Glycoform Differentiation by a Targeted, Self-Assembled, Pattern-Generating Protein Surface Sensor

Abstract

A method for generating targeted, pattern-generating, protein surface sensors via the self-assembly of modified oligodeoxynucleotides (ODNs) is described. The simplicity by which these systems can be created enabled the development of a sensor that can straightforwardly discriminate between distinct glycoform populations. By using this sensor to identify glycosylation states of a therapeutic protein, we demonstrate the diagnostic potential of this approach as well as the feasibility of integrating a wealth of supramolecular receptors and sensors into higher-order molecular analytical devices with advanced properties. For example, the facile device integration was used to attach the well-known anthracene-boronic acid (An-BA) probe to a biomimetic DNA scaffold and consequently, to use the unique photophysical properties of An-BA to improve glycoform differentiation. In addition, the noncovalent assembly enabled us to modify the sensor with a trinitrilotriacetic acid (tri-NTA)-Ni2+ complex, which endows it with selectivity toward a hexa-histidine tag (His-tag). The selective responses of the system to diverse His-tag-labeled proteins further demonstrate the potential applicability of such sensors and validate the mechanism underlying their function.

Cucurbit[7]uril Macrocyclic Sensors for Optical Fingerprinting: Predicting Protein Structural Changes to Identifying Disease-Specific Amyloid Assemblies

“…Overall, this recognition process generates a distinct fluorescence fingerprint that can be statistically analyzed by machine learning algorithms to identify individual target analytes. This strategy aligns with the array-based sensing, which is an attractive alternative to the conventional lock-and-key sensing that employs one specific receptor (e.g., antibodies) to detect one target analyte. − An array-based sensing strategy is modeled after the sensing mechanism of the mammalian olfactory system, where an array of cross-reactive receptors signals a specific pattern for each analyte. Given that these cross-reactive receptors can be synthetically generated, this strategy provides enormous flexibility, cost-effectiveness, and diversity to suit many sensing challenges.…”

Development of “Imprint-and-Report” Dynamic Combinatorial Libraries for Differential Sensing Applications

“…Synthetic host–guest systems are particularly well suited to sensor arrays, as they are rarely ideally selective, but small structural changes in the host can perturb binding preferences to a set of guests, providing a set of differential receptors. Accordingly, sensor arrays based on host–guest IDAs have been developed for a broad range of analytes. − Nonetheless, the workflow for developing a new sensor array has several significant challenges: Individual receptors must be identified, synthesized, and purified, and an appropriate environmentally sensitive dye must be identified for each receptor. Moreover, a set of receptors must be developed for each new set of analytes, which can often involve significant effort in multistep syntheses.…”

An Optical Probe for Real-Time Monitoring of Self-Replicator Emergence and Distinguishing between Replicators

“…To track the dynamic formation of several molecular species in solution, a new class of fluorescent molecular probes [25][26][27][28][29] , termed ID-probes 28 was recently developed. Unlike conventional small molecule-based probes, which generally bind a single analyte and produce a single fluorescence output, ID-probes combine several fluorophores and non-specific (or partially specific) recognition elements that enable them to interact with various different molecular species in a mixture and generate unique identification (ID) fingerprints for different analytes and their combinations.…”