Abstract
Identification of proteins is an important issue both in medical research and in clinical practice as a large number of proteins are closely related to various diseases. Optical sensor arrays with recognition ability have been flourished to apply for distinguishing multiple chemically or structurally similar analytes and analyzing unknown or mixed samples. This review gives an overview of the recent development of array-based discriminative optical biosensors for recognizing proteins and their applications in real samples. Based on the number of sensor elements and the complexity of constructing array-based discriminative systems, these biosensors can be divided into three categories, which include multi-element-based sensor arrays, environment-sensitive sensor arrays and multi-wavelength-based single sensing systems. For each strategy, the construction of sensing platform and detection mechanism are particularly introduced. Meanwhile, the differences and connections between different strategies were discussed. An understanding of these aspects may help to facilitate the development of novel discriminative biosensors and expand their application prospects.
Introduction
Proteins are fundamental components of cells and tissues of human bodies, and play important roles in various life processes, such as repairing tissue, transporting substances and maintaining the normal metabolism (Zhao et al., 2016; Wang et al., ). Studies have reported that proteins are involved in diagnosis of various affiliated diseases including Alzheimer's, Parkinson's, Huntington's, and prion diseases (Galdeano et al., ; Scala et al., ). Abnormal protein concentration levels in biofluids (serum, urine, etc.), cells or tissues can provide necessary information for the early diagnosis of various pathological conditions (Li and Liu, ; Kong et al., ). Thus, it is of great significance to quantitatively analyze and specially recognize proteins for applications in medical diagnostics, proteomics and pathogen detection.
Among many detection methods for proteins, discriminative optical sensors have exhibited advantages like high sensitivity, high-throughput and real-time online detection, which have gained increasing attention (Zhu et al., 2015; Zhang et al., 2017; Fan and Ding, ). Besides, such cross-reactive sensors enable the recognition of structurally or chemically similar analytes and even the identification of mixed or unknown samples (Lin et al., ; Bigdeli et al., ; Wang et al., ). One way to achieve discriminative sensing is to develop multi-element sensor arrays, which are inspired by mimicking mammalian taste and smell systems and usually consist of multiple cross-reactive elements that generate a combined recognition pattern for each analyte (Stewart et al., ; Peveler et al., ; Rana et al., ). Another way to realize discriminative sensing is to fabricate an environment-sensitive sensor array, which is constructed by changing the solvents (Cao et al., , ; Smith et al., ), probe concentrations (Li et al., ), or pH values and ionic strengths (Liu et al., ; Tomita et al., ; Zhou et al., 2017; Lin et al., ). The third type of discriminative sensing is multi-wavelength cross-reactive single-system-based sensors, which use multiple wavelengths instead of multi-elements to provide response signals (Wu et al., ; Rout et al., ). During the past few decades, these three types of optical sensors, especially the first type, have been widely employed for protein discrimination.
In this review, we focus on the array-based discriminative optical biosensors for identifying proteins according to the above-mentioned three strategies. The construction principle, sensing mechanism, sensitivity and accuracy, and practical application (protein identification in serum or urine and cell or bacterium discrimination) of various sensors are particularly introduced in detail. An understanding of these aspects may facilitate the development of novel discriminative optical biosensors and expand their application prospects.
Multi-Element-Based Sensor Arrays for Protein Recognition
The most widely adopted strategy of building sensor arrays is to use a number of cross-reactive sensors as elements to provide multiple response signals and generate recognition patterns for analytes. A variety of sensor elements like conjugated polymer, amphiphilic aggregates, nanoparticles, quantum dots, etc., have been used to generate multiple element sensor arrays for the purpose of protein identification.
Conjugated Polymers
Conjugated polymers (CPs) have been extensively explored for chemical and biological sensor design due to their highly delocalized electronic structures and unique optical and electronic properties (Chen et al., ; Zhao et al., 2017). The delocalized structures of CP backbones allow efficient intra- and inter-chain energy transfer that amplifies signals by the collective response compared with small molecule-fluorophores. Their optical properties (absorption and emission) are sensitive to minor conformational or environmental variations, enabling efficient detection of subtle differences when bound with various analytes in sensing processes. Water-soluble CPs with hydrophobic backbones and hydrophilic side-chains or ionic units can associate with different proteins through multivalent interactions, producing unique optical responses to different proteins (Feng et al., ).
Based on the non-specific interaction between conjugated polymers and proteins, Miranda et al. () reported using six functionalized poly(p-phenyleneethynylene)s (PPEs) to create a six-element sensor array for identifying 17 proteins which have diverse molecular weight, metal/non-metal-containing, isoelectric point (pI), and UV absorbencies. LDA results illustrated that the tested 17 proteins could be well-clustered into 17 different groups with a classification accuracy of 100%. Moreover, out of the 68 protein samples randomly selected from 17 proteins, only two samples were misclassified, and the identification accuracy was 97%. This work demonstrated that a PPE-based sensor array could effectively detect and distinguish proteins.
Wu and Schanze () constructed a fluorescent sensor array containing six conjugated polyelectrolytes (CPEs) and explored the aggregation state/size change upon binding with a set of different proteins by fluorescence correlation spectroscopy (Figure 1). This CPEs-based array could well identify seven proteins and successfully discriminate unknown protein samples with an accuracy of 93% by LDA. They found that the charge type (cation and anion) of CPEs played the most important role in protein recognition compared to other factors, such as charge density, molecular weight, and backbone structure. This kind of probes can be optimized by increasing the purity of polymers, conjugating more diverse functional groups to backbones or introducing novel CPE probes. Importantly, one of the challenges of this type of sensors is the need to eliminate potential interference when used for detection in complex biological environments.
Figure 1
Amphiphilic Aggregates
As we all know, amphiphilic molecules, such as surfactants, dendrimers, and block copolymers can form dynamic supramolecular aggregates, such as micelles and vesicles in aqueous solutions (Yan et al., 2010,
Using this strategy, Thayumanavan et al. have developed simple methods for constructing sensor arrays for protein recognition by using one kind of amphiphilic aggregates to encapsulate different fluorophores (Sandanaraj et al.,
Figure 2

Schematic representation for protein recognition: (A) A single amphiphilic polymer encapsulated different dyes and (B) A surfactant-polyelectrolyte ensemble encapsulated different dyes. Reprinted from Sandanaraj et al. (
Choi et al. (
Quantum Dots
Quantum dots (QDs) are fluorescent materials which possess advantages like high fluorescence quantum yields, narrow and symmetric emission band, broad absorption, high resistance to photobleaching, large “effective” Stokes shifts, versatile surface modification, etc. (Boeneman et al.,
QDs can form conjugates with ionic liquids or nanoparticles for constructing protein sensor arrays. Chen et al. (
Figure 3

(A) Chemical Structures of five different ionic liquids. Canonical score plots for identifying eight proteins at 500 nM based on (B) ionic liquids and (C) ionic liquids-QDs. Reprinted from Chen et al. (
Wang et al. (
QDs can also be modified with different ligands to distinguish proteins. Chang et al. (
Figure 4

(A) Schematic illustration of the ratiometric sensor array based on various functionalized QDs for protein discrimination. (B) Chemical structures of the four ligands modified on the surface of QDs. Reprinted from Chang et al. (
Gold Nanoclusters
Gold nanoclusters (Au NCs) are composed of several to hundreds of gold atoms, which have gained great attention due to their ultra-small size, excellent biocompatibility and unusual photophysical properties (Lin et al.,
Xu et al. (
Figure 5

(A) Photographs of the Au NCs in the absence and presence of human serums from five normal people (a–e), five hepatoma patients (f–j), and five thalassemia patients (k–o) under UV lamp. (B) LDA score plot for discriminating different human serums. Reprinted from Xu et al. (
In addition, Xu et al. (
Gold Nanoparticles
Gold nanoparticles (AuNPs) have been extensively applied in biosensors because of their unique optical, catalytic, chemical and electronical properties, and these properties can be modulated by changing the shape, size, surface modification or aggregation state of AuNPs (Daniel and Astruc,
DNA-Gold Nanoparticle Conjugates
Researchers have built lots of DNA-AuNP conjugates-based arrays for protein identification due to the different interactions among proteins, DNA and AuNPs. Besides, DNA as a non-specific receptor could provide unlimited sensor elements for array sensing, because a short DNA sequence (e.g., 15 bases) has up to billions of combinations (Wei et al.,
Figure 6

Schematic representation of the sensing principle of the aptamer-based sensor array. Reprinted from Lu et al. (
Later, Wei et al. (
In addition, Yang et al. (2013) developed a AuNPs-based colorimetric sensor array including five DNA-decorated catalytic AuNPs and one bare AuNPs for protein recognition. Each protein was first mixed with the sensing platform, and then HAuCl4 and NH2OH were added to make the nanoparticles grow. They selected three wavelengths related to the particle properties for each sensor element as absorbance data acquisition. This label-free 18-dimensional array (six sensor elements × three wavelengths) could effectively distinguish six different proteins, various concentrated proteins, protein mixtures and even samples in serum and urine. Later, they also used this type of sensor array to distinguish 4 different cell lines (Yang X. et al., 2014). In this type of sensor arrays, the addition of proteins can change the aggregation behaviors of DNA-AuNPs, remove DNA from AuNPs, or affect the catalytic performance of AuNPs. This protein detection method is simple, sensitive, and label-free, and it will provide new directions of developing array-based sensing systems and broaden the application field of nanoparticle-based sensors.
Fluorophore/Enzyme-Gold Nanoparticle Conjugates
Rotello et al. have used different positively-charged AuNPs and one negatively-charged fluorescent polymer conjugate, green fluorescent protein (GFP), or enzyme to develop several fluorophore/enzyme displacement sensor arrays. In 2007, they developed a sensor array based on six different non-covalent cationic AuNPs and an anionic fluorescent polymer conjugate (You et al., 2007). The fluorescence of polymer conjugates was quenched by AuNPs, and this platform showed distinct turn-on response patterns to different proteins because the target proteins disrupted the interaction between AuNPs and polymer conjugates. This array could not only quantitatively differentiate seven proteins at nanomolar concentrations, but also identify 52 unknown protein samples with an identification accuracy of 94.2% by LDA. Using this strategy, they developed another array-based sensing system containing three AuNP-polymer conjugates to effectively differentiate normal, cancerous, and metastatic cells (Bajaj et al.,
They also fabricated another effective sensor array containing five different positively-charged AuNPs and one negatively-charged GFP for protein recognition in buffer and human serum, where the fluorescence of GFP was quenched by AuNPs (De et al.,
In addition, they also constructed an enzyme-AuNP sensor array to improve the sensitivity through enzymatic catalysis (Miranda et al.,
The sensing mechanism of this type of sensor array is AuNPs could quench the fluorescence of polymer conjugates or GFP, or inhibit the activity of enzyme which turn off the fluorescence of fluorogenic substrate. Various proteins have different abilities to replace fluorophores/enzymes from AuNPs, thereby generating distinct turn-on signals, and then realizing the identification of proteins and cells. Using this strategy, the Rotello group has made outstanding contributions to the protein discrimination in human serum or urine and the identification of cells including healthy, cancerous, and metastatic cells.
Surfactant-Gold Nanoparticle Conjugates
Colorimetric sensor arrays have been constructed for protein recognition by efficient surfactant-based AuNPs. Surfactants used in this strategy have the following advantages: (1) they can change the zeta potential of AuNPs; (2) they can act as protein receptors; and (3) they can adjust the protein-induced aggregation of AuNPs. Using a very simple washing procedure, Rogowski et al. (
Other Nanoparticles
The unmodified noble metal nanoparticles, other metal nanoparticles and nanodots are also receiving extensive attention in the field of protein sensing. Zhang S. et al. (2015) fabricated a colorimetric sensor array utilizing seven unmodified noble metal nanoparticles (2 AgNPs and 5 AuNPs) with different sizes (Figure 7). The absorbance of the nanoparticles changed differently in the presence of ten proteins, which produced distinct response patterns visually distinguished by naked eyes. These proteins at different concentrations could be further successfully identified by LDA. Moreover, this array was able to discriminate seven bacteria and four cancer cells correctly. This assay illustrated that the sensor array based on unmodified noble metal nanoparticles has application potential in medical diagnostics.
Figure 7

Schematic representation of a sensor array based on seven noble metal nanoparticles for protein recognition. Reprinted from Zhang S. et al. (2015) with permission.
Kong et al. (
Tao et al. (
To construct a successful array-based optical sensing system, analytes and cross-reactive sensor elements should possess different interactions that lead to distinct responses. Multi-element-based sensor arrays for proteins have been widely developed and the detection mechanism, advantages and disadvantages for different types of arrays are summarized and analyzed in Table 1.
Table 1
| Type | Detection mechanism | Advantages | Disadvantages |
|---|---|---|---|
| Conjugated polymers | The formation of protein-CP complexes causes aggregation/size changes of CPs. | The direct interaction between CPs and proteins makes the array very sensitive. | The synthesis and purification of CPs is complicated. |
| Amphiphilic aggregates | Non-metalloprotein-binding induces the amphiphilic ensemble disassembly or assembly, and energy/electron transfer occurs from the probe to metalloproteins. | It is easy to fabricate such arrays by changing the encapsulated fluorophores or amphiphilic aggregates. | The amphiphilic molecule used needs to be charged and there are few fluorescent amphiphilic aggregates for protein recognition. |
| Quantum dots | The added proteins can disrupt the interaction between QDs and ionic liquids or QDs and nanoparticles. | It can improve the sensing sensitivity and discrimination ability of arrays due to their high quantum yields. | The interaction between QDs and proteins is not clear, which limits the construction of arrays that only use QDs for protein identification. |
| Gold nanoclusters | Protein-Au NCs complex is formed. | This type of array has ultra-small size, excellent biocompatibility, etc. | Gold is a precious metal, which makes the preparation of Au NCs expensive. |
| Gold nanoparticles | Proteins disrupt the interaction between DNA and AuNPs, or fluorophore/enzyme and NPs, or surfactant and AuNPs. | The optical properties could be well-modulated by changing the size, shape, surface modification or aggregation state of the AuNPs. | Gold is a high-cost metal and the construction of such arrays is complex due to the introduction of DNA fluorophores, or surfactants. |
Summary of different types of multi-element-based sensor arrays.
Environment-Sensitive Sensor Arrays for Protein Recognition
Environment-sensitive sensors are a type of sensors that are dependent on the physical and chemical properties of the surrounding environment. It is relatively easy to fabricate an environment-sensitive sensor array because it can be achieved by adjusting polarity, viscosity, pH, etc. (Vazquez et al.,
The discrimination of post-translational modifications (PTMs) in proteins has attracted widespread attention in the elucidation of human diseases as well as therapeutic protein improvements (Venne et al.,
Figure 8

Schematic illustration of fluorogenic interactions with proteins with/without PTMs. Reprinted from Tomita et al. (
In addition, pH-based sensor arrays using QDs or Au NCs were also developed. Yan et al. (2019) reported a sensor array containing negatively charged QDs as an indicator for protein discrimination in different pH buffer solutions. The results illustrated that proteins with different isoelectric points (pI < 7, pI = 7, or pI > 7) could be differentiated successfully. It is known that pI is defined as the pH value at which a protein has no net charge. A protein possesses net negative (positive) surface charge when pH is above (below) its pI, and thus has different electrostatic interactions with QDs, which contributes to the differentiation of different proteins. Furthermore, this sensor array was able to identify complex protein mixtures and HSA at different concentrations in water and urine. Subsequently, Xu et al. (
Multi-Wavelength-Based Single Sensing System for Protein Recognition
The key to develop multi-wavelength-based single system is to provide diverse signal variations at different wavelengths, where this system can generate distinct response patterns to various analytes at an array of channels (Lu et al.,
Multi-Channel Sensors
Multi-channel sensors have attracted much more attention because they can extract multidimensional signals from an individual multifunctional sensor element, which is called “lab-on-a-molecule” or “lab-on-a-nanoparticle” (Wu et al.,
For dual-channel sensors, Ma et al. (
Figure 9

(A) FL variation images of G-QDs and Y-QDs with and without proteins under the UV-light irradiation. (B) PCA canonical score plot for identifying corresponding proteins. Reprinted from Ma et al. (
For triple-channel sensors, they are very popular and have been largely used to construct protein sensors based on different materials. Lu et al. (
The Liu group fabricated a triple-channel colorimetric sensor based on DNA-AuNP conjugates (A21-AuNPs) for protein discrimination (Mao et al.,
Figure 10

Schematic representation of the triple-channel A21-AuNPs for protein sensing and the produced colorimetric pattern. Reprinted from Mao et al. (
QDs are also applied for constructing multi-channel sensors by collecting the signal changes of one type of QDs at different channels. Wu et al. (
Then, Xu et al. (
Figure 11

(A) Workflow of a triple-channel sensor for differentiation of proteins. (B) Schematic illustration of protein binding-induced displacement of BPB. Reprinted from Xu et al. (
For quadruple-channel sensors, Li et al. (
Figure 12

Schematic representation of the plasma-assisted quadruple-channel sensing device for protein discrimination. Reprinted from Li et al. (
Multi-Band Emission Sensors
Multi-band emission sensors are sensors that perform discriminative sensing based on signal changes at different emission wavelengths. The Margulies group put forward the concept of combinatorial fluorescent molecular sensor which was obtained by introducing several fluorescent units with various emission bands and different recognition units into the same molecular structure. The binding of different analytes caused distinct changes at different wavelengths, consequently resulting in distinguishable signatures (Rout et al.,
Using the surfactant encapsulating and modulating effect, our group has fabricated a series of multi-wavelength-based cross-reactive sensors for protein identification by designing a fluorescent probe with multi-band emission (pyrene, perylene, etc.) and introducing surfactant aggregates to tune their fluorescence emission. In our first try, we prepared a binary fluorescent ensemble based on a neutral bispyrene-based fluorophore and cationic surfactant dodecyltrimethylammonium bromide (DTAB) assemblies (Fan et al.,
Figure 13

(A) Fluorescence emission spectra of the bispyrene probe in different concentrated DTAB solutions. (B) Recognition patterns for different types of proteins. Reprinted from Fan et al. (
In order to further identify the proteins belong to the same type, we developed a mini sensor array (Cao et al.,
Figure 14

(A) Recognition patterns for different types of metalloproteins. (B) PCA score plot for identifying metalloproteins at 0.5 μM. Reprinted from Zheng et al. (2017) with permission.
To check the feasibility of the multi-wavelength cross-reactive strategy in identifying both non-metalloproteins and metalloproteins, we have designed a dual-fluorophore probe (bispyrene-modified perylene derivative) to provide more emission bands and signals. The cationic CTAB assemblies could effectively regulate the fluorescence emission of this dual-fluorophore probe from pyrene monomer emission to pyrene monomer-perylene co-emission (Bo et al.,
In addition, our group also synthesized an amphiphilic cholic acid-modified pyrene derivative, and found that it could form spherical aggregates and emit multiple fluorescence emission bands in aqueous solution (Fan et al.,
Conclusions and Outlook
In this review, we focused on different optical sensor arrays for protein discrimination and their applications in real samples. The three strategies for constructing such sensor arrays including multi-element-based sensor arrays, environment-sensitive sensor arrays and multi-wavelength-based single sensing systems for protein discrimination were described in detail. Besides, we tried to explain the connections and differences among different strategies.
Each type of array has its own advantages and disadvantages. For a multi-element-based sensor array, a series of sensor elements are usually required, and sometimes the number of sensor elements is even more than the number of analytes, making such arrays more complicated and time-consuming in the process of construction and data collection. But the recognition ability of this type of sensor array is easy to improve by increasing the sensor elements. The environment-sensitive sensor array is constructed by adjusting pH, polarity, viscosity, etc., and the multi-wavelength-based single system is based on an array of channels or emission bands, resulting in less dependent on design and synthesis of various probes (only one probe) compared with multi-element-based sensor arrays. Moreover, the third strategy using one single sensor system could significantly decrease sample consumption and simplify the data collection process. By comparison, the three types of sensor arrays have their own drawbacks. The construction and sensing process of the first type of array is the most time-consuming and costly, the second type of array is the most environment-sensitive and the least expandable, and the third type has highest requirements for the molecule design and instruments.
Although these three types of array-based sensors are different, they are closely related. For example, quantum dots (QDs) are involved in all three types but play different roles. In the first type, a variety of QDs are mainly used as sensor elements. But the second type involves only one type of QDs and the sensor elements are constructed by changing pH and ionic strengths. For the third type, the simplest one, the discrimination is achieved by collecting the signal changes of one type of QDs at different channels. It seems to be repetitive and unreasonable, but they actually serve their respective classifications very well.
Up to now, multi-element-based sensor arrays for protein identification have been boomingly developed, especially arrays constructed by nanomaterials as building blocks. The ability to realize strong discrimination ability of this type of sensor arrays based on as few as sensor elements is the big challenge and the future development trend. There have been some reports that realized using only two or three elements to achieve high-throughput detection of proteins. The other two types of optical biosensors have been relatively slowly developed. The challenge for the second type of environment-sensitive ones is the deep understanding of photophysical properties of a particular probe on the environments and design of new structural and effective probes. The development for the third type of multiple-wavelength cross-reactive single-system is highly dependent on the molecular design, which makes this type of sensor array grow slowly. But these two types also have broad application prospects because of easy preparation and simple data collection process. Particularly, the third type is more attractive due to the easy data collection and less consumption of samples. The aid of supramolecular assemblies on modulating photophysical properties of fluorescent probes makes this strategy more feasible. This type of optical sensor arrays will become a hot trend for developing discriminative sensors for proteins and other analytes.
Statements
Author contributions
JF and LQ designed and wrote the manuscript. HH and LD revised the manuscript. All authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication.
Funding
The authors appreciate the financial support from National Natural Science Foundation of China (21972086), the Fundamental Research Funds for the Central Universities (GK202001005), and the Program of Introducing Talents of Discipline to Universities (B14041). We also acknowledge the support from The Youth Innovation Team of Shaanxi Universities, the Scientific and Technological Innovation Programs of Higher Education Institutions in Shanxi (201802098, 2019L0818, and 2020L0504), the College Student's Innovation Fund of Shanxi Province (2020496), and Taiyuan Normal University (CXCY2002).
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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Summary
Keywords
protein, sensor array, nanoparticles, amphiphilic aggregate, environment-sensitive system
Citation
Fan J, Qi L, Han H and Ding L (2020) Array-Based Discriminative Optical Biosensors for Identifying Multiple Proteins in Aqueous Solution and Biofluids. Front. Chem. 8:572234. doi: 10.3389/fchem.2020.572234
Received
13 June 2020
Accepted
14 October 2020
Published
04 November 2020
Volume
8 - 2020
Edited by
Zheng Li, Shenzhen University, China
Reviewed by
Tao Yu, North Carolina State University, United States; Hugo José Nogueira Pedroza Dias Mello, São Paulo State University, Brazil
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© 2020 Fan, Qi, Han and Ding.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Junmei Fan jmfan@tynu.edu.cnLiping Ding dinglp33@snnu.edu.cn
This article was submitted to Analytical Chemistry, a section of the journal Frontiers in Chemistry
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