Duplex Stabilization and Energy Transfer in Zipper Porphyrin–DNA

Nguyen, ThaoNguyen; Brewer, Ashley; Stulz, Eugen

doi:10.1002/anie.200805657

Cited by 105 publications

(83 citation statements)

References 40 publications

(20 reference statements)

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“…11). When hybridized to an unmodified complementary DNA, or another modified strand to form a zipper-like heteropolymer, 185 the porphyrin stack was assembled in the major groove of DNA, forming a stable right-handed helical array, as indicated by CD studies and further molecular mechanics simulations.…”

Section: Varied Molecular Classes Of Dna Multichromophoresmentioning

confidence: 99%

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DNA-Multichromophore Systems

2012

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Section: Varied Molecular Classes Of Dna Multichromophoresmentioning

confidence: 99%

“…Energy transfer between the zinc porphyrin and the free porphyrin resulted in quenching of the fluorescence of the zinc porphyrin. 185 …”

Section: Varied Molecular Classes Of Dna Multichromophoresmentioning

confidence: 99%

DNA-Multichromophore Systems

2012

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“…The second dye category includes dyes that are modeled as fixed in their position and orientation with respect to dsDNA, such as the tC dye family (19), intercalating dyes from the YO and TO families (24–26,38) and intercalated and covalently-conjugated porphyrins (16,39–41). Intercalating dyes affect significantly the geometrical ground-state structure of free dsDNA by elongating and unwinding the canonical B-form dsDNA helix (24,42,43).…”

Section: Methodsmentioning

confidence: 99%

Structure-based model for light-harvesting properties of nucleic acid nanostructures

Pan

Boulais

Yang

et al. 2013

Nucleic Acids Research

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Programmed self-assembly of DNA enables the rational design of megadalton-scale macromolecular assemblies with sub-nanometer scale precision. These assemblies can be programmed to serve as structural scaffolds for secondary chromophore molecules with light-harvesting properties. Like in natural systems, the local and global spatial organization of these synthetic scaffolded chromophore systems plays a crucial role in their emergent excitonic and optical properties. Previously, we introduced a computational model to predict the large-scale 3D solution structure and flexibility of nucleic acid nanostructures programmed using the principle of scaffolded DNA origami. Here, we use Förster resonance energy transfer theory to simulate the temporal dynamics of dye excitation and energy transfer accounting both for overall DNA nanostructure architecture as well as atomic-level DNA and dye chemical structure and composition. Results are used to calculate emergent optical properties including effective absorption cross-section, absorption and emission spectra and total power transferred to a biomimetic reaction center in an existing seven-helix double stranded DNA-based antenna. This structure-based computational framework enables the efficient in silico evaluation of nucleic acid nanostructures for diverse light-harvesting and photonic applications.

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“…Comparison of the calculated structures of pyrene-DNA,49 porphyrin-DNA,65 pyrene-RNA,63 benzoyl-LNA 61 and aniline-DNA62 (from left to right).yFig. 14 (a) Four-way-branched porphyrin-DNA assembly (Reprinted with permission from ref.…”

mentioning

confidence: 98%

DNA as supramolecular scaffold for functional molecules: progress in DNA nanotechnology

et al. 2011

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Oligonucleotides have recently gained increased attraction as a supramolecular scaffold for the design and synthesis of functional molecules on the nanometre scale. This tutorial review focuses on the recent progress in this highly active field of research with an emphasis on covalent modifications of DNA; non-covalent interactions of DNA with molecules such as groove binders or intercalators are not part of this review. Both terminal and internal modifications are covered, and the various points of attachment (nucleobase, sugar moiety or phosphodiester backbone) are compared. Using selected examples of the recent literature, the diversity of the functionalities that have been incorporated into DNA strands is discussed.

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Duplex Stabilization and Energy Transfer in Zipper Porphyrin–DNA

Cited by 105 publications

References 40 publications

DNA-Multichromophore Systems

DNA-Multichromophore Systems

Structure-based model for light-harvesting properties of nucleic acid nanostructures

DNA as supramolecular scaffold for functional molecules: progress in DNA nanotechnology

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