Ensemble and single-molecule biophysical characterization of D17.4 DNA aptamer–IgE interactions

Poongavanam, Mohan Vivekanandan; Kisley, Lydia; Kourentzi, Katerina; Landes, Christy F.; Willson, Richard C.

doi:10.1016/j.bbapap.2015.08.008

Cited by 15 publications

(3 citation statements)

References 65 publications

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“…Our value of k 0 is much higher than the k 0 = 5.4 × 10 −6 s −1 for streptavidin/biotin complex [56], meaning that the DNA-Ab complexes are much weaker. However, the off-rate obtained is within the range reported for DNA-antibody or DNA-protein interactions, for example, the k off of D17.4 DNA aptamer/IgE complex was calculated to be (2.92 ± 0.18) × 10 −3 s −1 or (2.85 ± 0.14) × 10 −3 s −1 depending on the environmental conditions [57, 58]. Giuntoli et al [59] showed that the rate of dissociation from DNA of the Escherichia coli nucleoid protein Fis was approximately k off ~ 8 × 10 −3 s −1 .…”

Section: Discussionmentioning

confidence: 62%

Single-Molecule Interactions of a Monoclonal Anti-DNA Antibody with DNA

et al. 2016

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Interactions of DNA with proteins are essential for key biological processes and have both a fundamental and practical significance. In particular, DNA binding to anti-DNA antibodies is a pathogenic mechanism in autoimmune pathology, such as systemic lupus erythematosus. Here we measured at the single-molecule level binding and forced unbinding of surface-attached DNA and a monoclonal anti-DNA antibody MRL4 from a lupus erythematosus mouse. In optical trap-based force spectroscopy, a microscopic antibodycoated latex bead is trapped by a focused laser beam and repeatedly brought into contact with a DNA-coated surface. After careful discrimination of non-specific interactions, we showed that the DNA-antibody rupture force spectra had two regimes, reflecting formation of weaker (20–40 pN) and stronger (>40 pN) immune complexes that implies the existence of at least two bound states with different mechanical stability. The two-dimensional force-free off-rate for the DNA-antibody complexes was ~2.2 × 10−3 s−1, the transition state distance was ~0.94 nm, the apparent on-rate was ~5.26 s−1, and the stiffness of the DNA-antibody complex was characterized by a spring constant of 0.0021 pN/nm, suggesting that the DNA-antibody complex is a relatively stable, but soft and deformable macromolecular structure. The stretching elasticity of the DNA molecules was characteristic of single-stranded DNA, suggesting preferential binding of the MRL4 antibody to one strand of DNA. Collectively, the results provide fundamental characteristics of formation and forced dissociation of DNA-antibody complexes that help to understand principles of DNA-protein interactions and shed light on the molecular basis of autoimmune diseases accompanied by formation of anti-DNA antibodies.

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Section: Discussionmentioning

confidence: 62%

Single-Molecule Interactions of a Monoclonal Anti-DNA Antibody with DNA

et al. 2016

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“…Other drug candidates targeting IgE include DNA aptamer [ 118 ]. However, the structural basis for antagonizing IgE binding to FcεRI has not been well characterized [ 119 , 120 , 121 ].…”

Section: Ige-binding Therapeuticsmentioning

confidence: 99%

Tuning IgE: IgE-Associating Molecules and Their Effects on IgE-Dependent Mast Cell Reactions

Ando

Kitaura

2021

Cells

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The recent emergence of anti-immunoglobulin E (IgE) drugs and their candidates for humans has endorsed the significance of IgE-dependent pathways in allergic disorders. IgE is distributed locally in the tissues or systemically to confer a sensory mechanism in a domain of adaptive immunity to the otherwise innate type of effector cells, namely, mast cells and basophils. Bound on the high-affinity IgE receptor FcεRI, IgE enables fast memory responses against revisiting threats of venoms, parasites, and bacteria. However, the dysregulation of IgE-dependent reactions leads to potentially life-threatening allergic diseases, such as asthma and anaphylaxis. Therefore, reactivity of the IgE sensor is fine-tuned by various IgE-associating molecules. In this review, we discuss the mechanistic basis for how IgE-dependent mast cell activation is regulated by the IgE-associating molecules, including the newly developed therapeutic candidates.

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“…When the NaCl concentration was increased from 50 to 300 mM, a five-fold increase in the k D value was detected, which might be due to differences in the loop conformation, essential for the IgE binding. Moreover, it was shown that the Fc domain is positively charged, thereby the binding of the aptamer to IgE is partly based on electrostatic interaction which is significantly influenced by the ionic strength [135]. Increasing the temperature resulted in an apparent increase of the k D , since the conformational flexibility and the dye motion is in strong correlation with the temperature [133,135].…”

Section: Detection Principlementioning

confidence: 99%

Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications

Bognár

Gyurcsányi

2020

IJMS

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Nucleic acid aptamers show clear promise as diagnostic reagents, as highly specific strands were reported against a large variety of biomarkers. They have appealing benefits in terms of reproducible generation by chemical synthesis, controlled modification with labels and functionalities providing versatile means for detection and oriented immobilization, as along with high biochemical and temperature resistance. Aptamers against immunoglobulin targets—IgA, IgM, IgG and IgE—have a clear niche for diagnostic applications, therefore numerous aptamers have been selected and used in combination with a variety of detection techniques. The aim of this review is to overview and evaluate aptamers selected for the recognition of antibodies, in terms of their design, analytical properties and diagnostic applications. Aptamer candidates showed convincing performance among others to identify stress and upper respiratory tract infection through SIgA detection, for cancer cell recognition using membrane bound IgM, to detect and treat hemolytic transfusion reactions, autoimmune diseases with IgG and detection of IgE for allergy diseases. However, in general, their use still lags significantly behind what their claimed benefits and the plethora of application opportunities would forecast.

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Ensemble and single-molecule biophysical characterization of D17.4 DNA aptamer–IgE interactions

Cited by 15 publications

References 65 publications

Single-Molecule Interactions of a Monoclonal Anti-DNA Antibody with DNA

Single-Molecule Interactions of a Monoclonal Anti-DNA Antibody with DNA

Tuning IgE: IgE-Associating Molecules and Their Effects on IgE-Dependent Mast Cell Reactions

Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications

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