A Multi-Faceted Binding Assessment of Aptamers Targeting the SARS-CoV-2 Spike Protein.

The COVID-19 pandemic has underscored the critical need for the advancement of diagnostic and therapeutic platforms. These platforms rely on the rapid development of molecular binders that should facilitate surveillance and swift intervention against viral infections. In this study, we have evaluated by three independent research groups the binding characteristics of various published RNA and DNA aptamers targeting the spike protein of the SARS-CoV-2 virus. For this comparative analysis, we have employed different techniques such as biolayer interferometry (BLI), enzyme-linked oligonucleotide assay (ELONA), and flow cytometry. Our data show discrepancies in the reported specificity and affinity among several of the published aptamers and underline the importance of standardized methods, the impact of biophysical techniques, and the controls used for aptamer characterization. We expect our results to contribute to the selection and application of suitable aptamers for the detection of SARS-CoV-2.

A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has created an urgent need for new technologies to treat COVID-19. Here we report a 2'-fluoro protected RNA aptamer that binds with high affinity to the receptor binding domain (RBD) of SARS-CoV-2 spike protein, thereby preventing its interaction with the host receptor ACE2. A trimerized version of the RNA aptamer matching the three RBDs in each spike complex enhances binding affinity down to the low picomolar range. Binding mode and specificity for the aptamer-spike interaction is supported by biolayer interferometry, single-molecule fluorescence microscopy, and flow-induced dispersion analysis in vitro. Cell culture experiments using virus-like particles and live SARS-CoV-2 show that the aptamer and, to a larger extent, the trimeric aptamer can efficiently block viral infection at low concentration. Finally, the aptamer maintains its high binding affinity to spike from other circulating SARS-CoV-2 strains, suggesting that it could find widespread use for the detection and treatment of SARS-CoV-2 and emerging variants.

Enhanced DNA damage response through RAD50 in triple negative breast cancer resistant and cancer stem-like cells contributes to chemoresistance.

A growing body of evidence supports the notion that cancer resistance is driven by a small subset of cancer stem cells (CSC), responsible for tumor initiation, growth, and metastasis. Both CSC and chemoresistant cancer cells may share common qualities to activate a series of self-defense mechanisms against chemotherapeutic drugs. Here, we aimed to identify proteins in chemoresistant triple-negative breast cancer (TNBC) cells and corresponding CSC-like spheroid cells that may contribute to their resistance. We have identified several candidate proteins representing the subfamilies of DNA damage response (DDR) system, the ATP-binding cassette, and the 26S proteasome degradation machinery. We have also demonstrated that both cell types exhibit enhanced DDR when compared to corresponding parental counterparts, and identified RAD50 as one of the major contributors in the resistance phenotype. Finally, we have provided evidence that depleting or blocking RAD50 within the Mre11-Rad50-NBS1 (MRN) complex resensitizes CSC and chemoresistant TNBC cells to chemotherapeutic drugs.

Targeting hormone refractory prostate cancer by in vivo selected DNA libraries in an orthotopic xenograft mouse model.

The targeting of specific tissue is a major challenge for the effective use of therapeutics and agents mediating this targeting are strongly demanded. We report here on an in vivo selection technology that enables the de novo identification of pegylated DNA aptamers pursuing tissue sites harbouring a hormone refractory prostate tumour. To this end, two libraries, one of which bearing an 11 kDa polyethylene glycol (PEG) modification, were used in an orthotopic xenograft prostate tumour mouse model for the selection process. Next-generation sequencing revealed an in vivo enriched pegylated but not a naïve DNA aptamer recognising prostate cancer tissue implanted either subcutaneous or orthotopically in mice. This aptamer represents a valuable and cost-effective tool for the development of targeted therapies for prostate cancer. The described selection strategy and its analysis is not limited to prostate cancer but will be adaptable to various tissues, tumours, and metastases. This opens the path towards DNA aptamers being experimentally and clinically engaged as molecules for developing targeted therapy strategies.

Advances in the Study of Aptamer-Protein Target Identification Using the Chromatographic Approach.

Ever since the development of the process known as the systematic evolution of ligands by exponential enrichment (SELEX), aptamers have been widely used in a variety of studies, including the exploration of new diagnostic tools and the discovery of new treatment methods. Aptamers' ability to bind to proteins with high affinity and specificity, often compared to that of antibodies, enables the search for potential cancer biomarkers and helps us understand the mechanisms of carcinogenesis. The blind spot of those investigations is usually the difficulty in the selective extraction of targets attached to the aptamer. There are many studies describing the cell SELEX for the prime choice of aptamers toward living cancer cells or even whole tumors in the animal models. However, a dilemma arises when a large number of proteins are being identified as potential targets, which is often the case. In this article, we present a new analytical approach designed to selectively target proteins bound to aptamers. During studies, we have focused on the unambiguous identification of the molecular targets of aptamers characterized by high specificity to the prostate cancer cells. We have compared four assay approaches using electrophoretic and chromatographic methods for "fishing out" aptamer protein targets followed by mass spectrometry identification. We have established a new methodology, based on the fluorescent-tagged oligonucleotides commonly used for flow-cytometry experiments or as optic aptasensors, that allowed the detection of specific aptamer-protein interactions by mass spectrometry. The use of atto488-labeled aptamers for the tracking of the formation of specific aptamer-target complexes provides the possibility of studying putative protein counterparts without needing to apply enrichment techniques. Significantly, changes in the hydrophobic properties of atto488-labeled aptamer-protein complexes facilitate their separation by reverse-phase chromatography combined with fluorescence detection followed by mass-spectrometry-based protein identification. These comparative results of several methodological approaches confirmed the universal applicability of this method to studying aptamer-protein interactions with high sensitivity, showing superior properties compared with pull-down techniques.

Systematic evaluation of cell-SELEX enriched aptamers binding to breast cancer cells.

The sensitive and specific detection of pathogenic cells is essential in clinical diagnostics. To achieve this, molecular tools are required that unequivocally recognise appropriate cell surface molecules, such as biomarkers that come along with disease onset and progression. Aptamers are short single-stranded oligonucleotides that interact with cognate target molecules with high affinity and specificity. Within the last years they have gained an increased attention as cell-recognition tools. Here, we report a systematic analysis of a cell-SELEX procedure, for the identification of aptamers that recognise breast cancer cells. Besides a comparison of conventional (Sanger) with high-throughput sequencing techniques (next-generation sequencing), three different screening techniques have been applied to characterise the binding properties of selected aptamer candidates. This method has been found to be beneficial in finding DNA aptamers, rarely enriched in the libraries. Finally, four DNA aptamers were identified that exhibit broad-spectrum interaction patterns to different cancer cell lines derived from solid tumours.

Sensitive detection of cancer cells using light-mediated apta-PCR.

Apta-PCR is an ultrasensitive assay in which aptamers are exploited not only as biomolecular recognition elements, but also as reporter labels for amplification via real-time PCR. This methodology has been successfully applied to the detection of proteins, achieving limits of detection in the picomolar range. The introduction of caged aptamers that bear photo-labile groups, so called cages, at strategic positions so that their tertiary structure and thus their binding properties can be controlled by light, facilitates a more robust and attractive assay in terms of sample conservation and reusability. In this work, we report for the first time the use of caged aptamers for cell detection in an apta-PCR assay. Specifically, a sandwich format is used combining the capture of B-cells by an antibody with the specific detection of Burkitt's lymphoma cancer cells by a caged aptamer, acting as a reporter probe. Elution of the aptamer bound to the cancer cells is performed by light and the number of cells is then correlated with the amount of eluted caged aptamer using real-time PCR analysis. The reported technique shows an excellent sensitivity, achieving detection of as few as 77 cells, and due to the inherent robustness of the assay, this detection platform can be reused for further analyses, demonstrating potential applicability in proteomics and clinical diagnostics.

Spectroscopic and atomic force microscopy characterization of the electrografting of 3,5-bis(4-diazophenoxy)benzoic acid on gold surfaces.

The synthesis of a bipodal diazonium salt, 3,5-bis(4-diazophenoxy)benzoic acid, and the study of its electrochemical deposition on gold surfaces is presented. The presence of the organic layer on the gold surface was characterized using atomic force microscopy and X-ray photoelectron spectroscopy, demonstrating the presence of phenyl groups, indicative of the grafted layer as well as the formation of multilayers, dependent on the electrografting conditions.

Evaluation of techniques for generation of single-stranded DNA for quantitative detection.

A simple and efficient method for the generation of clean single-stranded DNA (ssDNA) with a high recovery and purity from a double-stranded polymerase chain reaction (PCR) product is required for nucleic acid sensing and microarray applications. Currently, the most widely used technique is thermal denaturation due to its simplicity and low cost, but this technique has drawbacks in terms of recovery and reproducibility. The work presented here compares this technique with alternative approaches for ssDNA generation exploiting affinity magnetic separation and exonuclease digestion. The ssDNA recovered was evaluated using gel electrophoresis and enzyme-linked oligonucleotide assay. Recoveries of between 50% and 70% of the theoretical maximum of generatable ssDNA were obtained with good reproducibility, demonstrating a marked improvement in performance as compared with thermal denaturation.

Electrochemical genosensor array for the simultaneous detection of multiple high-risk human papillomavirus sequences in clinical samples.

An electrochemical genosensor array for the simultaneous detection of three high-risk human papillomavirus (HPV) DNA sequences, HPV16, 18 and 45, exhibiting high sensitivity and selectivity is presented. The electrodes of a 4×4 array were modified via co-immobilization of a 1:100 (mol/mol) mixture of a thiolated probe and an oligoethyleneglycol-terminated bipodal thiol. Detection of synthetic and PCR products was carried out in a sandwich type format, with the target hybridized between a surface immobilized probe and a horseradish peroxidase-labelled secondary reporter probe. The detection limits obtained in the detection of each individual target were in the pM range, allowing the application of this sensor for the detection of samples obtained from PCR amplification of cervical scrape samples. The results obtained exhibited an excellent correlation with the HPV genotyping carried out within a hospital laboratory. Multiplexing and cross-reactivity studies demonstrated high selectivity over potential interfering sequences, facilitating application of the developed platform for the high-throughput screening of multiple high-risk DNA sequences.

Amperometric immunosensor for detection of celiac disease toxic gliadin based on Fab fragments.

Immunosensor sensitivity is strongly dependent on the density of free active epitopes per surface area, which could be achieved via well-oriented immobilization of antibody fragments as bioreceptor molecules. Here, we report on the development of an electrochemical gliadin immunosensor based on the spontaneous self-assembly of antigliadin Fab fragments (CDC5-Fab) on Au surfaces. The analytical performance of this immunosensor is compared with a similar containing whole CDC5 antibodies previously modified with thiol groups (CDC5-SH) as the recognition element. Fab fragments were generated by reduction of the disulfide bond of F(ab)(2) fragments obtained by bromelain digestion of CDC5 antibody. Surface plasmon resonance (SPR) was used to evaluate the degree of immobilization and recognition ability of immobilized CDC5-Fab and CDC5-SH on gold surfaces. The studied surface chemistries were evaluated in terms of time required for SAM formation, stability, susceptibility to nonspecific interactions, and sensitivity using surface plasmon resonance, electrochemical impedance spectroscopy (EIS), and amperometry. CDC5-Fab formed a stable monolayer on gold after 15 min and retained >90% of antigen recognition ability after 2 months of storage at 4 degrees C. Detection of gliadin of Fab modified electrodes was evaluated by impedance and amperometry. Labeless impedimetric detection achieved a LOD of 0.42 microg/mL while the amperometric immunosensor based on Fab fragments showed a highly sensitive response with an LOD of 3.29 ng/mL. The Fab based immunosensor offers the advantages of being highly sensitive, easy, and rapid to prepare, with a low assay time.

Amperometric sensing of ascorbic acid using a disposable screen-printed electrode modified with electrografted o-aminophenol film.

Electrode modification by electrochemical reduction of diazonium salts of different aryl derivatives is useful for catalytic, analytical and biotechnological applications. A simple and sensitive method for the electrocatalytic detection of ascorbic acid using disposable screen-printed carbon electrodes modified with an electrografted o-aminophenol film, via the electrochemical reduction of its in situ prepared diazonium salts in aqueous solution, is presented. The performance of two commercial SPEs as substrates for grafting of diazonium films has been compared and the grafting process optimized with respect to deposition time and diazonium salt concentration, with the modified surfaces being characterised using cyclic voltammetry. The functionalised screen-printed electrodes demonstrated an excellent electrocatalytic activity towards the oxidation of ascorbic acid shifting the overpotential from 298 and 544 mV to 160 and 244 mV, respectively vs. Ag/AgCl. DC amperometric measurements were carried out for the quantitative determination of ascorbic acid using the modified electrodes. The catalytic oxidation peak current was linearly dependent on the ascorbic acid concentration in the range of 2-20 microM, with a correlation coefficient 0.998, and a limit of detection of 0.86 microM was obtained with an excellent reproducibility (RSD% = 1.98, n = 8). The functionalised screen-printed electrodes exhibited notable surface stability, and were used as a simple and precise disposable sensor for the selective determination of ascorbic acid.

Amperometric determination of ascorbic acid in real samples using a disposable screen-printed electrode modified with electrografted o-aminophenol film.

Ascorbic acid (AA) is an antioxidant considered to play a crucial role in human health. Therefore, diverse methods for the determination of AA in foods have been developed, most of them time-consuming and requiring costly instrumentation. A simple and sensitive method for the quantification of AA in fresh fruits and vegetables and commercial juices using an amperometric sensor is presented on the basis of disposable screen-printed carbon electrodes (SPEs) modified with an o-aminophenol (o-AP) film selective for the detection of AA. The sensor exhibited a linear response for AA from 2-20 microM, with a correlation coefficient r2 = 0.998 and a limit of detection of 0.86 microM. Common possible interferents of the sample matrices were tested, and results showed high selectivity of the o-AP SPEs toward AA. The sensor exhibited an excellent reproducibility (RSD% = 1.98, n = 8) and surface stability. The method was validated by a comparison to a reference method, and excellent correlation is obtained.