TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy

• Dnyaneshwar B. Gophane and
• Snorri Th. Sigurdsson

Beilstein J. Org. Chem. 2015, 11, 219–227, doi:10.3762/bjoc.11.24

The Shono-type electroorganic oxidation of unfunctionalised amides. Carbon–carbon bond formation via electrogenerated N-acyliminium ions

• Alan M. Jones and
• Craig E. Banks

Beilstein J. Org. Chem. 2014, 10, 3056–3072, doi:10.3762/bjoc.10.323

• such as the nucleobases: protected cytosine, guanine 87, adenine, and thymine to afford azanucleoside products such as 88 (Scheme 20). The use of the Shono-type electrooxidation in peptide and peptidomimetic chemistry The preparation of a bridged tricyclic analogue to induce an α-helix conformation in

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

• /RNA binding sites allowed H-bonding-based recognition of some complementary polynucleotide sequences. However, the recognition pattern was not straight-forward; for instance N5-protonated phenanthridinium–adenine derivative 12 successfully recognized a complementary poly(U) sequence [72] (Scheme 23

• ), but this recognition was completely lost upon introduction of a permanent positive charge by methylation of phenanthridine-N5 13 [71]. Intriguingly, N5-methylated phenanthridine–adenine conjugate 13 exhibited preferred binding to peculiar protonated poly AH+ double stranded helix (Scheme 23) [71

• instance, adenine derivative 15 (Figure 6) selectively recognized the complementary nucleotide (UMP) by specific change in the UV–vis spectrum of phenanthridine subunits and high affinity [75]. Molecular modelling studies proposed a structure of the 15–UMP complex stabilized by a set of intra- and

An integrated photocatalytic/enzymatic system for the reduction of CO₂ to methanol in bioglycerol–water

• Michele Aresta,
• Angela Dibenedetto,
• Tomasz Baran,
• Antonella Angelini,
• Przemysław Łabuz and
• Wojciech Macyk

Beilstein J. Org. Chem. 2014, 10, 2556–2565, doi:10.3762/bjoc.10.267

• cofactors is nicotinamide adenine dinucleotide (NAD+), a cofactor of the oxydoreductase class of enzymes. NAD+, together with its reduced form, 1,4-NADH, plays an essential role in many metabolic processes of living cells. NADH is also important in industrial biocatalysis, namely in the process of reductive

Synthesis of novel conjugates of a saccharide, amino acids, nucleobase and the evaluation of their cell compatibility

• Dan Yuan,
• Xuewen Du,
• Junfeng Shi,
• Ning Zhou,
• Abdulgader Ahmed Baoum and
• Bing Xu

Beilstein J. Org. Chem. 2014, 10, 2406–2413, doi:10.3762/bjoc.10.250

• conjugates 1–4, the saccharide is glucuronic acid, the amino acid segment consists of Phe-Arg-Gly-Asp or naphthAla (3-(2-naphthyl)-alanine)-Phe-Arg-Gly-Asp, and the nucleobase is thymine or adenine. Our results show that the conjugates synthesized and examined in this work exhibit excellent cell

• exploration [26]. As an amino acid, Phe or naphthAla increases molecular aromatic–aromatic interactions [19][21][27]. Arg-Gly-Asp, which is a well-established tripeptidic epitope, that modulates mammalian cell adhesion through binding with integrins on the cell membrane [28][29]. Thymine or adenine, as a

• viability of HeLa cells incubated with (A) 1, (B) 2, (c) 5, (D) 6 at different concentrations for 3 days. Cell viability of HeLa cells incubated with (A) 3, (B) 4, (C) 7, (D) 8 at different concentrations for 3 days. Synthesis of nucleobase (thymine and adenine) and saccharide (glucuronic acid) derivatives

Reversibly locked thionucleobase pairs in DNA to study base flipping enzymes

• Christine Beuck and
• Elmar Weinhold

Beilstein J. Org. Chem. 2014, 10, 2293–2306, doi:10.3762/bjoc.10.239

• opposing adenine, resulting in ring opening and formation of an ethylene cross-linked base pair [29][30]. Other aziridine-substituted nucleobases have been incorporated enzymatically by a DNA polymerase, but elongation past the modified nucleoside has not been reported [31]. Another approach uses

• of base flipping to the overall binding affinity of the DNA adenine-N6 MTase from Thermus aquaticus (M.TaqI) as an example. Results Selective cross-linking of thionucleobase pairs in DNA by bis-alkylation with 1,2-diiodoethane Thionucleobases are excellent soft nucleophiles, and chemoselective

• combination of equations (1) and (2): We used the duplex 1I6S-Et-S4U2 containing a locked A/T base pair analog at the target position within the double-stranded 5’-TCGA-3’ recognition site of the DNA adenine-N6 MTase M.TaqI to determine the equilibrium constant Kflip for the base flipping step. 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

• for the studied series of compounds showed that the essential structural features for the ICD recognition are a) the presence of DNA-binding appendages (adenine side chain and positively charged side chain) on both DBTAA side chains, and b) the presence of a short propyl linker, which does not support

• intramolecular aromatic stacking between DBTAA and adenine. The observed AT-DNA-ICD pattern differs from previously reported ss-DNA (poly dT) ICD recognition by a strong negative ICD band at 350 nm, which allows for the dynamic differentiation between ss-DNA (poly dT) and coupled ds-AT-DNA. Keywords: AT-DNA

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

• processing metal-mediated base pairs [26][27], resulting, e.g., in the formation of cytosine–Ag(I)–adenine base pairs [28]. Structural analyses of short oligonucleotide duplexes comprising one or more metal-mediated base pairs indicate that the large conformational space of nucleic acids exists also for

Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid

• Keunsoo Kim,
• Venkateshwarlu Punna,
• Phaneendrasai Karri and
• Ramanarayanan Krishnamurthy

Beilstein J. Org. Chem. 2014, 10, 2131–2138, doi:10.3762/bjoc.10.220

• the adenine derivative. The synthetic improvements described here enable an easy access to isoGNA and allows for the further exploration of this structural unit in oligonucleotide chemistry thereby spurring investigations of its usefulness and applicability. Keywords: acyclic nucleic acids; glycerol

• proved problematic and no product was detected. Therefore, in the adenine case, we tried a direct SN2 reaction of N6-benzoyladenine with tosyl derivative 6, which was only moderately successful (30% yield of 7). Unexpectedly, in both the thymine and adenine cases, the subsequent debenzylation reaction

• , the reaction with N6-benzoyladenine proved problematic and did not proceed even with the tosyl derivative 14. The solubility issues with benzoylated adenine and the bulk of the O-TBDPS group may be the underlying reasons behind this difficulty. Therefore, we proposed to use a doubly N6-protected

Photo, thermal and chemical degradation of riboflavin

• Muhammad Ali Sheraz,
• Sadia Hafeez Kazi,
• Sofia Ahmed,
• Zubair Anwar and
• Iqbal Ahmad

Beilstein J. Org. Chem. 2014, 10, 1999–2012, doi:10.3762/bjoc.10.208

• two major coenzymes, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), account for the vitamin activity in human nutrition [13]. RF is among the most widely studied compounds in terms of photostability and degradation in aqueous and organic solvents. It shows strong absorption at 223

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

• analogs [12]. In this publication, we present a conformational analysis of pyrrolidine azanucleotide analogs 7–14 containing thymine and adenine as examples of pyrimidine and purine nucleobases, respectively (Figure 2), and show how the conformation is affected by the mode of the phosphonate moiety

• that the NMR spectra of 7–10 are strongly pD-dependent as demonstrated for example on the 1H NMR spectrum of adenine derivative 9 (Figure 4). As follows from pD titrations (Figure 5; for more details see Supporting Information File 1), phosphonomethyl analogs 7–10, both cis (8, 10) and trans (7, 9

• the compounds exist as zwitterions with a hydrogen bond between the negatively charged phosphonate moiety and the positively charged pyrrolidine nitrogen atom in the range of pD 3–9. The pD titration experiments have also revealed the deuteration/dedeuteration of adenine and thymine nucleobases. In

The chemoenzymatic synthesis of clofarabine and related 2′-deoxyfluoroarabinosyl nucleosides: the electronic and stereochemical factors determining substrate recognition by E. coli nucleoside phosphorylases

• Ilja V. Fateev,
• Konstantin V. Antonov,
• Irina D. Konstantinova,
• Tatyana I. Muravyova,
• Frank Seela,
• Roman S. Esipov,
• Anatoly I. Miroshnikov and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2014, 10, 1657–1669, doi:10.3762/bjoc.10.173

• synthesis of 2-chloro-9-(2-deoxy-2-fluoro-β-D-arabinofuranosyl)adenine (1, clofarabine) were studied. The first approach consists in the chemical synthesis of 2-deoxy-2-fluoro-α-D-arabinofuranose-1-phosphate (12a, 2FAra-1P) via three step conversion of 1,3,5-tri-O-benzoyl-2-deoxy-2-fluoro-α-D

• 2-chloro-9-(β-D-arabinofuranosyl)adenine (6) in 45 min, the formation of 2-chloro-9-(β-D-xylofuranosyl)adenine (7) proceeded very slowly attaining ca. 8% yield in 48 h. Keywords: chemoenzymatic synthesis; clofarabine; nucleoside phosphorylases; phosphopentomutase; recombinant E. coli ribokinase

• phosphate 12a or another route for its generation. Yamada et al. studied in detail the transformation of the fluoride 9 in a 3:1 mixture of the α- and β-anomers of the phosphates 12a and 12b. They employed this mixture in the condensation with adenine and 2,6-diaminopurine catalyzed by PNP from Bacillus

Pyrene-modified PNAs: Stacking interactions and selective excimer emission in PNA₂DNA triplexes

• Alex Manicardi,
• Lucia Guidi,
• Alice Ghidini and
• Roberto Corradini

Beilstein J. Org. Chem. 2014, 10, 1495–1503, doi:10.3762/bjoc.10.154

• which is present in the mutated form of the human cystic fibrosis (CFTR) gene, and which was previously studied in our lab using PNA and modified PNA probes [36][37]; this mutation is characterised by the presence of an adenine instead of guanine, and corresponds to one of the most frequent point

• ; for PNA3 this is attributable to steric hindrance between the adjacent pyrene units; PNA4 and PNA5 containing one pyrene unit in the C-term, at the end of a segment in which the triplex structure is destabilized by the presence on the PNA of one adenine unit, show less selectivity; furthermore a

Synthesis, characterization and DNA interaction studies of new triptycene derivatives

• Sourav Chakraborty,
• Snehasish Mondal,
• Rina Kumari,
• Sourav Bhowmick,
• Prolay Das and
• Neeladri Das

Beilstein J. Org. Chem. 2014, 10, 1290–1298, doi:10.3762/bjoc.10.130

• on plasmid DNA. The results also indicate that triptycene derivatives have more affinity toward guanine–cytosine bases than adenine–thymine bases of DNA. Further studies are currently underway in our lab and include the syntheses of newer derivatives of triptycene, a study of the mechanism of

Solid-phase-supported synthesis of morpholinoglycine oligonucleotide mimics

• Tatyana V. Abramova,
• Sergey S. Belov,
• Yulia V. Tarasenko and
• Vladimir N. Silnikov

Beilstein J. Org. Chem. 2014, 10, 1151–1158, doi:10.3762/bjoc.10.115

• synthesis of the MorGly oligonucleotide mimics [19]. When studying the tandem complementary complexes of MorGly homohexa- and pentamers, we found out that the adenine-containing MorGly oligomers formed more stable complexes with poly(U) than native oligodeoxyriboadenylates of the same length. Moreover, it

• dependence of the thermal stability of complementary complexes formed by the MorGly oligomers on the heterocyclic base composition (uracil or adenine) of the modified chain. It was shown while studying their tandem complexes that the impact of cooperative interactions at oligomer junctions on the thermal

• necessity of using monomers 2 (Scheme 1) as first subunits bound to the support through the oxalyl linker. We synthesized Boc-protected aminomethylmorpholino nucleosides 2a,d,e as shown in Scheme 1 starting from aminomethylmorpholino nucleosides 3a,d,e. The synthesis of adenine and uracil containing

Biosynthesis of rare hexoses using microorganisms and related enzymes

• Zijie Li,
• Yahui Gao,
• Hideki Nakanishi,
• Xiaodong Gao and
• Li Cai

Beilstein J. Org. Chem. 2013, 9, 2434–2445, doi:10.3762/bjoc.9.281

• oxygen. L-Talose and D-gulose The aldohexoses L-talose and D-gulose (C-3 epimer of D-galactose) are both very expensive owing to their scarcity in nature. L-Talofuranosyladenine, an adenine nucleoside derivative of L-talose, was found to be a slow-reacting substrate for calf intestinal adenosine

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

Flow synthesis of phenylserine using threonine aldolase immobilized on Eupergit support

• Jagdish D. Tibhe,
• Hui Fu,
• Timothy Noël,
• Qi Wang,
• Jan Meuldijk and
• Volker Hessel

Beilstein J. Org. Chem. 2013, 9, 2168–2179, doi:10.3762/bjoc.9.254

• , Germany). L-threonine, β-nicotinamide adenine dinucleotide disodium salt (NADH) were purchased from AppliChem GmbH (Darmstadt, Germany). Glycine, benzaldehyde, pyridoxal-5’-phosphate (PLP), Eupergit CM, 2-mercaptoethanol, 25% glutaraldehyde solution in water, ethylenediamine and other reagents were all

Functionalization of heterocyclic compounds using polyfunctional magnesium and zinc reagents

• Paul Knochel,
• Matthias A. Schade,
• Sebastian Bernhardt,
• Georg Manolikakes,
• Albrecht Metzger,
• Fabian M. Piller,
• Christoph J. Rohbogner and
• Marc Mosrin

Beilstein J. Org. Chem. 2011, 7, 1261–1277, doi:10.3762/bjoc.7.147

• chloranil amidocuprate 87 undergoes an oxidative coupling providing the adenine derivative 88 in 71% yield. A treatment with D-valinol (89) affords the desired CDK inhibitor, purvalanol A (84) in 65% yield (Scheme 15) [44]. 2.2 The preparation of polyfunctional heterocyclic magnesium reagents by the

• /Mg-exchange reaction. An oxidative amination leading to the biologically active adenine, purvalanol A (84). Preparation of polyfunctional arylmagnesium reagents using Mg in the presence of LiCl. Preparation of polyfunctional magnesium reagents starting from organic chlorides. Selective multiple

An overview of the key routes to the best selling 5-membered ring heterocyclic pharmaceuticals

• Marcus Baumann,
• Ian R. Baxendale,
• Steven V. Ley and
• Nikzad Nikbin

Beilstein J. Org. Chem. 2011, 7, 442–495, doi:10.3762/bjoc.7.57

• normally filled by the ADP’s adenine in the phosphorylated protein. The indolinone section is located in a deeper pocket with the heteroatoms being involved in H-bonding glutamate and tyrosine residues whilst the pyrrole ring and the diethylaminoethyl appendage are exposed to the solvent environment [8

Palladium- and copper-mediated N-aryl bond formation reactions for the synthesis of biological active compounds

• Carolin Fischer and
• Burkhard Koenig

Beilstein J. Org. Chem. 2011, 7, 59–74, doi:10.3762/bjoc.7.10

• . However, adenine was unreactive under these conditions, probably due to its low solubility [73]. Slight changes of the procedure, the use of a protic solvent, enabled the conversion of adenine (97) and cytosine (94) (Scheme 23). These conditions tolerated both electron-donating and electron-withdrawing

• lotrafiban (SB-214857). Intermolecular effort towards lotrafiban. Synthesis of matrix metalloproteases (MMPs) inhibitor. Regioselective 9-N-arylation of purines. N-Arylation of adenine and cytosine. 9-N-Arylpurines as enterovirus inhibitors. Xanthine analogues as kinase inhibitors. Synthesis of dual PPARα/γ

Synthesis of 5-(6-hydroxy-7H-purine-8-ylthio)- 2-(N-hydroxyformamido)pentanoic acid

• Yanmei Zhang,
• Greg Elliot,
• Adrian Saldanha,
• Igor Tsigelny,
• Dennis Carson and
• Wolf Wrasidlo

Beilstein J. Org. Chem. 2010, 6, 742–747, doi:10.3762/bjoc.6.93

• thiolated nucleoside to obtain the hybrid model compound. Keywords: adenylosuccinate synthetase (AdSS); thiolated nucleoside; Introduction During cell proliferation, adenine nucleotides for nucleic acid synthesis are generated through a de novo biosynthetic route, which requires the key enzyme

• adenylosuccinate synthetase (AdSS). Adenine nucleotides are also recycled by a salvage pathway which requires methylthioadenosine phosphorylase (MTAP). In some cancers this salvage pathway is lost making these cancers hypersensitive to cytotoxic effects of pharmacologic AdSS inhibitors [1]. However, no direct

Synthesis of some novel hydrazono acyclic nucleoside analogues

• Mohammad N. Soltani Rad,
• Ali Khalafi-Nezhad and
• Somayeh Behrouz

Beilstein J. Org. Chem. 2010, 6, No. 49, doi:10.3762/bjoc.6.49

• %). Moreover, N-benzyl adenine derivative 1o was obtained as the N(9)-isomer in 76% yield, while theophylline was mostly alkylated at N(7) to afford 1m (69%). All compounds were fully characterized and their structures confirmed by 1H and 13C NMR, elemental analysis, mass and IR spectroscopy. Although

Anthracene coupled adenine for the selective sensing of copper ions

• Kumaresh Ghosh and
• Tanushree Sen

Beilstein J. Org. Chem. 2010, 6, No. 44, doi:10.3762/bjoc.6.44

• exhibit Cu2+ induced ON-OFF type signaling patterns over the other representative metal ions studied. Compound 1 exhibits 97% quenching of emission in the presence of Cu2+ whilst derivative 2 shows 81% quenching under similar experimental conditions. Keywords: adenine-based anthracene; copper ion

• ]. Although there are various reports in this regard, synthetic receptors with improved binding efficiency are still in demand. In addition, the coordination of the metal ion with nucleobases plays an important role in the stability of the nucleic acid structure [25]. Among the nucleobases adenine provides

• five interactional sites for coordination with metal atoms. Although it has already been established that adenine moiety exhibits preferential coordination of silver ions [26], the formation of Cu(II) complexes of substituted adenines is also known in the literature [27]. Depending on the smaller size

Symmetrical and unsymmetrical α,ω-nucleobase amide-conjugated systems

• Sławomir Boncel,
• Maciej Mączka,
• Krzysztof K. K. Koziol,
• Radosław Motyka and
• Krzysztof Z. Walczak

Beilstein J. Org. Chem. 2010, 6, No. 34, doi:10.3762/bjoc.6.34

• particularly effective condensing agent. The subunits containing carboxylic groups were obtained by acidic hydrolysis of N-1 Michael adducts of uracils or N-9 Michael adducts of 6-chloropurine with methyl acrylate. The amines used were aliphatic/aromatic diamines, adenine, 5-substituted 1-(ω-aminoalkyl)uracils

• ). As amine components, readily accessible amines such as aliphatic α,ω-diamines, phenylene diamines, adenine, 5-substituted 1-(ω-aminoalkyl)uracils and 5′-amino-5′-deoxythymidine were chosen. To accomplish the synthesis of the title compounds, we developed a simple and effective method of coupling the