Spatial recognition and mapping of proteins using DNA aptamers

Stabilization of surface-bound antibodies for ELISA based on a reversable zeolitic imidazolate framework-8 coating

Immunoassays typically must be stored under refrigerated conditions because antibodies, after being immobilized to solid surfaces, tend to lose their recognition capabilities to target antigens under non-refrigerated conditions. This requirement hinders application of immunoassays in resource-limited settings including rural clinics in tropical regions, disaster struck areas, and low-income countries, where refrigeration may not be feasible. In this work, a facile approach based on a reversable zeolitic imidazolate framework-8 (ZIF-8) coating is introduced to stabilize surface-bound antibodies on enzyme-linked immunosorbent assay (ELISA) plates under non-refrigerated conditions. Using a sandwich ELISA for the detection of neutrophil gelatinase-associated lipocalin (NGAL), a urine biomarker for acute kidney injury, as a model system, ZIF-8 is demonstrated to be able to uniformly coat the surface-bound anti-NGAL IgG, and stabilize the dynamic range and detection sensitivity of the assay after storage at an elevated temperature (50 °C) for at least 4 weeks. The stabilization efficacy of the ZIF-8 coating is comparable to the current "gold standard" refrigeration approach, and superior to the commonly used sucrose coating method. This approach will greatly improve the shelf-life and stability of antibody-coated ELISAs and other types of assays which utilize surface-bound antibodies, thus extending biomedical research and medical diagnostics to resource-limited settings.

DNA building blocks for AFM tip functionalization: An easy, fast and stable strategy

Biosensing atomic force microscopy (AFM) offers the unique feature to determine the energy landscape of a bimolecular interaction at the real single molecule level. Furthermore, simultaneous and label-free mapping of molecular recognition and the determination of sample topography at the nanoscale gets possible. A prerequisite and one of the major parts in biosensing AFM are the bio-functionalized AFM tips. In the past decades, different approaches for tip functionalization have been developed. Using these functionalization strategies, several biological highly relevant interactions at the single molecule level have been explored. For the most common approach, the use of a heterobifunctional poly(ethylenglycol) crosslinker, a broad range of linkers for different chemical coupling strategies is available. Nonetheless, the time consuming functionalization protocol as well as the broad distribution of rupture length reduces the possibility of automation and may reduce the accuracy of the results. Here we present a stable and fast forward approach based on tetra-functional DNA tetrahedra. A fast functionalization and a sharp defined distribution of rupture length gets possible with low effort and high success rate. We tested the performance on the classical avidin biotin system by using tetrahedra with three disulfide legs for stable and site directed coupling to gold coated tips and a biotinylated end at the fourth vertex. A special advantage appears when working with a DNA aptamer as sensing molecule. In this case, the fourth strand can be extended by a certain DNA sequence complementary to the linkage part of an aptamer. This AFM tip functionalization protocol was applied on thrombin using DNA aptamers directed against the fibrinogen binding side of human thrombin.

Metal-Organic Framework Preserves the Biorecognition of Antibodies on Nanoscale Surfaces Validated by Single-Molecule Force Spectroscopy

Antibody biorecognition forms the basis for numerous biomedical applications such as diagnostic assays, targeted drug delivery, and targeted cancer imaging. However, antibodies, especially after being conjugated to surfaces or nanostructures, suffer from stability issues when stored under nonrefrigeration conditions. Therefore, enhancing the stability of antibodies on surfaces and nanostructures under ambient and elevated temperatures is of paramount importance for many nanobiotechnology applications. In this study, we introduce a simple and facile approach based on a metal-organic framework (MOF) coating to preserve the biorecognition capability of antibodies immobilized on nanoscale surfaces after exposure to elevated temperatures for a prolonged period. By using atomic force microscopy (AFM)-based force spectroscopy, we demonstrate that the MOF coating is able to preserve the binding force and binding frequency of the anti-CD-146 antibody attached to an AFM tip to CD-146 antigen on the surface of melanoma cells at the single-molecule level. We also demonstrate that the MOF coating outperforms another commonly used sucrose coatings in terms of maintaining the binding force and binding frequency of the antibody to antigen. Herein, the AFM tip functionalized with antibodies provides a nanoscale testbed (analogous to an antibody-conjugated nanostructure) to assess antibody biorecognition at the single-molecule level and preservation efficacy under antibody denaturing conditions. This MOF coating approach should be applicable to the preservation of a variety of antibody-conjugated nanostructures aiming for targeted drug delivery, targeted cancer imaging, and nanobiosensors. The improved stability and elimination of refrigeration requirements will facilitate wide applications of antibody-enabled nanobiotechnology in resource-limited environments and populations.

Investigation of the interaction between split aptamer and vascular endothelial growth factor 165 using single molecule force spectroscopy

Understanding the binding of split aptamer/its target could become a breakthrough in the application of split aptamer. Herein, vascular endothelial growth factor (VEGF), a major biomarker of human diseases, was used as a model, and its interaction with split aptamer was explored with single molecule force spectroscopy (SMFS). SMFS demonstrated that the interaction force of split aptamer/VEGF₁₆₅ was 169.44 ± 6.59 pN at the loading rate of 35.2 nN/s, and the binding probability of split aptamer/VEGF₁₆₅ was dependent on the concentration of VEGF₁₆₅ . On the basis of dynamic force spectroscopy results, one activation barrier in the dissociation process of split aptamer/VEGF₁₆₅ complexes was revealed, which was similar to that of the intact aptamer/VEGF₁₆₅ . Besides, the dissociation rate constant (k_off ) of split aptamer/VEGF₁₆₅ was close to that of intact aptamer/VEGF₁₆₅ , and the interaction force of split aptamer/VEGF₁₆₅ was higher than the force of intact aptamer/VEGF₁₆₅ . It indicated that split aptamer also possessed high affinity with VEGF₁₆₅ . The work can provide a new method for exploring the interaction of split aptamer/its targets at single-molecule level.

Elucidation of the effect of aptamer immobilization strategies on the interaction between cell and its aptamer using atomic force spectroscopy

The immobilization strategy of cell-specific aptamers is of great importance for studying the interaction between a cell and its aptamer. However, because of the difficulty of studying living cell, there have not been any systematic reports about the effect of immobilization strategies on the binding ability of an immobilized aptamer to its target cell. Because atomic force spectroscopy (AFM) could not only be suitable for the investigation of living cell under physiological conditions but also obtains information reflecting the intrinsic properties of individuals, the effect of immobilization strategies on the interaction of aptamer/human hepatocarcinoma cell Bel-7404 was successively evaluated using AFM here. Two different immobilization methods, including polyethylene glycol immobilization method and glutaraldehyde immobilization method were used, and the factors, such as aptamer orientation, oligodeoxythymidine spacers and dodecyl spacers, were investigated. Binding events measured by AFM showed that a similar unbinding force was obtained regardless of the change of the aptamer orientation, the immobilization method, and spacers, implying that the biophysical characteristics of the aptamer at the molecular level remain undisturbed. However, it showed that the immobilization orientation, immobilization method, and spacers could alter the binding probability of aptamer/Bel-7404 cell. Presumably, these factors may affect the accessibility of the aptamer toward its target cell. These results may provide valuable information for aptamer sensor platforms including ultrasensitive biosensor design.