The DNA three-way junction as a mould for tripartite chromophore assembly

Probst, Markus; Wenger, Daniel; Biner, Sarah M.; Häner, Robert

doi:10.1039/c1ob06400b

Cited by 37 publications

(34 citation statements)

References 65 publications

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“…Illustration of an energy-minimized model for a π-stacked assembly of two pyrenes (green) and one PBI (red) dye at the branch point of a DNA three-way junction. 490 aqueous solution. Obviously, for ionic self-assembly, the counterions have a crucial impact on the supramolecular packing as well as interaction with other molecules, which can be either of small size (e.g., chiral counterions) or macromolecular (e.g., polynucleotides).…”

Section: Self-assembly Of Pbi−dna Conjugatesmentioning

confidence: 99%

Perylene Bisimide Dye Assemblies as Archetype Functional Supramolecular Materials

et al. 2015

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CONTENTS 1. Introduction 962 1.1. Prologue 962 1.2. Parent Perylene Bisimide Chromophore 963 1.3. Core-Substituted Perylene Bisimides 964 1.4. Perylene Bisimides in the Solid State 966 1.5. Areas of Application 966 2. Linear, Dendritic, and Macrocyclic Covalent PBI Ensembles 968 2.1. Excitonic Coupling and Deactivation Processes of Photoexcited PBIs 969 2.2. Rigid PBI Dimers 971 2.3. Flexible PBI Ensembles 974 2.4. Cyclic PBI Ensembles 976 3. π-Stacked PBI Assemblies 979 3.1. Self-Assembly of Core-Unsubstituted PBIs in Solution 979 3.2. Organization of Core-Unsubstituted PBIs in the Bulk Solid State 984 3.3. Self-Assembly of Amphiphilic PBIs in Aqueous Media and Solid Bulk State 987 3.4. Self-Assembly of Core-Substituted PBIs 991 3.5. Self-Assembly of Dye Arrays Composed of Multiple PBIs 995 3.6. Self-Assembly of Multichromophoric PBI Conjugates Containing Other Dyes 996 4. Hydrogen-Bond Directed Self-Assembly 1000 4.1. Self-Assembly Directed by Imide−Imide H-Bonding Interactions 1000 4.2. Self-Assembly Directed by Side-Chain Amide−Amide H-Bonding Interactions 1003 4.3. Self-Assembly Directed by Other H-Bonding Interactions 1006 4.4. Coassembly Directed by Imide−Melamine H-Bonding Interactions 1008 4.5. Coassembly Directed by Melamine−Cyanurate/Barbiturate H-Bonding Interactions 1011

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Section: Self-assembly Of Pbi−dna Conjugatesmentioning

confidence: 99%

Perylene Bisimide Dye Assemblies as Archetype Functional Supramolecular Materials

et al. 2015

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“…Replacement of an entire base pair with a W*V or W*W pair, however, resulted in a significantly smaller destabilization. Considering that the aromatic surfaces of W and V are smaller than those of other non-nucleosidic polyaromatic DNA building blocks, such as pyrenes, phenanthrenes, or perylenebis-(imides), [70,71] W and V efficiently stabilize DNA hybrids by interstrand stacking interactions. 10*16).…”

Section: Resultsmentioning

confidence: 99%

2,1,3‐Benzothiadiazole‐Modified DNA

Garo

Häner

2012

Eur J Org Chem

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The use of 2,1,3‐benzothiadiazole (BTD) as a structural element with advanced electronic properties for DNA hybrids is described. Bis(alkynyl)‐ and bis(carboxamide)‐derived BTD units are shown to support duplex stability through interstrand stacking interactions. Placement of the BTD units opposite to a natural base, however, leads to considerable destabilization. The bis(alkynyl)‐derived BTD W is strongly fluorescent, and quantum yields of up to 0.20 are observed. Its fluorescence behavior is strongly dependent on the neighboring nucleobases. The quenching effect of the natural bases decreases in the order G >> A ≥ T ≥ C and correlates very well with the free energies for charge separation (ΔGCS) through photoinduced electron transfer, as calculated by the Rehm–Weller equation. Fluorescence of W is completely quenched when it is placed against the bis(carboxamide)‐derived BTD V. The described BTD‐based compounds W and V represent valuable building blocks for the construction of highly ordered, DNA‐based materials with special optical and electronic properties.

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“…The DNA three‐way junction (3WJ) consisting of three complementary oligonucleotide branches has been widely utilized as a building block to construct DNA architectures and dynamic assemblies . It has also been exploited as a scaffold for the controlled arrangement of functional molecules, including a wide range of different chromophores . Target‐responsive DNA 3WJs can also be designed into DNA devices for molecular diagnostic, sensing, and imaging applications .…”

Section: Introductionmentioning

confidence: 99%

Catalytic Hairpin Assembly‐Programmed DNA Three‐Way Junction for Enzyme‐Free and Amplified Electrochemical Detection of Target DNA

Wei

Liu

et al. 2015

Chemistry An Asian Journal

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DNA three-way junctions (DNA 3WJ) have been widely used as important building blocks for the construction of DNA architectures and dynamic assemblies. Herein, we describe for the first time a catalytic hairpin assembly-programmed DNA three-way junction (CHA-3WJ) strategy for the enzyme-free and amplified electrochemical detection of target DNA. It takes full advantage of the target-catalyzed hairpin assembly-induced proximity effect of toehold and branch-migration domains for the ingenious execution of the strand displacement reaction to form the DNA 3WJ on the electrode surface. A low detection limit of 0.5 pM with an excellent selectivity was achieved for target DNA detection. The developed CHA-3WJ strategy also offers distinct advantages of simplicity in probe design and biosensor fabrication, as well as enzyme-free operation. Thus, it opens a promising avenue for applications in bioanalysis, design of DNA-responsive devices, and dynamic DNA assemblies.

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The DNA three-way junction as a mould for tripartite chromophore assembly

Cited by 37 publications

References 65 publications

Perylene Bisimide Dye Assemblies as Archetype Functional Supramolecular Materials

Perylene Bisimide Dye Assemblies as Archetype Functional Supramolecular Materials

2,1,3‐Benzothiadiazole‐Modified DNA

Catalytic Hairpin Assembly‐Programmed DNA Three‐Way Junction for Enzyme‐Free and Amplified Electrochemical Detection of Target DNA

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