Halogen-containing thiazole orange analogues – new fluorogenic DNA stains

• Aleksey A. Vasilev,
• Meglena I. Kandinska,
• Stanimir S. Stoyanov,
• Stanislava B. Yordanova,
• David Sucunza,
• Juan J. Vaquero,
• Obis D. Castaño,
• Stanislav Baluschev and
• Silvia E. Angelova

Beilstein J. Org. Chem. 2017, 13, 2902–2914, doi:10.3762/bjoc.13.283

• moieties is somehow limited [5][6][7]. Such a restriction occurs when TO derivatives bind to nucleic acids by intercalation between the base pairs [6][8] or presumably between individual bases in single-stranded nucleic acids and in both cases a dramatic increase of the fluorescence is observed. The

• solutions in TE buffer led to clear bathochromic (in the range 6 to 10 nm) and hypohromic shifts and this is illustrated as an example for 5b in Figure 2. Such a spectral change is generally accepted as evidence for the intercalation of dye molecules into DNA [39][40][41]. Emission All dyes have a

• fluorescence maxima of the free dyes in TE buffer upon addition of dsDNA. The fluorescence maxima of dye–dsDNA complexes suggest an increased relative intensity of the 0–0 transition, which further confirms the intercalation of the ligands in all cases studied. The measured enhancement in the fluorescence

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• derivative 5 binds to the double-stranded (dA)10–T10 template with a self-assembly ratio of 112%. Such a high value of a self-assembly ratio can be rationalized by a triple-helix-like binding, intercalation, or a mixture of both. Remarkably, compound 5 also shows dual staining pattern in living HeLa cells

• % to the double-stranded template is significantly higher compared to the single-stranded templates and must be assigned either to a triple-helix-like binding or intercalation, or a mixture of both (Table 3). In summary, compounds 3 and 5 show a self-assembling behavior in the presence of the

• -like binding, intercalation, or a mixture of both. Confocal microscopy revealed a similar cellular staining pattern for compounds 4 and 5. Both derivatives predominantly accumulate in mitochondria of living HeLa cells and the adenine conjugate 5 accumulates also in the nucleoli of the cells. Our

Solvent-free copper-catalyzed click chemistry for the synthesis of N-heterocyclic hybrids based on quinoline and 1,2,3-triazole

• Martina Tireli,
• Silvija Maračić,
• Stipe Lukin,
• Marina Juribašić Kulcsár,
• Dijana Žilić,
• Mario Cetina,
• Ivan Halasz,
• Silvana Raić-Malić and
• Krunoslav Užarević

Beilstein J. Org. Chem. 2017, 13, 2352–2363, doi:10.3762/bjoc.13.232

• constituent of compounds with diverse applications, some of which display potent cytostatic activity through different mechanisms of action such as DNA intercalation, apoptosis, abrogation of cell migration, inhibition of angiogenesis and disregulation of nuclear receptor signaling [34][35]. Moreover, it was

Main group mechanochemistry

• Agota A. Gečiauskaitė and
• Felipe García

Beilstein J. Org. Chem. 2017, 13, 2068–2077, doi:10.3762/bjoc.13.204

• mechanochemical methods [72]. In the context of main group compounds, recent studies have highlighted efficient routes to: (i) alkaline earth carbides and their intercalation compounds, including the first successful synthesis of Mg2C3 from its elements [73][74]; (ii) nanomaterials, where main group elements act

Encaging palladium(0) in layered double hydroxide: A sustainable catalyst for solvent-free and ligand-free Heck reaction in a ball mill

• Wei Shi,
• Jingbo Yu,
• Zhijiang Jiang,
• Qiaoling Shao and
• Weike Su

Beilstein J. Org. Chem. 2017, 13, 1661–1668, doi:10.3762/bjoc.13.160

• , which matches the results well for the intercalation of nitrate (NO3−) into MgAl-LDHs in literature [48]. In the MgAl-LDHs-PdCl42− sample, the (003) plane shifted to the lower position of 8.8°, resulting to an expansion of interlayer spacing of 1.01 nm from 0.82 nm. These phenomena suggest that PdCl42

Interactions between cyclodextrins and cellular components: Towards greener medical applications?

• Loïc Leclercq

Beilstein J. Org. Chem. 2016, 12, 2644–2662, doi:10.3762/bjoc.12.261

• . have attached an anthrylamine to a β-CD [113]. The obtained anthryl(alkylamino)-β-CD was used as chemically switched DNA intercalator. However, as the anthryl residue is locked in the CD cavity, its intercalation into DNA is not possible in aqueous solution. Upon addition of a ligand that is tightly

• bound in the CD cavity (e.g., 1-adamantanol), the host molecule releases the anthryl unit, which then leads to strong intercalation with the double-stranded DNA molecule leading to structural distortions (Scheme 5). This behavior was clearly established from 1H NMR spectroscopy (shifts and broadening of

Experimental and theoretical investigations into the stability of cyclic aminals

• Edgar Sawatzky,
• Antonios Drakopoulos,
• Martin Rölz,
• Christoph Sotriffer,
• Bernd Engels and
• Michael Decker

Beilstein J. Org. Chem. 2016, 12, 2280–2292, doi:10.3762/bjoc.12.221

• chemistry, DNA intercalation, etc.) or in synthetic tetrahydroquinazolines as cholinesterase (ChE) inhibitors [15][16][17] as well as ChE inhibitors based on the scaffold of the naturally occurring alkaloid physostigmine from the calabar bean physostigma venenosum [18][19] (Figure 1). This is just a small

Application of Cu(I)-catalyzed azide–alkyne cycloaddition for the design and synthesis of sequence specific probes targeting double-stranded DNA

• Svetlana V. Vasilyeva,
• Vyacheslav V. Filichev and
• Alexandre S. Boutorine

Beilstein J. Org. Chem. 2016, 12, 1348–1360, doi:10.3762/bjoc.12.128

• of the probe fluorescence has been observed in our previous work [2][3]. Thus, only F1-NH2-MM14 is sequence-specific. We ascribe this low specificity of F1-NH2-TO to strong intercalation properties of the TO fluorophore that can intercalate into DNA independently of the polyamide. UV-visible

A journey in bioinspired supramolecular chemistry: from molecular tweezers to small molecules that target myotonic dystrophy

• Steven C. Zimmerman

Beilstein J. Org. Chem. 2016, 12, 125–138, doi:10.3762/bjoc.12.14

• early career efforts in molecular recognition, especially molecular tweezers. Although designed to complex DNA, these hosts proved more applicable to the field of host–guest chemistry. This early experience and interest in intercalation ultimately led to the current efforts to develop small molecule

• ; intercalation; macrocycles; multi-target drug discovery; RNA recognition; RNase mimic; Review Early childhood and overview I was born on October 8, 1957 in Evanston, Illinois, the second of three boys. Our parents, Howard E. Zimmerman and Jane Zimmerman, née Kirschenheiter, were very much in love and also

• example, one summer that process involved taking J. D. Watson’s “Molecular Biology of the Gene” [5] on the subway to a Long Island beach on weekends. The beautiful structure of DNA and its intercalation complexes of aromatic dyes were especially intriguing. In broader reading, I sought to understand

Pyridinoacridine alkaloids of marine origin: NMR and MS spectral data, synthesis, biosynthesis and biological activity

• Louis P. Sandjo,
• Victor Kuete and
• Maique W. Biavatti

Beilstein J. Org. Chem. 2015, 11, 1667–1699, doi:10.3762/bjoc.11.183

• moieties and an acridine core are two pharmacophoric motifs inhibiting the proliferation of cancer cells through intercalation into DNA [42][94][95]. Compounds with such a feature can also cleave the DNA double helix or inhibit the action of TOPO [42][94][95]. These abilities have been observed in

A one-pot multistep cyclization yielding thiadiazoloimidazole derivatives

• Debabrata Samanta,
• Anup Rana,
• Jan W. Bats and
• Michael Schmittel

Beilstein J. Org. Chem. 2014, 10, 2989–2996, doi:10.3762/bjoc.10.317

• –C6 = 49.0°). The phenyl ring attached to the N3 atom is nearly coplanar (C1–N3–C3–C4 = 2.5°) with the thiadiazole ring allowing additional delocalization. This coplanar arrangement might help for intercalation into biological molecules using e.g., π–π stacking, C–H···π or ion–dipole interactions

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

• 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

• charge at the heterocyclic nitrogen N-5, and strong electron affinity and polar groups at the 3 and/or 8 position of the phenanthridine can efficiently and predictably regulate the spectroscopic response (UV–vis and fluorescence) of the chromophore [48]. The understanding of the intercalation process

• ethidium bromide and its neutral analogue, revealing detailed description of the forces included in the intercalation process, stressing the dispersion energy as a control factor [50]. Moreover, a number of kinetic measurements provided for the binding of ligands to DNA additionally clarify mechanistic

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

• which could not be observed. It is, however, obvious that a severe disturbance of either the complex formation between the probe lipo-oligonucleotide 4 and the target nucleic acid 9 and/or the intercalation of the Sybr Green dye by the overhang take place. This might be the reason for the instability of

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

• /RNA intercalation, minor or major groove binding, and external electrostatic binding [1]. However, non-covalent interactions involving small molecules (Mw < 600) can only rely on a small number of interacting groups, while the steric parameters of DNA/RNA binding sites are also quite limited

• ] (Supporting Information File 1). Study of interactions of DBTAA derivatives with ds-DNA/RNA in aqueous medium Previous studies [11] revealed intriguing recognition of single stranded DNA dT sequences by AP3 (but not AP6, APH), whereby intercalation of AP3, AP6, APH in double stranded ct-DNA was excluded. Here

• intercalation of DBTAA. However, for the accurate elucidation of the precise mechanism, knowledge of the DNA/RNA binding mode is a prerequisite. Processing of the titration data by means of the Scatchard equation [17][18] gave the binding constants and the density of the binding sites (Table 2, log Ks and ratio

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

• less polar environment compared to its placement in single-stranded PNA. Although the related benzophenoxazine dye Nile blue binds to DNA by intercalation, the binding results in a bathochromic shifting and a quenched fluorescence [39][40]. Based on this, together with the fact that PNA–DNA duplexes

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 backbone and base-pairing properties [9]. We are continuing our investigation of isoGNA oligonucleotides within the context of chimeric sequences and collaborative intercalation studies and thus have a continuing need for the synthesis of isoGNA building blocks. While iso-glycerol nucleosides are

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

• showed some displacement of the intercalated EtBr, as evident from the steady-state fluorescence data (Supporting Information File 1, Figure S2). This indicates that the mode of interaction of the compounds with DNA may not be intercalation except for the triptycene derivatives 5 and 6. No noticeable

Novel supramolecular affinity materials based on (−)-isosteviol as molecular templates

• Christina Lohoelter,
• Malte Brutschy,
• Daniel Lubczyk and
• Siegfried R. Waldvogel

Beilstein J. Org. Chem. 2013, 9, 2821–2833, doi:10.3762/bjoc.9.317

• “collapsed” structure in which the triptycene units are twisted by 60° and approaching each other, prohibiting the formation of significant voids for intercalation of analytes. Results of the gravimetric measurements with HFF-QCMs Triphenylene ketal 3 and the triptycene derivatives 8, 14, 15, 17, 19 and the

Liquid-crystalline heterodimesogens and ABA-heterotrimesogens comprising a bent 3,5-diphenyl-1,2,4-oxadiazole central unit

• Govindaswamy Shanker,
• Marko Prehm and
• Carsten Tschierske

Beilstein J. Org. Chem. 2012, 8, 472–485, doi:10.3762/bjoc.8.54

• aromatics are organized on average antiparallel to each other with complete intercalation of the aromatic units, i.e., the cyanobiphenyls and diphenyl-1,2,4-oxadiazole units appear not to be segregated (Figure 4a). In the aliphatic regions the alkyl chains are interdigitated and conformationally disordered

Laterally substituted symmetric and nonsymmetric salicylideneimine-based bent-core mesogens

• Sonja Findeisen-Tandel,
• Wolfgang Weissflog,
• Ute Baumeister,
• Gerhard Pelzl,
• H. N. Shreenivasa Murthy and
• Channabasaveshwar V. Yelamaggad

Beilstein J. Org. Chem. 2012, 8, 129–154, doi:10.3762/bjoc.8.15

• (Figure 2). The layer thicknesses amount to d = 4.0 nm (OH 1a) and d = 4.2 (OH 1b). Based on a calculated molecular length of L ~ 5.4 nm, the molecular long axes are tilted with respect to the layer normal by about 42°, excluding an intercalation of the terminal chains. EHC cells consisting of two thin

Synthesis of (−)-julocrotine and a diversity oriented Ugi-approach to analogues and probes

• Ricardo A. W. Neves Filho,
• Bernhard Westermann and
• Ludger A. Wessjohann

Beilstein J. Org. Chem. 2011, 7, 1504–1507, doi:10.3762/bjoc.7.175

• -4CR was utilized for the synthesis of a molecular probe prototype of 1, which can be used for intercalation studies (Scheme 3). For this propose, the natural product scaffold should be attached through a spacer to a reporter tag, which is normally a luminescent group or a dye. The advanced

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

• this chromophore to DNA. We interpret the similarity of the absorption properties together with the results from the thermal dehybridization studies, as discussed above, as a result of the intercalation of the Nile Blue dye in duplex DNA. To further explore the optical properties we recorded steady

• chains and the triazolyl group represents the most critical issue for intercalation. From both molecular models it became obvious that this tether is long and flexible enough allowing the Nile Blue chromophore to intercalate in a nearly perfectly stacked position between the adjacent base pairs. This