Combining bacteriophage engineering and linear dichroism spectroscopy to produce a DNA hybridisation assay

Ali, Aysha; Little, Haydn A.; Carter, Jake G.; Douglas, Craig; Hicks, Matthew R.; Kenyon, D. M.; Lacomme, Christophe; Logan, Richard T; Dafforn, TR; Tucker, James H. R.

doi:10.1039/d0cb00135j

Cited by 4 publications

(13 citation statements)

References 26 publications

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“…We demonstrate that LD can provide unique insights into the structure and assembly process for the extended foldamer structures which can be used to optimize future foldamer designs. This data lays the foundations for the use of the foldamers in bioassays developed using LD as the detector …”

Section: Introductionmentioning

confidence: 89%

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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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Section: Introductionmentioning

confidence: 89%

“…This data lays the foundations for the use of the foldamers in bioassays developed using LD as the detector. 46…”

Section: ■ Introductionmentioning

confidence: 99%

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

et al. 2021

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“…( Michel et al, 2020 ; Trotter et al, 2020 ; Sun et al, 2019 ; Chen et al, 2019 ). This system has been previously developed for detection using antibodies ( Pacheco-Gómez et al, 2012 ) and DNA ( Ali et al, 2020 ) and offers high levels of sensitivity alongside speed and simplicity. Here we extend our work on this signal read-out methodology to encompass DNA aptamer-based detection.…”

Section: Introductionmentioning

confidence: 99%

“…We accordingly demonstrated that this novel LD sensing methodology could be used to detect pathogenic E. coli using antibodies ( Pacheco-Gómez et al, 2012 ) as well as DNA from pathogens. ( Ali et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

“…In the case of DNA sensing using LD spectroscopy, we generated a “sandwich assay” where the DNA target bridges between two M13 bacteriophages in order to disrupt alignment. ( Ali et al, 2020 ). We found it sufficient to covalently attach DNA strands to the M13 bionanoparticles that were complementary to different sequence regions of the target to bring about a change in LD signal.…”

Section: Introductionmentioning

confidence: 99%

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A plug-and-play aptamer diagnostic platform based on linear dichroism spectroscopy

et al. 2023

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A plug-and-play sandwich assay platform for the aptamer-based detection of molecular targets using linear dichroism (LD) spectroscopy as a read-out method has been demonstrated. A 21-mer DNA strand comprising the plug-and-play linker was bioconjugated onto the backbone of the filamentous bacteriophage M13, which gives a strong LD signal due to its ready alignment in linear flow. Extended DNA strands containing aptamer sequences that bind the protein thrombin, TBA and HD22, were then bound to the plug-and-play linker strand via complementary base pairing to generate aptamer-functionalised M13 bacteriophages. The secondary structure of the extended aptameric sequences required to bind to thrombin was checked using circular dichroism spectroscopy, with the binding confirmed using fluorescence anisotropy measurements. LD studies revealed that this sandwich sensor design is very effective at detecting thrombin down to pM levels, indicating the potential of this plug-and-play assay system as a new label-free homogenous detection system based on aptamer recognition.

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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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Combining bacteriophage engineering and linear dichroism spectroscopy to produce a DNA hybridisation assay

Abstract: A novel DNA sensing method based on LD spectroscopy and using bionanoparticle scaffolds is described, as demonstrated by the rapid detection of DNA strands associated with bacterial and viral pathogens.

Cited by 4 publications

References 26 publications

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

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

A plug-and-play aptamer diagnostic platform based on linear dichroism spectroscopy

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

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