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The acridizinium fluorophore was employed as water-soluble substitute for anthracene in PET probes and donor-pi-acceptor systems that may be used as fluorescent light-up probes and ratiometric probes in aqueous media.

The association of dicationic polycyclic ligands, namely, four diazoniapentaphene derivatives, three diazoniaanthra[1,2-a]anthracenes, diazoniahexaphene, and a partly saturated hydroxy-substituted diazoniapentaphene with double-stranded and triple-helical DNA, was investigated by spectrophotometric and viscosimetric titrations, CD and LD spectroscopy, DNA melting experiments, and molecular modeling studies. All experimental and theoretical data reveal an intercalative DNA-binding mode of the diazoniapentaphenes and diazoniaanthra[1,2-a]anthracenes; the latter have approximately 10-fold higher affinity for the DNA duplex. CD spectroscopic investigations and molecular modeling studies show that only one azonianaphthalene part of the ligand is intercalated between the DNA base pairs, whereas the remaining part of the ligand points outside the intercalation pocket. In contrast, the diazoniahexaphene is a DNA groove binder, which binds selectively to [poly(dAdT)]2. At low ligand-to-DNA ratios (r0.15), the diazoniahexaphene also behaves as an intercalator; however, all spectroscopic and viscosimetric data are consistent with significant groove binding of this ligand at r0.2. Studies of the interaction of diazoniapolycyclic ions with triplex DNA reveal a preferential binding of both diazoniapentaphenes and diazoniaanthra[1,2-a]anthracenes to the triplex and stabilization thereof. These properties are more pronounced in the case of the hexacyclic diazoniaanthra[1,2-a]anthracenes; however, the diazoniahexaphene shows no preferential binding to the triplex. The DNA binding properties of the diazoniapentaphene derivatives remain essentially the same upon variation of the positions of nitrogen atoms or substitution with methyl groups. In contrast, the interactions of the diazoniaanthra[1,2-a]anthracence isomers with triplex DNA are slightly different. Notably, the 14a,16a-diazoniaanthra[1,2-a]anthracene is among the most efficient triplex stabilizers, with a 9-fold larger binding affinity for the triplex than for the DNA duplex. Moreover, the diazoniapentaphene and diazoniaanthra[1,2-a]anthracene derivatives represent the first examples of triplex-DNA binders that do not require additional aminoalkyl side chains for efficient triplex stabilization.

The interaction of the linear dibenzo[b,g]quinolizinium (5a) and the angular dibenzo[a,f]quinolizinium (6) with DNA was studied in detail in order to evaluate the influence of the shape of polycyclic quinolizinium ions on their DNA-binding properties. First, the synthesis and the thermally induced dimerization of 5a were reinvestigated because the preparation and isolation of the bromide salt of 5a according to literature procedures turned out to be problematic. The dibenzo[b,g]quinolizinium bromide [5a(Br)] tends to dimerize in solution with a highly selective and unprecedented formation of the corresponding anti-head-to-head dimer. Nevertheless, it was observed that careful exclusion of bromide ions from the reaction mixture suppresses the formation of the dimer. Moreover, the dimer may be transformed to the monomer by a remarkably rapid photoinduced electron-transfer reaction with 1-methoxynaphthalene. The association of 5a and 6 with nucleic acids was investigated by spectrophotometric and spectrofluorimetric DNA titrations, CD and LD spectroscopy, DNA thermal denaturation studies, and competition-dialysis techniques. Both dibenzoquinolizinium ions 5a and 6 exhibit an intercalative mode of binding to double-stranded DNA with moderate binding constants (K = 1-7 x 10(5) M(-1)) and a slight preference for association with GC-rich DNA regions. The structures of the intercalation complexes were calculated by molecular modeling methods. Competition-dialysis studies reveal that the isomers 5a and 6 bind selectively to triple-helical DNA (poly[dA]-poly[dT]2) as compared to selected synthetic and native double-stranded nucleic acids. Notably, the selectivity of the linear dibenzo[b,g]quinolizinium 5a toward triplex DNA is higher than the one of the angular derivative 6. In contrast, the DNA thermal denaturation studies reveal a higher stabilization of triple-helical DNA in the presence of 6 (DeltaTm3-->2 = 28 degrees C at r = 0.5) as compared to the stabilization by 5a (DeltaTm3-->2 = 14 degrees C at r = 0.5). This comparison emphasizes the importance of the extended pi system for the interaction of annelated quinolizinium ions with DNA. Moreover, the comparison between 5a and 6 demonstrates the significant influence of the shape of the pi system on the duplex- and triplex-stabilizing properties of the dibenzoquinolizinium ions.

The photoinduced DNA damage by the berberine derivative coralyne is presented. The irradiation of coralyne in the presence of plasmid DNA namely, pBR322, leads to remarkably fast DNA damage by single-strand cleavage, as determined by agarose-gel electrophoresis. Even upon exposure to sunlight, almost all of the supercoiled plasmid is converted to the open circular form in less than a minute [c(pBR322) = 3.5 x 10(-9) M; c(coralyne) = 4.3 x 10(-5) M]. The efficiency of the DNA strand cleavage is not decreased in the presence of radical-trapping reagents such as tert-butanol or DMSO. Moreover, the extent of the DNA damage is the same under aerobic conditions and at reduced oxygen concentration. Thus, the formation of reactive intermediates such as hydroxyl radicals or singlet oxygen is excluded. These results show that the exposure of coralyne and derivatives thereof to light, even with moderate light intensity, needs to be avoided during experiments in which their biological activity is assessed by plasmid unwinding assays.

[reaction: see text] N-Arylamino-substituted acridizinium (benzo[b]quinolizinium) derivatives are almost nonfluorescent in water or organic solvents; however, upon addition of calf thymus DNA or bovine serum albumin the fluorescence intensity increases by a factor of 10 to 50. Thus, these dyes exhibit ideal properties to be used as DNA- and protein-sensitive "light-up probes".

For the fabrication of micrototal analysis systems (/spl mu/TAS) methods of micropatterning, sealing, and for the manufacturability, as well as techniques for connecting the microstructures to the macroworld are of particular significance. The idea is to create a monolithic instrument which consists of an assembly of three-dimensional integrated modules (e.g. fluidic networks, electrical and optical sensors, microelectronic circuits) to support the advantage of efficient interconnections. To demonstrate the feasibility of an application specific lab-on-microchip, published in Ref.1, results obtained with a fabricated micro flow cytometer and monolithically integrated optical detectors based on amorphous silicon are reported. In this work, we use an a-Si:H pin diode for the optoelectronic detection of organic fluorescence sensors, namely anthracene derivatives, which are driven through the fluidic channel network hydrodynamically.

[reaction: see text] Four pH-sensitive fluorescence probes are presented which consist of an anthracene fluorophore and a pi-conjugated oxazoline, benzoxazole, or pyridine substituent. The protonation of the heterocycles increases their acceptor properties and results in significant red-shifts of the absorption and emission maxima of the anthracene chromophore. The comparison between 2-[2'-(6'-methoxyanthryl)]-4,4-dimethyl-2-oxazoline and 2-[2'-(anthryl)]-4,4-dimethyl-2-oxazoline reveals that the donor-acceptor substitution pattern of the fluorophore is not required to achieve a red shift upon protonation. The benzoxazole and pyridine substituents offer a particular advantage due to their persistence under acidic conditions. Thus, these compounds may be used as efficient pH-sensitive fluorescence switches. Nevertheless, the switching of benzoxazole 2c requires relatively strong acidic conditions. The anthrylpyridinium exhibits a red-shifted emission in chloroform; however, it is nonfluorescent in aqueous or alcoholic solution. Although the oxazoline is not persistent under permanent acidic conditions, this heterocycle may be useful as a substituent in fluorescence indicators since it may be used to detect acid concentrations of 10(-4)-10(-5) M, which are close to the biologically relevant range.

Mechanistic investigations of the photoinduced DNA damage by acridizinium salts (4a-azonia-anthracene derivatives) are presented. Irradiation of 9-bromoacridizinium in the presence of defined double- and single-stranded DNA oligomers under aerobic conditions leads to both frank strand breaks and alkali-labile sites as determined by polyacrylamide gel electrophoresis (PAGE). The extent of the DNA damage increases significantly in D(2)O and occurs selectively at guanosine residues. These observations reveal the formation of singlet oxygen ((1)O(2)) as reactive species, which oxidizes the DNA bases, above all the guanine bases. Further evidence for (1)O(2) formation was obtained from laser-flash spectroscopic investigations, which show intersystem crossing (S(1) to T(1)) of the excited states of the parent acridizinium and of the 9-bromo- and 9-amino-substituted derivatives. The resulting triplet state is efficiently quenched by oxygen (k(q)10(9) s(-)(1)M(-)(1)) to yield (1)O(2). Under anaerobic conditions, no significant alkali-labile lesions are observed, but frank strand breaks are induced; however, to lesser extent than under aerobic conditions. The DNA damage is suppressed in the presence of a radical scavenger, namely t-BuOH, and hydroxyl radicals are shown to be the reactive intermediates by trapping experiments with terephthalic acid. Moreover, the intercalated acridizinium molecules are not involved in the DNA damage reactions. The intercalated acridizinium salt leads to a primary PET reaction with the DNA bases; however, a fast BET transfer is proposed that regains the dye and the DNA, so that the excited intercalated dye does not contribute significantly to the overall DNA damage.

Science of Synthesis: Houben-Weyl Methods of Molecular Transformations is the entirely new edition of the acclaimed reference series Houben-Weyl, the standard synthetic chemistry resource since 1909. This new edition is published in English and will comprise 48 volumes published between the years 2000 and 2008. Science of Synthesis is a quality reference work developed by a highly esteemed editorial board to provide a comprehensive and critical selection of reliable organic and organometallic synthetic methods. This unique resource is designed to be the first point of reference when searching for a synthesis strategy. Features: * Contains the expertise of presently 450 leading chemists worldwide. * Critically evaluates the preparative applicability and significance of the synthetic methods. * Discusses relevant background information and provides detailed experimental procedures For full information on the Science of Synthesis series, visit the Science of Synthesis Homepage Series Editors: D. Bellus, S. V. Ley, R. Noyori, M. Regitz, E. Schaumann, I. Shinkai, E. J. Thomas, B. M. Trost, P. J. Reider

The feasibility of micro total analysis systems (μTAS) on microchips based on the concept of a monolithic instrument is demonstrated. In such a device a microfluidic layer system is deposited in a backend process on a conventional CMOS integrated circuit with the aim to achieve cost and performance enhancements through integration and miniaturization. Experimental results on elementary functional components of a μTAS are presented including a narrow channel electroosmotic micropump, a micro mass flow meter using the thermal anemometric principle, a micro cytometer with integrated optical detection, and elementary structures for on-chip micro-capillary electrophoresis.

The title compound exhibits a selective enhancement of its fluorescence intensity in the presence of AT-rich DNA.

Silaindanes were obtained by reaction of hexakis[2-(dimethylaminomethyl)phenyl]cyclotrisilane (3) with 3 equiv. of various styrenes. Analogous treatment of 3 with p-methoxystryrene yielded a mixture of the corresponding silaindane and a 2:1 adduct between bis[2-(dimethylaminomethyl)phenyl]silylene (4) and the styrene. Competition experiments show that the addition rate of 4 to the triple bond of diarylacetylenes is accelerated by electron-withdrawing substituents. The reaction constant (ρ=+0.85±0.21) indicates that 4 acts as a nucleophile in these reactions. The rate determining step in these reactions of cyclotrisilane 3 is the formation of silylene 4. The rate constant for this first order process was determined to be (6.3±0.4)×10−4 s−1 at 60°C.

The DNA-damaging effect of the potent dopaminergic neurotoxin ‘TaClo’ (1-trichloromethyl-1,2,3,4-tetrahydro-β-carboline) is reported. After irradiation (300 nm, 350 nm) of cell-free pBR322 DNA in the presence of TaClo, single-strand breaks were observed by gel electrophoresis. It seems likely that TaClo undergoes a light-induced formation of reactive species (probably radicals). In comparison with TaClo, the bromo derivative exhibits an increased toxic action while the fluoro derivative shows a weaker effect towards DNA. In the presence of Cu(II) at 37°C in the dark, DNA strand scissions were found to occur, too. The formation of Cu(I), as detected by UV-absorption at 480 nm using the Cu(I) complexing ligand BCS, hints at the formation of a reactive species by a Cu(II)/Cu(I) mediated redox cycle. Until now, the chemical nature of this reactive species has not been elucidated.

It was demonstrated that the interaction of the aminoacridizinium salts 2a-2d with DNA depends on the substitution pattern of the chromophore. Spectrophotometric and fluorometric titrations of the acridizinium salts 2a-2d with natural and synthetic polynucleotides reveal that the degree of interaction of the acridizinium salts 2a-2d with the nucleic acid differs significantly. The binding mode of the dyes with DNA was evaluated by circular dichroism and linear dichroism spectroscopy and compared with the parent system 2c. Whereas the 9-aminoacridizinium (2a) mainly intercalates into DNA, the salts 2b-c show a higher degree of association to the DNA backbone. The intercalated aminoacridizinium 2a caused few strand breaks upon UVA exposure, whereas the salts 2b-2d exhibit relatively efficient DNA-damaging properties. All acridizinium salts showed a sequence-selective strand cleavage for guanine-rich DNA regions.

The readily available cationic dye 3-Br binds to DNA as was shown by UV, fluorescence and CD spectroscopy. The electronic spectra of the quinolizinium salt 3 exhibit significant bathochromic shifts and a decrease of the absorbance and emission intensity on addition of calf thymus DNA. Moreover, fluorometric titration of [poly(dCdG)]2 with salt 3 resulted in a significant decrease of the emission intensity, whereas addition of [poly(dAdT)]2 led only to a marginal perturbation of the emission spectrum. Analysis of the binding constants with the different polynucleotides revealed that quinolizinium 3-Br binds preferentially to GC base pairs. Irradiation of DNA in the presence of quinolizinium 3-Br resulted in efficient single-strand cleavage of the nucleic acid.

The reaction of 9-N,N-dimethylaminomethylanthracene 1 with aromatic carboxylic acids gave crystalline salts (2a, 2b, 3a and 3b), which were irradiated in the solid state. Whereas salt 3a was selectively transformed to the dimer 4a, the other salts were photoinert. The results were rationalized on the basis of X-ray structure analysis. In the presence of oxygen, solid-state irrradiation of anthracene salt 3b leads to selective photooxygenation. The selectivity of both solid-state photoreactions was not observed in solution.

Cationic dyes have been shown to bind efficiently to DNA [1] and lead to photoinduced DNA damage [2]. Such photobiological features may be used to detect or characterize the nucleic acid [3]. Furthermore the intentional photoinduced damage of DNA, e. g. in tumor cells, may be applied in phototherapy [4,5]. Among the cationic aromatic compounds that have been investigated along these lines are coralyne (1) [6] and related quinolizinium salts [7]. During our studies on photobiological properties of aromatic heterocycles we showed that readily available benzo[b]-quinolizinium salts (acridizinium salts) 2 exhibit pronounced DNA-binding and DNA-photodamaging properties [8]. To further investigate the photobiological features of quinolizinium derivatives we synthesized indolo[2,3-b]- quinolizinium salt (3a) [9]. The interactions of this aromatic dye with DNA seemed to be of special interest since it resembles closely the structure of the known anti-tumor compound Celiptium® 4. Herein, we present preliminary investigations of the interactions of quinolizinium dye 3a with DNA.

N,N'-Dicyclohexyl-N-(6'-methoxyanthryl-2-carbonyl)urea (1a) exhibits a strong solvatochromism with respect to its fluorescence properties. The emission maxima of 1a correlate well with the anion-stabilizing properties of the solvent. This feature allows the detection of analytes with high acceptor numbers, such as alcohols and carboxylic acids, and the detection of analytes such as fluoride ions which form strong hydrogen bonds with the amido hydrogen atom.

An N-methylphenanthrolinium-annelated spirooxazine derivative 2(SO) whose DNA-intercalating properties are reversibly changed by a photochromic reaction was prepared. Upon irradiation at 350 nm the spirooxazine is transformed to the corresponding photomerocyanine 2(PM) that binds to DNA. After irradiation with visible light the spirooxazine 2(SO), which exhibits no significant DNA-binding properties, is regained. The association of 2(PM) with DNA was examined by CD and absorption spectroscopy, fluorescent intercalator displacement and viscometric titration.

A benzo[b]quinolizinium-benzo-15-crown-5 ether conjugate 2a is presented that enables the fluorimetric detection of Mg(2+) and DNA by a significant light-up effect, along with a change of the emission wavelength with different analytes (Mg(2+): 495 nm; DNA: 550 nm). The mechanism of the excited-state deactivation of 2a was investigated by steady-state fluorescence spectroscopy in media of varied viscosity and compared with the photophysical properties of methoxyphenyl-substituted benzo[b]quinolizinium 2b (m,p-diOMe), 2c (m-OMe), and 2d (p-OMe) as reference compounds. Compounds 2a-c, which share the m-alkoxyphenyl substituent as the common feature, have low emission quantum yields (Φ(F)10(-2) in water) but exhibit a significant increase of their fluorescence intensity in viscous glycerol solutions. In contrast, the viscosity of the medium does not influence the emission properties of the parent phenyl-substituted benzo[b]quinolizinium 2e and of the p-methoxyphenyl-substituted derivative 2d. Based on these observations it is concluded that the excited-state deactivation in 2a-c is mainly due to the rotation of the m-alkoxy group about the C(ar)-O bond. The interaction of 2a-c with DNA or Mg(2+) ions was studied by spectrophotometric titrations and CD spectroscopy. Notably, the association of 2a or 2b with DNA or 2a with Mg(2+) ions induces a strong fluorescence enhancement (15- and 40-fold for DNA, 450-fold for Mg(2+)), which is rationalized by the suppression of the torsional-relaxation of the alkoxy-substituent in the excited state. Additionally, the cation-induced light-up effect of 2a is selective towards Mg(2+) ions as compared with other cations such as NH(4)(+), Li(+), Na(+), K(+) and Ba(2+).

A styrylbenzothiazole substrate that has no significant affinity towards DNA was transformed photochemically into a DNA-binding benzothiazoloquinolinium ion. The photoreaction may be performed directly in the presence of DNA thus establishing the DNA-ligand interaction in situ with temporal control.

9-[2-(1,4-Dioxa-7,13-dithia-10-azacyclopentadecyl)phenyl]amino-benzo[b]quinolizinium enables the unambiguous fluorimetric and polarimetric detection of Hg(2+) in the close proximity of double-stranded nucleic acids without interfering background signals from the complexes of this compound with Hg(2+) or DNA alone.

The synthesis and the investigation of the Cu(II)-binding, the DNA-binding, and the DNA-damaging properties of a conjugate between the benzo[b]quinolizinium ion and the bis(pyridin-2-ylmethyl)amino receptor are presented. Photometric and fluorimetric titrations as well as CD spectroscopic analysis reveal that the 9-bis(pyridin-2-ylmethyl)aminobenzo[b]quinolizinium ligand intercalates into DNA (K(b) = 1.9 x 10(4) M(-1)) and exhibits a high selectivity towards complexation of Cu(2+) in water (K(b) = 4.3 x 10(4) M(-1)). This combination of functionalities allows to localize Cu(2+) in close proximity of DNA, where these metal ions induce efficient DNA damage, as shown by the single-strand cleavage of supercoiled plasmid DNA. Notably, the DNA cleavage does not require additional reagents nor light.

Allylamine, an unsaturated short carbon chain amine was used to mediate ss-DNA attachment to an H-terminated polycrystalline diamond thin film surface for biosensoric applications. At first, allylamine was photochemically tethered onto the diamond film surface; ss-DNA was then attached via the allylamine linkage. The DNA molecules are then hybridized with the complementary DNA molecules containing fluorescence labels followed by denaturing. Time-of-fight secondary ion mass spectrometry and fluorescence spectroscopy are used to confirm the allylamine bonding and the covalent DNA bonding to the diamond film surface, respectively.

The integration of a selective Hg2+ receptor unit, 1,4-dioxa-7,13-dithia-10-azacyclopentadecane, into the 9-aminoacridizinium fluorophore provides a fluorescent probe which allows a selective ratiometric detection of Hg2+ in water.

A donor-substituted acridizinium salt was synthesized, and an enhanced regioselectivity in the [4+4] photocyclo-addition to give exclusively the head-to-tail products was observed.

[reaction: see text] A chiral periodic mesoporous organosilica (ChiMO) was prepared, in which a 1,2-bis-(ureido)cyclohexyl linker (38 wt %) is introduced into the walls of the hybrid organic-inorganic material. This silica was used as a host for 11-formyl-12-methyldibenzobarrelene (2), and the stereoselectivity of the di-pi-methane rearrangement of 2 within this host-guest complex was studied. At low conversions, the only product was the corresponding dibenzosemibullvalene. An enantiomeric excess of 24% at 11% conversion was obtained using the ChiMO as host. These values compare well with those achieved using a system based on conventional faujasites (LiY and NaY) as hosts incorporating a chiral auxiliary. We tested S-phenylglycine, S-proline, S-camphanic acid, and S-mandelic acid as chiral auxiliaries. In contrast to the behavior of the ChiMO material, adsorption of dibenzobarrelene in purely siliceous mesoporous MCM-41 silica (3.2 nm pore size) containing ephedrine failed, a failure that can be explained as arising from the large internal silanol population and high hydrophilicity of the siliceous MCM-41 sample.

DNA intercalators represent an important class of compounds with a high potential as DNA-targeting drugs. In this review it is demonstrated that annelated quinolizinium derivatives such as coralyne and derivatives thereof intercalate into DNA and that this structural motif allows several variations of the substitution pattern without loss of intercalating properties. The commonly applied methods for the evaluation of the DNA association, mainly spectroscopic studies, are pointed out. In addition, studies on the biological activities of annelated quinolizinium derivatives, such as topoisomerase poisoning or cell toxicity, are highlighted.

The associative interactions of indolo[2,3-b]-quinolizinium bromide with DNA and its DNA photocleavage properties were studied in detail. Absorption and emission spectroscopy, linear dichroism, and energy-transfer measurements indicate that the indoloquinolizinium binds to DNA primarily by intercalation, with a preference for GC base pairs. In agreement with this data, the results of primer extension analysis indicate that photocleavage occurrs prevalently at the GC nucleotides. Molecular modeling studies confirm that intercalative stacking between adjacent base pairs is energetically favorable. However, it is also observed that the location of the dye in the minor groove of the DNA is energetically even more favorable. Upon UVA irradiation, the indoloquinolizinium causes single-strand cleavage with an efficiency that varies with the dye-DNA ratio. This observation is rationalized in terms of more efficient photocleavage by the externally bound dye compared with the intercalated one. The kinetics of strand degradation under aerobic and anaerobic conditions suggest that a Type I reaction occurs, that is, radical-mediated DNA damage.

1,2-Disilacyclobut-3-enes are synthesized quantitatively from cyclotrisilane 1 and alkynes; the solid-state structure of 4d is determined by single-crystal X-ray diffraction.

The association of 12a,14a-diazoniapentaphene dibromide (5) with DNA and its ability to photoinduce DNA damage was studied. Spectrophotometric and fluorimetric titrations show that the title compound (5) binds to DNA (K ≈ 5·10 5 M -1 ) with the highest affinity towards GC-rich regions. The highest affinity was observed for GC base pairs. Compound 5 binds to DNA primarily by intercalation as shown by LD spectroscopy and energy-transfer experiments. Moreover, efficient DNA damage was observed on UVA irradiation in the presence of 5. Preliminary experiments suggest that singlet oxygen may be involved in the photoinduced DNA damage.