Linear dichroism of visible-region chromophores using M13 bacteriophage as an alignment scaffold

Tridgett, Matthew; Moore-Kelly, Charles; Duprey, Jean‐Louis H. A.; Iturbe, Lorea Orueta; Tsang, Chi; Little, Haydn A.; Sandhu, Sandeep Kaur; Hicks, Matthew R.; Dafforn, Timothy R.; Rodger, Alison

doi:10.1039/c8ra05475d

Cited by 7 publications

(6 citation statements)

References 38 publications

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“…Even though Cy3 and AF555 are spectroscopically similar, the energy transfer between the pyrazoline moiety and Cy3 seems to be more efficient compared to AF555 because only 2.6-fold (RNA1) and 3.2-fold (RNA2) fluorescence intensity increases were yielded with AF555. Although structural details of both AF-maleimides are reported in literature [27], the exact structure was not provided by the manufacturer of the dyes. Therefore, the varying energy transfer efficiency cannot conclusively be explained, but we assume differing Förster radii or competing photochemical processes could be possible explanations for the lower efficiency.…”

Section: Resultsmentioning

confidence: 99%

Fluorogenic and Bioorthogonal Modification of RNA Using Photoclick Chemistry

Krell

Wagenknecht

2020

Biomolecules

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A bromoaryltetrazole-modified uridine was synthesized as a new RNA building block for bioorthogonal, light-activated and postsynthetic modification with commercially available fluorescent dyes. It allows “photoclick”-type modifications by irradiation with light (300 nm LED) at internal and terminal positions of presynthesized RNA with maleimide-conjugated fluorophores in good yields. The reaction was evidenced for three different dyes. During irradiation, the emission increases due to the formation of an intrinsically fluorescent pyrazoline moiety as photoclick product. The fluorogenecity of the photoclick reaction was significantly enhanced by energy transfer between the pyrazoline as the reaction product (poor emitter) and the photoclicked dye as the strong emitter. The RNA-dye conjugates show remarkable fluorescent properties, in particular an up to 9.4 fold increase of fluorescence, which are important for chemical biology and fluorescent imaging of RNA in cells.

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Section: Resultsmentioning

confidence: 99%

Fluorogenic and Bioorthogonal Modification of RNA Using Photoclick Chemistry

Krell

Wagenknecht

2020

Biomolecules

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“…23,24 These studies are based on the orientation of molecules in solution. The advancements in Couette flow LD cells 25,26 and the use of stretchable polymer films 27,28 have enabled this progress. These innovations have transformed LD into an effective tool in synthetic biology, facilitating tasks like engineering biological assays for DNA detection through bacteriophage utilization.…”

Section: ■ Introductionmentioning

confidence: 99%

Angle-Resolved Linear Dichroism to Probe the Organization of Highly Ordered Collagen Biomaterials

Krins,

Wien,

Schmeltz

et al. 2024

Biomacromolecules

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Controlling the assembly of high-order structures is central to soft-matter and biomaterial engineering. Angle-resolved linear dichroism can probe the ordering of chiral collagen molecules in the dense state. Collagen triple helices were aligned by solvent evaporation. Their ordering gives a strong linear dichroism (LD) that changes sign and intensity with varying sample orientations with respect to the beam linear polarization. Being complementary to circular dichroism, which probes the structure of chiral (bio)molecules, LD can shift from the molecular to the supramolecular scale and from the investigation of the conformation to interactions. Supported by multiphoton microscopy and X-ray scattering, we show that LD provides a straightforward route to probe collagen alignment, determine the packing density, and monitor denaturation. This approach could be adapted to any assembly of chiral (bio)macromolecules, with key advantages in detecting large-scale assemblies with high specificity to aligned and chiral molecules and improved sensitivity compared to conventional techniques.

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“…Small molecules that are unable to be aligned through shear flow, due to an insufficient force exerted on the molecule, are instead able to be aligned through their adsorption onto a polymer film which is mechanically stretched. The stretching aligns the long axis of the molecule parallel to the stretch direction. ,− …”

Section: Introductionmentioning

confidence: 99%

“…While the use of LD as a tool for studying the orientation of chromophores in biopolymers such as DNA, protein assemblies, and M13 bacteriophage is well established, ,,,,− as far as we are aware, flow LD has extremely limited use for the analysis of synthetic polymers. This is partly because synthetic polymers do not usually form secondary and tertiary structures such as double helical DNA and coiled-coil, cross-beta, or protein fibers which enhance biomolecular polymer rigidity and hence flow orientation.…”

Section: Introductionmentioning

confidence: 99%

Linear Dichroism Activity of Chiral Poly(p-Aryltriazole) Foldamers

et al. 2021

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Controllable higher-order assembly is a central aim of macromolecular chemistry. An essential challenge to developing these molecules is improving our understanding of the structures they adopt under different conditions. Here, we demonstrate how flow linear dichroism (LD) spectroscopy is used to provide insights into the solution structure of a chiral, self-assembled fibrillar foldamer. Poly(para-aryltriazole)s fold into different structures depending on the monomer geometry and variables such as solvent and ionic strength. LD spectroscopy provides a simple route to determine chromophore alignment in solution and is generally used on natural molecules or molecular assemblies such as DNA and M13 bacteriophage. In this contribution, we show that LD spectroscopy is a powerful tool in the observation of self-assembly processes of synthetic foldamers when complemented by circular dichroism, absorbance spectroscopy, and microscopy. To that end, poly(paraaryltriazole)s were aligned in a flow field under different solvent conditions. The extended aromatic structures in the foldamer give rise to a strong LD signal that changes in sign and in intensity with varying solvent conditions. A key advantage of LD is that it only detects the large assemblies, thus removing background due to monomers and small oligomers.

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Linear dichroism of visible-region chromophores using M13 bacteriophage as an alignment scaffold

Abstract: Here we characterise four dyes and assess the complementarity of linear dichroism and FRET in biomimetic light-harvesting antennae optimisation.

Cited by 7 publications

References 38 publications

Fluorogenic and Bioorthogonal Modification of RNA Using Photoclick Chemistry

Fluorogenic and Bioorthogonal Modification of RNA Using Photoclick Chemistry

Angle-Resolved Linear Dichroism to Probe the Organization of Highly Ordered Collagen Biomaterials

Linear Dichroism Activity of Chiral Poly(p-Aryltriazole) Foldamers

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