DNA-Based Scaffolds for Sensing Applications

Ranallo, Simona; Porchetta, Alessandro; Ricci, Francesco

doi:10.1021/acs.analchem.8b05009

Cited by 92 publications

(76 citation statements)

References 173 publications

(229 reference statements)

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“…Our strategy to rationally regulate DNA nanostructures formation with antibodies starts from the consideration that the isothermal assembly and disassembly of such nanostructures can be induced by regulator strands that can be released by specifically designed DNA-based circuits 17,29 . To first design an antibody-controlled DNA-based circuit we took advantage of the specific Y-shaped geometry that all IgG antibodies share with two identical binding sites separated by about 6–14 nm 30–32 and by the possibility to easily conjugate different recognition elements on the backbone of synthetic nucleic acid strands 33 . More specifically, we have started our design from a conventional toehold strand displacement reaction, which is the most employed process in DNA-based circuits 34–36 .…”

Section: Resultsmentioning

confidence: 99%

Orthogonal regulation of DNA nanostructure self-assembly and disassembly using antibodies

2019

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Here we report a rational strategy to orthogonally control assembly and disassembly of DNA-based nanostructures using specific IgG antibodies as molecular inputs. We first demonstrate that the binding of a specific antibody to a pair of antigen-conjugated split DNA input-strands induces their co-localization and reconstitution into a functional unit that is able to initiate a toehold strand displacement reaction. The effect is rapid and specific and can be extended to different antibodies with the expedient of changing the recognition elements attached to the two split DNA input-strands. Such an antibody-regulated DNA-based circuit has then been employed to control the assembly and disassembly of DNA tubular structures using specific antibodies as inputs. For example, we demonstrate that we can induce self-assembly and disassembly of two distinct DNA tubular structures by using DNA circuits controlled by two different IgG antibodies (anti-Dig and anti-DNP antibodies) in the same solution in an orthogonal way.

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Section: Resultsmentioning

confidence: 99%

Orthogonal regulation of DNA nanostructure self-assembly and disassembly using antibodies

2019

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“…Design of Ab-directed DNA-templated synthesis. Our strategy to achieve Ab-directed DNA-templated synthesis takes advantage of the following features: first, the Y-shaped geometry that all IgG antibodies share, with two identical binding sites separated by about 6-14 nm [33][34][35] ; second, the possibility to easily conjugate different recognition elements to synthetic nucleic acid strands 36 . More specifically, we conjugated a reactive group and a recognition element (i.e., antigen) to each of a pair of templating synthetic oligonucleotides (Fig.…”

Section: Resultsmentioning

confidence: 99%

Using antibodies to control DNA-templated chemical reactions

et al. 2020

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DNA-templated synthesis takes advantage of the programmability of DNA-DNA interactions to accelerate chemical reactions under diluted conditions upon sequence-specific hybridization. While this strategy has proven advantageous for a variety of applications, including sensing and drug discovery, it has been so far limited to the use of nucleic acids as templating elements. Here, we report the rational design of DNA templated synthesis controlled by specific IgG antibodies. Our approach is based on the co-localization of reactants induced by the bivalent binding of a specific IgG antibody to two antigen-conjugated DNA templating strands that triggers a chemical reaction that would be otherwise too slow under diluted conditions. This strategy is versatile, orthogonal and adaptable to different IgG antibodies and can be employed to achieve the targeted synthesis of clinically-relevant molecules in the presence of specific IgG biomarker antibodies.

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“…The so-called DNAMeter exhibits several unique features. First, the intrinsic modularity and precise self-assembly of the DNA scaffold allows the accurate positioning of specific reference fluorophores, reporter fluorophores and quenchers 32,[48][49][50] . As a result, a facile ratiometric quantification of tensile forces can be achieved.…”

Section: Discussionmentioning

confidence: 99%

Quantifying Tensile Forces at Cell–Cell Junctions with a DNA-based Fluorescent Probe

Zhao

Xie

et al. 2020

Preprint

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Cells are physically contacting with each other. Direct and precise quantification of forces at cell-cell junctions is still challenging. Herein, we have developed a DNA-based ratiometric fluorescent probe, termed DNAMeter, to quantify intercellular tensile forces. These lipidmodified DNAMeters can spontaneously anchor onto live cell membranes. The DNAMeter consists of two self-assembled DNA hairpins of different force tolerance. Once the intercellular tension exceeds the force tolerance to unfold a DNA hairpin, a specific fluorescence signal will be activated, which enables the real-time imaging and quantification of tensile forces. Using Ecadherin-modified DNAMeter as an example, we have demonstrated an approach to quantify, at the molecular level, the magnitude and distribution of E-cadherin tension among epithelial cells.Compatible with readily accessible fluorescence microscopes, these easy-to-use DNA tension probes can be broadly used to quantify mechanotransduction in collective cell behaviors.

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DNA-Based Scaffolds for Sensing Applications

Cited by 92 publications

References 173 publications

Orthogonal regulation of DNA nanostructure self-assembly and disassembly using antibodies

Orthogonal regulation of DNA nanostructure self-assembly and disassembly using antibodies

Using antibodies to control DNA-templated chemical reactions

Quantifying Tensile Forces at Cell–Cell Junctions with a DNA-based Fluorescent Probe

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