Multichannel DNA Sensor Array Fingerprints Cell States and Identifies Pharmacological Effectors of Catabolic Processes

Abstract

Cells at disease onset are often associated with subtle changes in the expression level of a single or few molecular components, making traditionally used biomarker-driven clinical diagnosis a challenging task. We demonstrate here the design of a DNA nanosensor array with multichannel output that identifies the normal or pathological state of a cell based on the alteration of its global proteomic signature. Fluorophore-encoded single-stranded DNA (ssDNA) strands were coupled via supramolecular interaction with a surface-functionalized gold nanoparticle quencher to generate this integrated sensor array. In this design, ssDNA sequences exhibit dual roles, where they provide differential affinities with the receptor gold nanoparticle as well as act as transducer elements. The unique interaction mode of the analyte molecules disrupts the noncovalent supramolecular complexation, generating simultaneous multichannel fluorescence output to enable signature-based analyte identification via a linear discriminant analysis-based machine learning algorithm. Different cell types, particularly normal and cancerous cells, were effectively distinguished using their fluorescent fingerprints. Additionally, this DNA sensor array displayed excellent sensitivity to identify cellular alterations associated with chemical modulation of catabolic processes. Importantly, pharmacological effectors, which could modulate autophagic flux, have been effectively distinguished by generating responses from their global protein signatures. Taken together, these studies demonstrate that our multichannel DNA nanosensor is well suited for rapid identification of subtle changes in a complex mixture and thus can be readily expanded for point-of-care clinical diagnosis, high-throughput drug screening, or predicting the therapeutic outcome from a limited sample volume.

Cell-Based Chemical Safety Assessment and Therapeutic Discovery Using Array-Based Sensors

“…Single-stranded DNA (ssDNA) can be readily chemically synthesized to generate a large library, making these materials attractive motifs for sensing [ 98 ]. Agasti et al complexed three cationic surface-functionalized AuNPs with different fluorophore-labeled ssDNA strands to form a robust multichannel array-based sensing platform [ 99 ]. Cells with different states were lysed to extract the total protein components.…”

“…( d ) Sensor array generated distinguishable fluorescent fingerprints between cells treated with autophagy inhibitors and inducers, and the accuracy of discrimination under LDA was 98%. Reproduced with permission from [ 99 ]. Copyright 2019 American Chemical Society.…”

Programmable Engineering of DNA-AuNP Encoders Integrated Multimodal Coupled Analysis for Precision Discrimination of Multiple Metal Ions

“…Inspired by the olfactory recognition process, cross-responsive strategies (CRS) combining different recognition receptors to produce a composite unique fingerprint-like signal of a target analyte have been developed. ,− CRSs based on AuNPs are a particular case due to their simplicity and practicality . Several CRSs based on AuNPs have been employed for identifying multiple analytes through synthesized or screened recognition receptors on the surface of AuNPs, such as metal ions, − small molecules, − biomacromolecules, ,− and cells. ,− However, these CRS’s recognition receptors based on AuNPs cannot get the whole comprehensive information from the target when limited in number and type, diminishing the detection accuracy and throughput compared with the olfactory system. These factors severely restrict the broad application of CRSs based on AuNPs.…”

Machine Learning-Assisted Array-Based Detection of Proteins in Serum Using Functionalized MoS2 Nanosheets and Green Fluorescent Protein Conjugates

“…Pattern-based sensing relying on optical response offers an alternative way for the analysis of several analytes, including proteins, , bacteria, , diseased cell lines, , amino acids, nitroexplosives, − neurotransmitters, − biothiols, − etc. This type of sensor has a simplified setup, containing receptor units, which interact with the analyte of interest.…”