Specific DNA duplex formation at an artificial lipid bilayer: fluorescence microscopy after Sybr Green I staining

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2014, 10, 2307–2321, doi:10.3762/bjoc.10.240

• it had been shown that a membrane-bound duplex formation between the lipo-oligonucleotide 7 (5’-d(1a-ATC CAG TTA TGA)-3’) and the oligomer 5 failed. Now, we repeated the first experiment (4 + 5) successfully and run a z-scan of the bilayer after 45 min of incubation with a laser irradiation of the

• + SG. In a second series of experiments we used an unlabelled target DNA (6) for duplex formation at the lipid bilayer and added only a DMSO solution of Sybr Green I to the cis compartment of the bilayer slide. As can be seen from Figure 7 also the hybridization of an unlabelled target oligomer 6 with

• the lipo-oligonucleotide 4 can be proved by adding the dye and irradiation at 488 nm. In case of the incorporation of the lipo-oligonucleotide 7 into the bilayer and addition of the non-complementary unlabelled oligomer 6 (negative control experiment), no duplex formation occurs (data not shown). From

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

• achieved by consecutive treatments with triethylamine and aqueous NH3/NH4OAc. Treatment of the released oligomer with 1 mol L−1 TBAF in THF removed the 2'-O-(2-cyanoethyl) protecting group and the deprotected oligomer was isolated by precipitation from EtOH with NaOAc. Experimental General. RP-HPLC

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

• protecting groups (acetate, isobutyrate, diphenylcarbamoyl groups), the N6-Boc protecting group on adenine was impervious. We tried different acidic conditions (trifluoroacetic acid, acetic acid with heat, AlCl3 [23][24][25]), but all of these conditions started to degrade the oligomer without completely

• prepare the phosphoramidite 28, and proceeded with the oligomer synthesis for our studies. However, this was far from satisfactory, and the continued demand for isoGNA oligomers within our group and our collaborative work prompted us to look for an improvement of the preparation of the adenine building

Supercritical carbon dioxide: a solvent like no other

• Jocelyn Peach and
• Julian Eastoe

Beilstein J. Org. Chem. 2014, 10, 1878–1895, doi:10.3762/bjoc.10.196

• . have a large body of both practical and theoretical work around polymer solubility in carbon dioxide [84]. The first reported use of ab initio modelling to design oxygenated hydrocarbon polymers for use in CO2 was in 2009, where one oligomer and two polymers were synthesised and found to be soluble in

Photoswitchable precision glycooligomers and their lectin binding

• Daniela Ponader,
• Sinaida Igde,
• Marko Wehle,
• Katharina Märker,
• Mark Santer,
• David Bléger and
• Laura Hartmann

Beilstein J. Org. Chem. 2014, 10, 1603–1612, doi:10.3762/bjoc.10.166

• oligomer shape and concomitantly in the sugar ligands accessibility. Indeed, dramatic shrinking of rigid-rod polymers for example, occurs upon photoirradiation when several azobenzenes are introduced in the main-chain, the embedded photoswitches acting as hinges [17][18]. In the present study, an

• % binding (IC50) was derived for the different glycooligomers (Table 2). All galactose-containing glycooligomers can bind to PA-IL. The mannose-containing control oligomer does not show any binding. This confirms that the backbone itself does not undergo non-specific interactions with the receptor, as we

• . This indicates a change in the accessibility of the sugar ligands for receptor binding, with the Z-oligomer having a less accessible conformation. Following the same model as for the trivalent ligand, the divalent ligand has the opportunity to bind in a bivalent fashion in its E-form (Figure 3a) while

Influence of perylenediimide–pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity

• Christian B. Winiger,
• Simon M. Langenegger,
• Oleg Khorev and
• Robert Häner

Beilstein J. Org. Chem. 2014, 10, 1589–1595, doi:10.3762/bjoc.10.164

• method to demonstrate the formation of double versus single stranded DNA structure. Therefore, the formation of defined short duplexes has been further investigated using polyacrylamide gel electrophoresis (PAGE) experiments. Oligomer single strands 1, 6 and 7 migrate with the same velocity as the 13 bp

• reference (Figure 7). Strands 1 and 6, however, form a duplex and thus have lower electrophoretic mobility, similar to an 18–20 bp reference. Oligomer 7 has the same DNA sequence as 6, but with 4 PDI molecules instead of 4 pyrenes (see Table 1). Thus when combined, single strands 1 and 7 do not form a

• spectra (scaled) of duplexes 1*2 to 1*6 at 20 °C. Conditions: see Table 1. Temperature-dependent UV–vis absorption spectrum of 1*2. Conditions: see Table 1. Fluorescence spectra of oligomer 1 (black), duplex 1*2 (blue) and duplex 1*6 (red) at 20 °C. Excitation: 370 nm. Conditions: see Table 1. PAGE

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

• generated when a purine (A/G) or a pyrimidine (C/T) base is stripped off from the DNA strand and this is considered as the most common type of DNA damage lesions. We generated one abasic site in a 48-base pair long oligomer duplex by treating the DNA (Figure 3) with Uracil DNA Glycosylase (UDG) enzyme

• , which excises one uracil residue present in the middle of the oligomer duplex (Figure 3). The oligomer duplexes after UDG treatment were incubated with 200 µM of the compound (1–8) for 24 hours in 10 µL reaction mixture. We found that none of the compounds were able to generate single strand breaks at

• incubation with 5 units of HindIII and BamHI separately for 1 hour at 37 °C. The results of incubation were confirmed by agarose gel electrophoresis. Quantitative estimation was done using the following equation. *1.42 = correction factor for supercoiled plasmid. Abasic site cleavage assay The oligomer

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

• of the oligomer chain (Figure 2) depended on the utilized synthetic method. We found that the MorGly oligomers containing the residues of type A formed less stable complementary complexes than oligomers containing residues of type B. Another interesting fact demonstrated in the article [20] was the

• 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

• labile linker between the solid support and the growing oligomer chain (Figure 3) during SPPS in combination with the tert-butyloxycarbonyl (Boc)- and acyl-protected morpholino nucleosides. After completion of the synthesis, the cleavage of the oligomer from the solid support and the deprotection of

Molecular architecture with carbohydrate functionalized β-peptides adopting 3₁₄-helical conformation

• Nitin J. Pawar,
• Navdeep S. Sidhu,
• George M. Sheldrick,
• Dilip D. Dhavale and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2014, 10, 948–955, doi:10.3762/bjoc.10.93

• indicated by a negative and shifted (204 nm) Cotton signal. This is likely due to the triple benzyl protection on the sugar units and the resulting high sterical demand in combination with hydrophobicity [60]. A similar effect was noticed for β3-peptide 7 that differs from oligomer 1 only in the β3-sugar

• side chain configuration. The deprotected oligomer 8 having the (6R)-configuration of sugar-β-amino acids is not structured as expected for β-peptides with mixed β3-side chain configurations. Overall, there is a indication for the influence of the benzyl groups in β3-peptides 1 and 7 on the secondary

Staudinger ligation towards cyclodextrin dimers in aqueous/organic media. Synthesis, conformations and guest-encapsulation ability

• Malamatenia D. Manouilidou,
• Yannis G. Lazarou,
• Irene M. Mavridis and
• Konstantina Yannakopoulou

Beilstein J. Org. Chem. 2014, 10, 774–783, doi:10.3762/bjoc.10.73

• environment, rigid spacer/linker), have not been explored so far toward formation of CD dimers. For any realistic application of CD oligomers, especially for drug encapsulation, some key requirements can be set: (i) ease of preparation, (ii) efficient purification, (iii) aqueous solubility of the oligomer

• shown recently [30] that depending on the linker connecting the CD moieties, self-inclusion occurs in water, frequently associated with inversion of one glucopyranose unit, that may totally incapacitate the cavity and annihilate the prospective utility of the oligomer as a multivalent host. These

Triphenylene discotic liquid crystal trimers synthesized by Co₂(CO)₈-catalyzed terminal alkyne [2 + 2 + 2] cycloaddition

• Bin Han,
• Ping Hu,
• Bi-Qin Wang,
• Carl Redshaw and
• Ke-Qing Zhao

Beilstein J. Org. Chem. 2013, 9, 2852–2861, doi:10.3762/bjoc.9.321

• mesomorphism. Keywords: Co2(CO)8 catalyzed cycloaddition; columnar mesophase; discotic liquid crystal; triphenylene; oligomer; Introduction Discotic liquid crystals (DLCs) with nematic phase have been commercially utilized in the liquid crystal display industry as optical compensating films for widening the

Oligomeric epoxide–amine adducts based on 2-amino-N-isopropylacetamide and α-amino-ε-caprolactam: Solubility in presence of cyclodextrin and curing properties

• Julian Fischer and
• Helmut Ritter

Beilstein J. Org. Chem. 2013, 9, 2803–2811, doi:10.3762/bjoc.9.315

• and 8 gave oligomer 9 and that of 7 and 8 gave oligomer 10, respectively. Thereby, to reduce branching via the hydroxy or amide groups with the epoxide functions and to obtain amine end groups, 5 and 7 were added in low excess compared to the diepoxide (molecular ratio 1.2:1 (5/7:8)). To investigate

• the solution properties of 9 and 10 in water, turbidity measurements were performed (Figure 1). It was observed, that 9 was soluble in cold water and exhibited a cloud point of about 27 °C due to heating. To evaluate the effect of CD complexation on the solubility of that oligomer 9, 150 mol % of

• shifted back to the initial temperature of about 27 °C. Oligomer 10 also exhibited LCST characteristics (Figure 2). It could be noticed that the solubility properties differ on heating and on cooling. While on heating a cloud point of about 35 °C was measured, on cooling a cloud point of about 30 °C was

Synthesis of homo- and heteromultivalent carbohydrate-functionalized oligo(amidoamines) using novel glyco-building blocks

• Felix Wojcik,
• Sinaida Lel,
• Alexander G. O’Brien,
• Peter H. Seeberger and
• Laura Hartmann

Beilstein J. Org. Chem. 2013, 9, 2395–2403, doi:10.3762/bjoc.9.276

• mentioned reaction conditions was determined (Figure 2b; Lac). With optimized reaction conditions in place, large amounts of glycosylated building blocks are required to support solid phase oligomer synthesis. Large scale production of glycosylated building blocks 8, 9, 10 and 13 relied on the previously

• three different glycooligomers 14–16 (Figure 3) to show the potential of the building block approach for the straightforward synthesis of a variety of differently glycosylated structures. The oligomer synthesis is based on standard peptide synthesis protocols and amide formation via activation of the

• ligands such as the Lac disaccharide, we synthesized structure 15 presenting three Lac ligands placed right next to each other in a short oligomer chain. Indeed, depending on the building blocks applied and oligomer structures targeted, different activating reagents are required. Glycooligomer 15

Synthesis of mucin-type O-glycan probes as aminopropyl glycosides

• David Benito-Alifonso,
• Rachel A. Jones,
• Anh-Tuan Tran,
• Hannah Woodward,
• Nichola Smith and
• M. Carmen Galan

Beilstein J. Org. Chem. 2013, 9, 1867–1872, doi:10.3762/bjoc.9.218

• -protected glycosyl acceptor 11 to afford trisaccharide 25 in 78% yield (Scheme 3). With the trisaccharide in hand, we proceeded to globally deprotect the assembled oligomer using a similar tandem reaction sequence as before that involved no column chromatography in between steps. In brief, selective

Molecular assembly of amino acid interlinked, topologically symmetric, π-complementary donor–acceptor–donor triads

• M. B. Avinash,
• K. V. Sandeepa and
• T. Govindaraju

Beilstein J. Org. Chem. 2013, 9, 1565–1571, doi:10.3762/bjoc.9.178

• combinations, when tethered to a polymer or oligomer [2]. This preferential aromatic interaction was proposed to be a consequence of frontier orbital congruence for the HOMO of pyrene with the LUMO of NDI. Alternatively, NDI is one of the highly π-acidic molecules with an estimated molecular quadrupole moment

Incorporation of perfluorohexyl-functionalised thiophenes into oligofluorene-truxenes: synthesis and physical properties

• Neil Thomson,
• Alexander L. Kanibolotsky,
• Joseph Cameron,
• Tell Tuttle,
• Neil J. Findlay and
• Peter J. Skabara

Beilstein J. Org. Chem. 2013, 9, 1243–1251, doi:10.3762/bjoc.9.141

• photophysical properties of the resulting oligomer. There are also less common examples of functionalisation at the C3, C8 and C13 positions [9]. Alkyl substituents attached to hetero- and carbocyles, which make up the conjugated backbone of oligomers and polymers, can also affect the properties of the material

Superstructures of fluorescent cyclodextrin via click-reaction

• Arkadius Maciollek,
• Helmut Ritter and
• Rainer Beckert

Beilstein J. Org. Chem. 2013, 9, 827–831, doi:10.3762/bjoc.9.94

• diameter of randomly methylated β-CD, blue: mixture of monomer and oligomer after adding potassium adamantane-1-carboxylate, red: supramolecular polymer of 3. AF4 elution diagram of 3. Synthesis of fluorescent cyclodextrin 3 by click-chemistry.

Influence of cyclodextrin on the solubility and the polymerization of (meth)acrylated Triton^® X-100

• Melanie Kemnitz and
• Helmut Ritter

Beilstein J. Org. Chem. 2012, 8, 2176–2183, doi:10.3762/bjoc.8.245

• the poly(ethylene glycol) substituent is hydrophilic. Because of this amphiphilic character, Triton® X-100 can be described as a short AB block co-oligomer [1]. Long amphiphiles are relatively flexible and provide a lower critical micelle concentration (CMC) [2]. The CMC of Triton® X-100 is 0.22 mM [3

meta-Oligoazobiphenyls – synthesis via site-selective Mills reaction and photochemical properties

• Raphael Reuter and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2012, 8, 877–883, doi:10.3762/bjoc.8.99

• example, biological settings. As a synthetic strategy it would be highly desirable to be able to build up the oligomer in a modular, protecting-group-free manner. In this respect, we planed a combination of the Mills reaction [27] with Suzuki cross-coupling, which we have successfully employed in previous

• studies (Figure 2) [28]. A key issue, however, was a site-selective transformation in order to differentiate both ends of the oligomer. The installment of an ester group on one site of the biphenyl unit should steer the critical Mills reactivity not only by steric, but also by electronic factors to the

• reacted with mCPBA in THF to yield the nitroso derivative 10 in a good yield of 69%. With all the necessary building blocks in hand, the assembly of oligomer 2 was started with a Suzuki reaction of 9 with 3-aminophenylboronic acid pinacolate (11) to prepare biphenyl 12 (Scheme 3). The reaction proceeded

Chemo-enzymatic modification of poly-N-acetyllactosamine (LacNAc) oligomers and N,N-diacetyllactosamine (LacDiNAc) based on galactose oxidase treatment

• Christiane E. Kupper,
• Ruben R. Rosencrantz,
• Birgit Henßen,
• Helena Pelantová,
• Stephan Thönes,
• Anna Drozdová,
• Vladimir Křen and
• Lothar Elling

Beilstein J. Org. Chem. 2012, 8, 712–725, doi:10.3762/bjoc.8.80

• to an amino-functionalised poly-LacNAc oligomer were performed and the products characterised by LC–MS and NMR analysis. Remarkably, elongation of terminally oxidised poly-LacNAc glycans by β3GlcNAc- and β4Gal-transferase was also successful. In this way, a set of novel, modified poly-LacNAc

• quantitative yield. In this way defined oxidised poly-LacNAc oligomer structures are easily obtained by galactose oxidase treatment and subsequent heating of the reaction mixture. The corresponding 6-aldehyde LacNAc oligomers were used as substrates in further elongation reactions with glycosyltransferases

• conversion of 6-aldehydes under alkaline conditions to the corresponding α,β-unsaturated aldehydes. By means of ultrafiltration instead of heating, at moderate pH values, the chemical formation of α,β-unsaturated aldehydes was avoided, giving rise to a series of poly-LacNAc oligomer 6-aldehydes as a novel

Thiophene-based donor–acceptor co-oligomers by copper-catalyzed 1,3-dipolar cycloaddition

• Stefanie Potratz,
• Amaresh Mishra and
• Peter Bäuerle

Beilstein J. Org. Chem. 2012, 8, 683–692, doi:10.3762/bjoc.8.76

• -halogenothiophene 3 and 2-ethynylthiophene (4) in the presence of sodium azide and a copper(I) catalyst to yield co-oligomer 1,4-di(thien-2-yl)-1,2,3-triazole (5) (Scheme 2). We first used the Fokin protocol [34], which worked well for phenyl halides and in which 1.2 equiv of sodium azide, 10 mol % of cupric

• -oligomer 19, which is a result of the instability of the intermediate azide. The electron-donating methyl group in the 5-position of the thiophene ring destabilizes the corresponding azide, therefore low conversion to 15 was observed. The yield was increased with decreasing temperature. Electron

• the 2-vinylthiophene subunit at 1.15 V and 1.13 V vs Fc/Fc+, respectively. For co-oligomer 11, the oxidation potential was significantly higher (1.23 V) and indicates formation of a radical cation localized on the thiophene subunits. In the negative regime, no reduction wave for the 1,2,3-triazole

Synthesis of mesomeric betaine compounds with imidazolium-enolate structure

• Nina Gonsior,
• Fabian Mohr and
• Helmut Ritter

Beilstein J. Org. Chem. 2012, 8, 390–397, doi:10.3762/bjoc.8.42

• . found: C, 54.32; H, 5.93; N, 23.83. Synthesis of Oligomer 7 with both, monomer balance (7a) and monomer imbalance (7b) p-Bromanil (1) (557 mg, 1.31 mmol) and 1,4-bis(1H-imidazol-1-yl)butane (4) (1 equiv (a) and 2 equiv (b), respectively) were dissolved in 45 mL of acetonitrile at 60 °C and heated to

• diagram of 3/m-β-CD complex. Classification of betaine 3. Thermogravimetric analyses of polymer networks 6a–c and oligomers 7a,b. Reaction of p-bromanil (1) with 1-butylimidazole (2). Mechanism of molecular association of the complex. Synthesis of polymer 6 and oligomer 7 based on imidazolium-enolate

Improved syntheses of high hole mobility phthalocyanines: A case of steric assistance in the cyclo-oligomerisation of phthalonitriles

• Daniel J. Tate,
• Rémi Anémian,
• Richard J. Bushby,
• Suwat Nanan,
• Stuart L. Warriner and
• and Benjamin J. Whitaker

Beilstein J. Org. Chem. 2012, 8, 120–128, doi:10.3762/bjoc.8.14

• schematically in Scheme 2. In the intermediates 8 (Scheme 2, X = C5H11O, Y = growing oligomer chain) the exocyclic carbon/nitrogen double bond marked * presumably has the (Z)-stereochemistry shown. This is the favoured stereochemistry for most imides of aromatic ketones, although the opposite stereochemisty is

Syntheses and properties of thienyl-substituted dithienophenazines

• Annemarie Meyer,
• Eva Sigmund,
• Friedhelm Luppertz,
• Gregor Schnakenburg,
• Immanuel Gadaczek,
• Thomas Bredow,
• Stefan-S. Jester and
• Sigurd Höger

Beilstein J. Org. Chem. 2010, 6, 1180–1187, doi:10.3762/bjoc.6.135

• (long) polymers, and can, as a matter of principle, be obtained in higher purity with respect to defects/polymerization faults. Moreover, they act as model systems allowing estimation of the pure polymer properties by extrapolation of the oligomer properties to infinite molecular weight [4]. Beside pure

• , when compared with the optical spectra of the quater- and sexithiophene [28] (Table 2, 19 and 20), a clear red-shift could be observed for both oligomer series, regardless if they are based on 10 or 11, due to the intramolecular donor-acceptor character of the compounds. Quantum chemical calculations

Miniemulsion polymerization as a versatile tool for the synthesis of functionalized polymers

• Daniel Crespy and
• Katharina Landfester

Beilstein J. Org. Chem. 2010, 6, 1132–1148, doi:10.3762/bjoc.6.130

• . Torini et al. carried out the reaction between a diisocyanate dissolved in oil and a diol dissolved in water and added after miniemulsification of the first monomer in the aqueous continuous phase [113]. Owing to the side reaction with water, only an oligomer with molecular weight ranging from 500 to