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

• switching of optical properties in DNA can be achieved selectively at 310 nm (forward) and 450 nm (backward); both wavelengths are outside the normal nucleic acid absorption range. Moreover, this nucleoside was proven to be photochemically stable and allows switching back and forth several times. These

• . Diarylethenes have been applied in a noncovalent chiroptical photoswitchable DNA complex [33] and combined with 7-deazaadenosine to obtain a nucleosidic diarylethene switch [34]. Recently, we reported, very preliminarily, the preparation and optical properties of nucleoside 4 [30]. Herein, we give a full

• account and present the detailed synthesis of diarylethene-modified nucleosides 4, 5 and 6 (Scheme 1), and the characterization of their photochromic behavior. It turned out to be most promising to continue the DNA work with the modified and photochromic nucleoside 4, which was, thus, incorporated into

Enantioselective supramolecular devices in the gas phase. Resorcin[4]arene as a model system

• Caterina Fraschetti,
• Matthias C. Letzel,
• Antonello Filippi,
• Maurizio Speranza and
• Jochen Mattay

Beilstein J. Org. Chem. 2012, 8, 539–550, doi:10.3762/bjoc.8.62

• [VR∙H∙dC]+ complex does not uptake B, whereas its diastereoisomers are able to efficiently capture B and to proceed to the nucleoside displacement. This very sensitive system strongly resembles the electronic concept of a logic gate. Indeed, depending on the relative configuration of the

• supramolecular device and of the neutral gas B, the transported nucleoside can or cannot be released. This effect is outstanding for the [VR/S∙H∙dC]+ aggregates, which, if “stimulated” by a reactant characterized by the correct configuration, can selectively release one enantiomer of a chiral guest and keep the

Azobenzene dye-coupled quadruply hydrogen-bonding modules as colorimetric indicators for supramolecular interactions

• Yagang Zhang and
• Steven C. Zimmerman

Beilstein J. Org. Chem. 2012, 8, 486–495, doi:10.3762/bjoc.8.55

• ]. Indeed, several syntheses of the DAN unit are now available [29][30][31][32][33][34]. The original UG unit contains a labile nucleoside unit, but a DeUG unit [35] and more recently a DeUG module bearing a range of synthetic handles for further elaboration [36] were both reported with more scalable

Selectivity in C-alkylation of dianions of protected 6-methyluridine

• Ngoc Hoa Nguyen,
• Christophe Len,
• Anne-Sophie Castanet and
• Jacques Mortier

Beilstein J. Org. Chem. 2011, 7, 1228–1233, doi:10.3762/bjoc.7.143

• parameters that are critical for the design of new nucleoside drug candidates [4][5][6][7][8]. These cyclic compounds are expected to have a beneficial biological impact especially toward enzymatic repair processes [9]. As part of an ongoing program directed by one of us (C. L.) toward the synthesis and

• construction of C-substituted nucleosides are based on ring lithiation of nucleoside derivatives followed by their reaction with appropriate electrophiles. Thus, sequential lithiation of 2',3'-O-isopropylideneuridine (6) with LDA in THF (Figure 1) and electrophilic quenching with n-bromobutane was reported to

• organolithiums [14], and indeed, 7 failed to react, in our experiments, with 4-bromo-but-1-ene to give 9. We then turned our attention to the metalation of the 5'-O-TBDMS protected nucleoside 10 (Figure 2). Treatment with LDA (5 equiv) in THF at −70 °C followed by addition of D2O provided 12 in 82% yield

Synthesis, reactivity and biological activity of 5-alkoxymethyluracil analogues

• Lucie Brulikova and
• Jan Hlavac

Beilstein J. Org. Chem. 2011, 7, 678–698, doi:10.3762/bjoc.7.80

• , cytotoxic and antibacterial, is also reported. Keywords: 5-alkoxymethyluracil; biological activity; nucleosides; Review Introduction Modifications of nucleic acid components play a significant role in the field of nucleic acids research. In particular, nucleoside analogues find broad therapeutic

• nucleoside 1, Bergstrom and co-workers reported a presumed mechanism for its formation (Scheme 1) [8]. In addition, they also focused their research on isopropyloxy analogue 2. Reaction of 3,3,3-trifluoropropene with 5-chloromercuri-2'-deoxyuridine (4) in methanol gave two major products (E)-5-(3,3,3

• localization agents, Iwashina and co-workers investigated the radiolabelled 5-(1-methoxy-2-iodoethyl) nucleoside 31 (Figure 4) [15] which was obtained by radio-iodination of 5-(1-methoxy-2-iodoethyl)-2'-deoxyuridine (28) via isotope exchange by the pivalic acid melt method. In addition to the above mentioned 5

Oxalyl retro-peptide gelators. Synthesis, gelation properties and stereochemical effects

• Janja Makarević,
• Milan Jokić,
• Leo Frkanec,
• Vesna Čaplar,
• Nataša Šijaković Vujičić and
• Mladen Žinić

Beilstein J. Org. Chem. 2010, 6, 945–959, doi:10.3762/bjoc.6.106

• Janja Makarevic Milan Jokic Leo Frkanec Vesna Caplar Natasa Sijakovic Vujicic Mladen Zinic Laboratory for Supramolecular and Nucleoside Chemistry, Ruđer Bošković Institute, P.O.B. 180, HR-10002 Zagreb, Croatia 10.3762/bjoc.6.106 Abstract In this work we report on gelation properties, self

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

• a nucleoside. A prototype compound was designed and docked into the catalytic domain of the AdSS enzyme bridging the region between the magnesium center of the protein to the nucleoside region. The synthesis involves coupling a brominated peptide fragment capable of complexing magnesium to a

• 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

Kinetic studies and predictions on the hydrolysis and aminolysis of esters of 2-S-phosphorylacetates

• Milena Trmčić and
• David R. W. Hodgson

Beilstein J. Org. Chem. 2010, 6, 732–741, doi:10.3762/bjoc.6.87

• use of bromoacetate-based cross-linking agents with thiophosphate nucleophiles 3, where our aim was to generate nucleoside-pyrophosphate mimics as potential glycosyl transferase inhibitors under aqueous conditions. Initially, we focus on the use of the bromoacetic acid esters of N-hydroxybenzotriazole

A novel and efficient method to prepare 2-aryltetrahydrofuran-2-ylphosphonic acids

• Vsevolod V. Komissarov,
• Anatoly M. Kritzyn and
• Jouko J. Vepsäläinen

Beilstein J. Org. Chem. 2010, 6, No. 63, doi:10.3762/bjoc.6.63

• [1][2][3][4]. As a part of our ongoing project, it seemed important to synthesize compounds with phosphonate and phenyl groups at one end of the hydrocarbon chain and a nucleic base residue at the other end. Previously, it was shown that compounds with similar structures inhibit purine nucleoside

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

• using phenylhydrazine. To interpret the dominant formation of (E)-hydrazone derivatives rather than (Z)-isomers, PM3 semiempirical quantum mechanic calculations were carried out which indicated that the (E)-isomers had the lower heats of formation. Keywords: acyclic nucleoside; chemotherapeutic agent

• antineoplastic (e.g. bisantrene [4][10]), contain a hydrazone moiety in their structure. Furthermore, various structurally related miconazole bioactive hydrazones are known as antimicrobial and antifungal agents [11][12]. The significance of nucleoside chemistry in drug discovery is well-known and fully

• established in medicinal chemistry [13][14][15][16]. Acyclic nucleosides constitute a special class of nucleoside analogues which have attracted great interest due to their broad-spectrum chemotherapeutic activities against cancer and infections caused by viruses, microbes and other pathogenic microorganisms

The C–F bond as a conformational tool in organic and biological chemistry

• Luke Hunter

Beilstein J. Org. Chem. 2010, 6, No. 38, doi:10.3762/bjoc.6.38

• amount of research into fluorinated nucleoside analogues as potential treatments for cancer and viral infection [21][22]. Fluorine is an obvious choice for incorporating into sugar-modified nucleoside analogues, since fluorine can be considered a reasonable mimic of either a hydrogen atom or a hydroxyl

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

• ]. Moreover, α,ω-nucleobase amide-conjugated molecules possess the tendency to form meta-stable complexes with DNA and thus can perturb the cell replication. For example, amide-linked heterodimer synthons consisting of acyclic nucleoside units and 5′-amino-2′,5′-dideoxythymidine are PNA/DNA chimeras (V) [4

• of 1ea shown as thermal ellipsoids at 50% probability [17][18]. DMT-MM in its presumably more stable conformation [20]. TEM images of symmetrical α,ω-nucleobase amide-conjugated systems: A – two splitting nucleoside nanofibres growing out from crystalline phase (11), the rectangular area (A) shows

(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

• derivatives with tendency to adopt specific compact conformations (foldamers). Linear naturally-occurring SAA homo-oligomers SAAs occur extensively in nature as subunits of oligosaccharides in cell walls such as N-acetylneuraminic 1 and muramic acids 2, as well as in some nucleoside antibiotics (e.g

• positively charged isothiouronium inter-nucleoside linkages into otherwise negatively charged DNA (Figure 17) [83][84]. The binding of these artificial DNAs (DNmt or DNT) to its complementary DNA strand occurs as with the unmodified DNA·DNA duplex but with enhanced nuclease resistance. In order to design

Dipyridodiazepinone derivatives; synthesis and anti HIV-1 activity

• Nisachon Khunnawutmanotham,
• Nitirat Chimnoi,
• Arunee Thitithanyanont,
• Patchreenart Saparpakorn,
• Kiattawee Choowongkomon,
• Pornpan Pungpo,
• Supa Hannongbua and
• Supanna Techasakul

Beilstein J. Org. Chem. 2009, 5, No. 36, doi:10.3762/bjoc.5.36

• : AIDS; anti HIV-1 RT; dipyridodiazepinone; nevirapine; synthesis; Introduction Dipyridodiazepinone nevirapine (1) [1] (Figure 1) is a potent non-nucleoside inhibitor of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) and is approved as a therapeutic agent for the treatment of AIDS

Sordarin, an antifungal agent with a unique mode of action

• Huan Liang

Beilstein J. Org. Chem. 2008, 4, No. 31, doi:10.3762/bjoc.4.31

• immunosuppressed patients, especially those suffering from AIDS or cancer, fungal infections have become a significant, often life-threatening problem [1][2]. Present treatments rely on antifungals such as polyene antibiotics (amphotericin B), nucleoside analogs (5-fluorocytosine) and azoles (fluoconazole

Understanding the mechanism of Pd-catalyzed allylic substitution of the cyclic difluorinated carbonates

• Jun Xu,
• Xiao-Long Qiu and
• Feng-Ling Qing

Beilstein J. Org. Chem. 2008, 4, No. 18, doi:10.3762/bjoc.4.18

• substitution features a reversal of regioselectivity caused by fluorine. Background Carbocyclic nucleosides (CNAs), in which the furanose oxygen atoms of the 4'-oxonucleosides are substituted by CH2, have received considerable attention because they exhibit greater metabolic stability toward nucleoside

• is more hindered than the C2 position. Interestingly, we also found that treatment of the trans-trans dimer 8 with PPh3 / 3-benzoylthymine sodium at rt provided the nucleoside analogue 5 in 30% yield. No product was detected when PPh3 was absent (Scheme 3). Thus, we think that the reaction occurred

N-1 regioselective Michael- type addition of 5-substituted uracils to (2-hydroxyethyl) acrylate

• Sławomir Boncel,
• Dominika Osyda and
• Krzysztof Z. Walczak

Beilstein J. Org. Chem. 2007, 3, No. 40, doi:10.1186/1860-5397-3-40

• utilization of synthetic subunits, we have obtained ester-conjugated acyclic nucleoside, namely 3-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-propionic acid 2-[3-(5-bromo-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-propionyloxy]-ethyl ester (4) (Scheme 2). The reaction was performed in THF at room

• of the product was confirmed by 1H and 13C NMR spectroscopy. See Figure 1 in Supporting Information File 1 for the assignment of particular protons in NMR spectrum of the model ester-conjugated nucleoside. Conclusion In summary, a simple and efficient method of N-1 alkylation of uracil rings using

• spectrum of the model ester-conjugated nucleoside (4). Michael-type addition of 5-substituted uracil derivatives to 2-hydroxyethyl acrylate. Synthesis of the model ester-conjugated acyclic nucleoside. Conditions for the Michael-type addition of 5-substituted uracil derivatives to 2-hydroxyethyl acrylate

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

• coumarin or ferrocene labeled nucleosides. Fluorescent properties of coumarin labeled nucleosides are determined. Conclusion New coumarin and ferrocene labeled nucleosides were prepared via intermolecular Staudinger ligation. This reaction joins the fluorescent coumarin and biospecific nucleoside to the

• new molecule with promising fluorescent and electrochemical properties. The isolated yields of products depend on the structure of azidonucleoside and carboxylic acids. A detailed study of the kinetics of the Staudinger ligation with nucleoside substrates is in progress. Background Modified

• , [22][23] including specific labeling of nucleic acids, [24] proteomic studies [25][26] and modification of cell surfaces. [17][18] We applied the Staudinger ligation for nucleoside labeling procedures, using coumarin and ferrocene derivatives as labels. According to our knowledge, applications of this

The first salen- type ligands derived from 3',5'-diamino- 3',5'-dideoxythymidine and -dideoxyxylothymidine and their corresponding copper(II) complexes

• Daniel Koth,
• Michael Gottschaldt,
• Helmar Görls and
• Karolin Pohle

Beilstein J. Org. Chem. 2006, 2, No. 17, doi:10.1186/1860-5397-2-17

• , Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands 10.1186/1860-5397-2-17 Abstract Background There are many nucleoside metal complexes known. According to observations made, only very few of them reveal their central ion to be co-ordinated by the sugar part of their

• containing three (DNA nucleosides) and four (RNA nucleosides) chiral centers respectively. Though the coordination of metal ions to nucleosides is well known, mostly the nucleobase interacts with the metal centre, and the chiral part of the nucleoside is not involved in the coordination. [1][2] Although a

• use as ligand in a copper(II) complex. [6] As far as we are aware, a metal complex with a 3',5'-diimino substituted nucleoside as a ligand has not been published by another source yet, and neither has its carbohydrate analogue. This study reports the synthesis of 3',5'-diamino-3',5'-dideoxy- and 3',5

Investigation of acetyl migrations in furanosides

• O. P. Chevallier and
• M. E. Migaud

Beilstein J. Org. Chem. 2006, 2, No. 14, doi:10.1186/1860-5397-2-14

• acetyl moieties. Such direct transesterification is intermolecular and while it has been observed in nucleoside-phosphoramidite and glycoside chemistry,[20][21][22][23] this alkoxide-promoted intermolecular acetyl migration process has been overlooked in furanosides. The isolated quantities of 1c and 1d

Stereoselective α-fluoroamide and α-fluoro- γ-lactone synthesis by an asymmetric zwitterionic aza-Claisen rearrangement

• Kenny Tenza,
• Julian S. Northen,
• David O'Hagan and
• Alexandra M. Z. Slawin

Beilstein J. Org. Chem. 2005, 1, No. 13, doi:10.1186/1860-5397-1-13

• intermediate in the synthesis of the anti-HIV nucleoside β-FddA1 6. [17][18] Results and discussion In order to undertake the appropriate zwitterionic aza-Claisen rearrangement reactions an efficient method for the production of the α-fluoro acid chloride substrates was required. A number of routes to 2

• iodolactonisation to generate α-fluoro-γ-butyrolactones, with good diastereoselectivities (~80–100% de). These molecules are useful intermediates for further derivatisation in the area of nucleoside analogue synthesis and the method is complementary to asymmetric electrophilic fluorination strategies for the