CIDNP; nucleotide–amino acid conjugates

• model compound conjugates of the amino acid, nucleotide, and dye residues, where key participants (dye, amino acid, and nucleoside) have to be drawn together mimicking the biologically important DNA repair processes. To fulfill the requirements of the photo-induced TR CIDNP experiments, a synthetic

• conjugates consisting of amino acid, nucleotide, and dye residues including linkers of different lengths (Figure 1). Target compounds 1–8 have been synthesized by the phosphotriester block liquid phase synthesis (LPS). Results and Discussion Design of model compounds Our previous studies revealed a great

SF002-96-1, a new drimane sesquiterpene lactone from an Aspergillus species, inhibits survivin expression

• Silke Felix,
• Louis P. Sandjo,
• Till Opatz and
• Gerhard Erkel

Beilstein J. Org. Chem. 2013, 9, 2866–2876, doi:10.3762/bjoc.9.323

• % CO2. Reporter gene assays The 1092 bp human survivin promoter (region between nucleotide 1821 and nucleotide 2912 within the human survivin gene; GenBankTM accession number U75285) was amplified by polymerase chain reaction from genomic DNA isolated from MonoMac6 cells using oligonucleotides derived

An overview of the synthetic routes to the best selling drugs containing 6-membered heterocycles

• Marcus Baumann and
• Ian R. Baxendale

Beilstein J. Org. Chem. 2013, 9, 2265–2319, doi:10.3762/bjoc.9.265

Activation of cryptic metabolite production through gene disruption: Dimethyl furan-2,4-dicarboxylate produced by Streptomyces sahachiroi

• Dinesh Simkhada,
• Huitu Zhang,
• Shogo Mori,
• Howard Williams and
• Coran M. H. Watanabe

Beilstein J. Org. Chem. 2013, 9, 1768–1773, doi:10.3762/bjoc.9.205

• performed using ABI BigDye chemistry at the Gene Technologies Lab, Texas A&M University. The computer-based analysis and comparisons of nucleotide and protein sequences were performed with BLAST, FASTA, CLUSTALW and GENEDOC programs. See Supporting Information File 1 for details on bacterial strains

Methylidynetrisphosphonates: Promising C₁ building block for the design of phosphate mimetics

• Vadim D. Romanenko and
• Valery P. Kukhar

Beilstein J. Org. Chem. 2013, 9, 991–1001, doi:10.3762/bjoc.9.114

• blocks in the synthesis of the nucleotide analogues with enhanced affinity for receptors and better charge correlation with transition states for selected kinases. Two synthetically useful approaches to the parent trisphosphonic acid HC(PO3H2)3 have been developed. One of the procedures is based on the

• conception of supercharged nucleotide analogues in which an additional negative charge is provided without elongation of the polyphosphate chain. But there are still a lot of other aspects of their chemistry that remain to be investigated. From a synthetic point of view, since the introduction of a

Synthesis and physicochemical characterization of novel phenotypic probes targeting the nuclear factor-kappa B signaling pathway

• Paul M. Hershberger,
• Satyamaheshwar Peddibhotla,
• E. Hampton Sessions,
• Daniela B. Divlianska,
• Ricardo G. Correa,
• Anthony B. Pinkerton,
• John C. Reed and
• Gregory P. Roth

Beilstein J. Org. Chem. 2013, 9, 900–907, doi:10.3762/bjoc.9.103

• -oriented within the NF-κB pathway and are specific modulators of the intracellular signaling protein, nucleotide-binding oligomerization domain-1 (NOD1). Within each project area first-in-class chemical probes were identified and characterized as new research-tool compounds. The synthetic routes for each

• performs in a noncanonical manner and inhibits NF-κB activity outside of the known, well-characterized pathways [7]. Determination of the precise signaling mechanism is the subject of ongoing research in our laboratories. Discovering modulators of NF-κB signaling via selective nucleotide-binding

• oligomerization domain-1 (NOD1) inhibition (ML130 and ML146): The second program targeted proteins in the mammalian innate immune system that confer defense by detection of specific microbial ligands, or pathogen-associated molecular pattern microbial sensors known to house NOD1 (nucleotide-binding

Recent progress in the discovery of small molecules for the treatment of amyotrophic lateral sclerosis (ALS)

• Allison S. Limpert,
• Margrith E. Mattmann and
• Nicholas D. P. Cosford

Beilstein J. Org. Chem. 2013, 9, 717–732, doi:10.3762/bjoc.9.82

• proteins associated with ALS. Trans-activating response (TAR) DNA-binding protein 43 (TDP-43) is a nucleotide-binding protein important for gene transcription and mRNA splicing, transport, and stabilization [38]. Mutations in the TARDBP gene, which encodes TDP-43, are responsible for up to 6.5% of fALS [1

• binding of TDP-43 to nucleotides. Cassel et al. [42] developed a high-throughput screening assay whereby TDP-43 nucleotide binding could be assessed. A screen of 7360 compounds yielded a series of small molecules that disrupt oligonucleotide binding to TDP-43 protein [42]. Later, this series of 4

Synthesis and evaluation of cell-permeable biotinylated PU-H71 derivatives as tumor Hsp90 probes

• Tony Taldone,
• Anna Rodina,
• Erica M. DaGama Gomes,
• Matthew Riolo,
• Hardik J. Patel,
• Raul Alonso-Sabadell,
• Danuta Zatorska,
• Maulik R. Patel,
• Sarah Kishinevsky and
• Gabriela Chiosis

Beilstein J. Org. Chem. 2013, 9, 544–556, doi:10.3762/bjoc.9.60

• clinical trials, has been the ATP-competitive inhibitors that bind to the N-terminal nucleotide binding pocket [4][5]. Hsp90 belongs to the family of GHKL (G = DNA gyrase subunit B; H = Hsp90; K = histidine kinases; L = MutL) ATPases, which is distinguished by a unique bent shape of its nucleotide binding

• interest is the purine scaffold, including its representative PU-H71 (1a). This agent, currently in clinical investigation for cancer, binds to the N-terminal nucleotide binding pocket of Hsp90 [12]. We have shown that PU-H71 selects for tumor Hsp90 species, and therefore labeled derivatives of PU-H71 may

Synthesis of a derivative of α-D-Glcp(1->2)-D-Galf suitable for further glycosylation and of α-D-Glcp(1->2)-D-Gal, a disaccharide fragment obtained from varianose

• Carla Marino,
• Carlos Lima,
• Karina Mariño and
• Rosa M. de Lederkremer

Beilstein J. Org. Chem. 2012, 8, 2142–2148, doi:10.3762/bjoc.8.241

• bacteria to protozoa and in the fact that, being absent in mammals, the metabolism of Galf is a good target for chemotherapy [9][10][11]. In particular, the unique UDP-galactopyranose mutase necessary for the production of the Galf nucleotide has been thoroughly studied and characterized in several

Studies on the substrate specificity of a GDP-mannose pyrophosphorylase from Salmonella enterica

• Lu Zou,
• Ruixiang Blake Zheng and
• Todd L. Lowary

Beilstein J. Org. Chem. 2012, 8, 1219–1226, doi:10.3762/bjoc.8.136

• enzyme. When taken into consideration with other previously published work, it appears that this enzyme has potential utility for the chemoenzymatic synthesis of GDP-Manp analogues, which are useful probes for studying enzymes that employ this sugar nucleotide as a substrate. Keywords: chemoenzymatic

• synthesis; kinetics; methylation; pyrophosphorylase; sugar nucleotide; Introduction Modified sugar nucleotide analogues are valuable probes to study glycosyltransferases and other enzymes that use these activated glycosylating agents as substrates [1][2][3][4][5]. The synthesis of natural and non-natural

• attractive strategy is to employ a chemoenzymatic approach, in which a synthetic sugar 1-phosphate derivative is converted to the sugar nucleotide by a pyrophosphorylase (Figure 1B) [14][15]. This approach is increasingly used for the synthesis of sugar nucleotides, but a limitation is that the specificity

Diarylethene-modified nucleotides for switching optical properties in DNA

• Sebastian Barrois and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2012, 8, 905–914, doi:10.3762/bjoc.8.103

• with a representative set of chromophore-modified oligonucleotides and found that the DNA-polymerase-catalyzed nucleotide incorporation opposite to attached chromophores at the 5-position of uridine follows Watson–Crick selectivity [49]. In the meantime, DNA polymerases have been evolved that have an

(Pseudo)amide-linked oligosaccharide mimetics: molecular recognition and supramolecular properties

• José L. Jiménez Blanco,
• Fernando Ortega-Caballero,
• Carmen Ortiz Mellet and
• José M. García Fernández

Beilstein J. Org. Chem. 2010, 6, No. 20, doi:10.3762/bjoc.6.20

• access pseudoamide-type oligosaccharide mimics. Calystegine B2 analogues 38 and 39 with urea-linked disaccharide structure. Rotameric equilibrium shift of 40 by formation of a bidentate hydrogen bond. Nucleotide analogues with thiourea and S-methylisothiouronium linkers. Rotameric equilibria for β-(1→6

Synthetic incorporation of Nile Blue into DNA using 2′-deoxyriboside substitutes: Representative comparison of (R)- and (S)-aminopropanediol as an acyclic linker

• Daniel Lachmann,
• Sina Berndl,
• Otto S. Wolfbeis and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2010, 6, No. 13, doi:10.3762/bjoc.6.13

• visible spectrum) for use in “click” conjugation have been reported meanwhile [18]. The dye carrying the azide group was reacted with an alkyne group that was incorporated into the oligonucleotides as a nucleotide substituent. (S)-3-Amino-1,2-propanediol was used as an acyclic linker and substitute for

Synthesis of phosphonate and phostone analogues of ribose-1-phosphates

• Pitak Nasomjai,
• David O'Hagan and
• Alexandra M. Z. Slawin

Beilstein J. Org. Chem. 2009, 5, No. 37, doi:10.3762/bjoc.5.37

• step in the biosynthesis involves the fluorinase, an enzyme that catalyses nucleophilic attack of fluoride ion on SAM (3) to generate 5′-FDA (4). The initial fluorinated product 5′-FDA (4) is then depurinated by a purine nucleotide phosphorylase (PNP) to give 5-fluoro-5-deoxyribose-1-phosphate (5

Synthesis of coumarin or ferrocene labeled nucleosides via Staudinger ligation

• Ivana Kosiova,
• Andrea Janicova and
• Pavol Kois

Beilstein J. Org. Chem. 2006, 2, No. 23, doi:10.1186/1860-5397-2-23

• reaction in nucleoside and nucleotide chemistry are rare. Results and discussion We used intermolecular Staudinger ligation [27] for the preparation of fluorescent and electrochemically labeled nucleosides. As the label we used either coumarin-4-acetic acids 1a-c or ferrocene derivative 17 (Figure 1

Colchitaxel, a coupled compound made from microtubule inhibitors colchicine and paclitaxel

• Karunananda Bombuwala,
• Thomas Kinstle,
• Vladimir Popik,
• Sonal O. Uppal,
• James B. Olesen,
• Jose Viña and
• Carol A. Heckman

Beilstein J. Org. Chem. 2006, 2, No. 13, doi:10.1186/1860-5397-2-13

• stacked on it in such a way that the nucleotide-binding site is embedded in the interface [8]. Ravelli and coworkers found colchicine binding site to be buried in the β subunit, boxed in by β-strands of the second domain and helices #7 and #8. The A ring of colchicine contacts residue 241[9], consistent