Design of Specific Nucleic Acid‐Based Biosensors for Protein Binding Activity

Abstract

Nucleic acid-based biosensors for the detection of specific proteins combine the typical programmability of synthetic DNA systems with artificially controlled DNA-protein communication. The high-affinity interaction between a target protein and a specific ligand, such as an aptamer sequence, or a double stranded DNA domain, or a small peptide, is paired with a nature-mimicking molecular mechanism allowing for probing, processing, and translating protein binding activity into a measurable signal. In this Review, two main strategies developed in the context of protein-responsive nucleic acid-based biosensors are discussed. One is the design of proximity-based assays harnessing the spatial colocalization of functional probes within the volume of a multivalent protein. The other is the engineering of dynamic DNA structures that undergo a controlled conformational or structural change upon protein binding. Examples of applications from optical and electrochemical detection of antibodies in biofluids to fluorescence imaging of transcription factors in living cells are reported, and suggestions along with possible future directions in the field are discussed.

Development of Nucleic‐Acid‐Based Electrochemical Biosensors for Clinical Applications

“…These include small size, high chemical and thermal stability, easy and precise modification, programmable structure, and scalable production. [47,48] These properties make DNA-based probes ideally suited for use in biosensors for both target recognition and signal transduction, [49,50] and for the development of commercial and scalable diagnostics. [13,[50][51][52] Herein, we classify DNA probes, which are increasingly used in biosensor developments, into two categories: (1) reccognition probes and (2) reporting probes (Figure 2).…”

“…[47,48] These properties make DNA-based probes ideally suited for use in biosensors for both target recognition and signal transduction, [49,50] and for the development of commercial and scalable diagnostics. [13,[50][51][52] Herein, we classify DNA probes, which are increasingly used in biosensor developments, into two categories: (1) reccognition probes and (2) reporting probes (Figure 2). Recognition probes detect biomarkers through target-specific binding.…”

“…These include small size, high chemical and thermal stability, easy and precise modification, programmable structure, and scalable production [47, 48] . These properties make DNA‐based probes ideally suited for use in biosensors for both target recognition and signal transduction, [49, 50] and for the development of commercial and scalable diagnostics [13, 50–52] …”

Universal nanocomposite coating with antifouling and redox capabilities for electrochemical affinity biosensing in complex biological fluids

“…[4][5][6] Nevertheless, the current feasibility of electrochemical biosensors for point-of-care testing (POCT) is significantly restricted due to several key challenges: (i) limited performance: the inefficiency in conjugation of biorecognition elements results in suboptimal sensitivity and specificity 7,8 ; (ii) biofouling: uncontrolled biofouling inevitably deteriorates the electrode morphology, leading to a rapid loss in sensitivity 9,10 ; (iii) lack of built-in redox properties: the absence of intrinsic redox capability necessitates the use of additional steps and external redox-probes. 11,12 These limitations result in a scarcity of studies reporting on electrochemical affinity biosensors capable of performing direct detection in unprocessed biofluids. 13,14 Consequently, these traditional biosensors are plagued by non-specificity and reduced sensitivity, making them highly susceptible to external factors and thereby restricting their commercial viability.…”

Recent Progress on Optical Biosensors Developed for Nucleic Acid Detection Related to Infectious Viral Diseases

“…Nucleic acid-based biosensors serve as effective screening tools for determination of a trace low-molecular-mass analytes (i.e., drugs, toxins, and pesticides) as an important aspect of studies in drug discovery and environmental processes [ 9 ]. On the other hand, protein binding activity can be processed, and transformed into a measurable signal using nucleic acid-based biosensors that can recognize and detect a specific targeted protein [ 10 , 11 , 12 ].…”