Helical Arrangement of Interstrand Stacked Pyrenes in a DNA Framework

Malinovskii, Vladimir L.; Samain, Florent; Häner, Robert

doi:10.1002/ange.200700891

Cited by 55 publications

(41 citation statements)

References 66 publications

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“…[64] Die bestimmten Energien für die beiden Waagentypen, 5 mit einem unsubstituierten und 6 mit einem CF 3 [65] auf Basis eines einfachen elektrostatischen Solvatisierungmodells. [66] Insgesamt sind die beobachteten Substituenteneffekte in guter Übereinstimmung mit den oben besprochenen Ergebnissen der Rechnungen von Kim,…”

Section: Modellstudienunclassified

Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen

2011

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Dieser Aufsatz beschreibt Phänomene der molekularen Erkennung von aromatischen Ringen in chemischen und biologischen Systemen in einem multidimensionalen Ansatz. Neue Ergebnisse aus der Wirt‐Gast‐Chemie, biologischen Affinitätsassays und Biostrukturanalysen, Datenbanksuchen in der Cambridge Structural Database (CSD) und der Protein Data Bank (PDB) und hochentwickelten Rechnungen, die seit dem Erscheinen eines früheren Aufsatzes in 2003 veröffentlicht wurden, sind hier zusammengefasst. Die Themen Aren‐Aren‐, Perfluoraren‐Aren‐, Schwefel‐Aren‐, Kation‐π‐ und Anion‐π‐Wechselwirkungen sowie Wasserstoffbrücken zu aromatischen Systemen werden behandelt. Das gewonnene Wissen kommt besonders der strukturbasierten Hit‐zur‐Leitstruktur‐Entwicklung und der Leitstrukturoptimierung sowohl in der pharmazeutischen als auch in der Pflanzenschutzindustrie zugute. Zudem erleichtert es die Entwicklung neuer Materialien und supramolekularer Systeme und soll zu weiteren Anwendungen von Wechselwirkungen mit aromatischen Ringen zur Kontrolle des stereochemischen Verlaufs chemischer Umsetzungen inspirieren.

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Section: Modellstudienunclassified

Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen

2011

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“…For example, nucleobases have been successfully exploited in the creation of a variety of supramolecular nanostructures of different chromophores, such as porphyrin, [9] pyrene, [10] thiophene, [11] anthracene, [12] oligo(p-phenylenevinylene)s [13] and other small organic molecules. [14] Similarly, DNA has also been used as the structural scaffold for the helical organization of a series of chromophores including pyrene, [15][16][17][18][19] porphyrin, [20] biphenyl, [21] oligo(p-phenylenevinylene)s [22] etc. and dyes including azobenzene derived dyes, [23] perylene bisimide [24][25][26] etc.…”

Section: Introductionmentioning

confidence: 99%

Non‐covalent Versus Covalent Control of Self‐Assembly and Chirality of Nile Red‐modified Nucleoside and DNA

Varghese

Wagenknecht

2010

Chemistry A European J

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A DNA-based covalent versus a non-covalent approach is demonstrated to control the optical, chirooptical and higher order structures of Nile red (Nr) aggregation. Dynamic light scattering and TEM studies revealed that in aqueous media Nr-modified 2'-deoxyuridine aggregates through the co-operative effect of various non-covalent interactions including the hydrogen bonding ability of the nucleoside and sugar moieties and the pi-stacking tendency of the highly hydrophobic dye. This results in the formation of optically active nanovesicles. A left-handed helically twisted H-type packing of the dye is observed in the bilayer of the vesicle as evidenced from the optical and chirooptical studies. On the other hand, a left-handed helically twisted J-type packing in vesicles was obtained from a non-polar solvent (toluene). Even though the primary stacking interaction of the dye aggregates transformed from H-->J while going from aqueous to non-polar media, the induced supramolecular chirality of the aggregates remained the same (left-handed). Circular dichroism studies of DNA that contained several synthetically incorporated and covalently attached Nr-modified nucleosides revealed the formation of helically stacked H-aggregates of Nr but--in comparison to the noncovalent aggregates--an inversed chirality (right-handed). This self-assembly propensity difference can, in principle, be applied to other hydrophobic dyes and chromophores and thus open a DNA-based approach to modulate the primary stacking interactions and supramolecular chirality of dye aggregates.

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“…[15] It has also been reported that the shift of the excimer emission band can be used as a signal to detect hybridization, as the excimer fluorescence could redshift or blue-shift upon hybridization by the interstrandstacked pyrenes. [16] Although both monomer and excimer emission of pyrene-labeled probes has been investigated in detail, the often complex response depends on the structure of the probe.…”

Section: Introductionmentioning

confidence: 99%

Detection of RNA Hybridization by Pyrene‐Labeled Probes

et al. 2009

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Powerful pyrene probes: Two kinds of pyrene-labeled oligonucleotides (HNA- and RNA-skeleton probes) were explored. The enhanced fluorescence intensity in the monomer region and the disappearance of aggregate/excimer emission in duplexes has been successfully used to detect the hybridization of oligonucleotides. By covalently attaching pyrene chromophores with different linkers onto altritol nucleotides or ribonucleotides, and by varying the number of these pyrene modified altritol nucleotides and ribonucleotides in HNA (hexitol nucleic acid) and RNA, respectively, we have explored the general applicability of pyrene absorbance and especially fluorescence as a probe to monitor RNA hybridization. The results reveal that the backbone of the probes, the number of pyrene units attached and the nature of the tether can all substantially affect the absorbance and fluorescence properties of the probes both in single strand and double strand form. Moreover, the strength of hybridization is also affected. The disappearance of pyrene aggregate/excimer emission and simultaneous increase in monomer emission intensity of the multipyrene-labeled probes has been successfully used to monitor the hybridization of oligonucleotides, including a hairpin structure. Differences in optical response between the HNA- and RNA-skeleton probes upon hybridization indicate that the interaction of pyrene with the nucleobases in both types of duplexes is different.

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Helical Arrangement of Interstrand Stacked Pyrenes in a DNA Framework

Cited by 55 publications

References 66 publications

Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen

Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen

Non‐covalent Versus Covalent Control of Self‐Assembly and Chirality of Nile Red‐modified Nucleoside and DNA

Detection of RNA Hybridization by Pyrene‐Labeled Probes

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