Water-dispersed luminescent quantum dots for miRNA detection

Trends in Analytical Chemistry 111 (2019) 197e205

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Trends in Analytical Chemistry journal homepage: www.elsevier.com/locate/trac

Water-dispersed luminescent quantum dots for miRNA detection Olga A. Goryacheva a, b, Anastasiya S. Novikova a, Daniil D. Drozd a, Pavel S. Pidenko a, Tatiana S. Ponomaryeva a, Artem A. Bakal a, Pradyumna K. Mishra c, Natalia V. Beloglazova a, b, d, Irina Yu. Goryacheva a, * a

Department of General and Inorganic Chemistry, Chemistry Institute, Saratov State University, Astrakhanskaya 83, Saratov, 410012, Russia Centre of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, Ghent, 9000, Belgium c Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, 462001, India d Nanotechnology Education and Research Center, South Ural State University, 454080, Lenin Prospect 76, Chelyabinsk, 454080, Russia b

a r t i c l e i n f o

a b s t r a c t

Article history: Available online 3 January 2019

This review targets valuable insight into the application of water dispersed luminescent quantum dots (QDs) for detection of microRNA (miRNA). Recently, considerable efforts have been devoted to obtain QDs for biosensing and bioimaging. Quantum dots with bright stable photoluminescence, synthesized directly in the water phase, offered an unparalleled advantage for the assay development involving small size, high colloidal stability, and presence of groups for bioconjugation. In this review we have delineated the fundamental principles guiding the rational design, synthesis, and application of photoluminescent water-dispersed QDs. Diverse analysis methods for miRNA detection based on the photoluminescence, €rster resonance energy transfer and electrochemiluminescence energy electrochemiluminescence, Fo transfer with different enhancement strategies are discussed. © 2019 Elsevier B.V. All rights reserved.

Keywords: Quantum dots MicroRNA Photoluminescence Electrochemiluminescence €rster resonance energy transfer Fo Electrochemiluminescence energy transfer

1. Introduction MicroRNAs (mi-RNAs) are an abundant class of small noncoding RNAs, which consist of 18e25 nucleotides. These molecules are critical in many biological processes, including regulation of gene expression [1e3]. Targeting most protein-coding transcripts, miRNAs participate in various developmental and pathological processes in mammals [4]. They were first found in 1993 in transparent nematode C. elegans [5,6] and afterward in plants, animals and viruses. Up to now, more than 2500 miRNAs were identified in humans [7]. Mi-RNAs are considered to be promising biomarkers because dysregulation of their expression is correlated with the development and progress of many diseases. Up- or downregulation of the miRNAs expression affects cellular processes such as proliferation or apoptosis. This dysregulation correlates with the development and progress of a diverse range of chronic human ailments, including cancer [4,8]. The unique properties of miRNAs both complicate and simplify approaches for their detection. Small size, high sequence homology

* Corresponding author. E-mail address: [email protected] (I.Yu. Goryacheva). https://doi.org/10.1016/j.trac.2018.12.022 0165-9936/© 2019 Elsevier B.V. All rights reserved.

among family members and extremely low abundance in test samples have always posed great challenges for the development of any detection method [9,10]. On the other hand, their chemical stability, polyanionic nature, hybridizability, persistence length, extraordinary binding specificity, tolerance to chemical reactivity and virtually unlimited programmability by virtue of nucleotide sequence simplify and unify the operations for detection of miRNA in biological matrices [10,11]. Among different labels, luminescent semiconductor nanocrystals (quantum dots, QDs) [16e19] are widely used for individual [12,13] and multiple [10,14,15] miRNA detection. QDs' photostability allows the use of laser excitation and very long exposure, providing a high sensitivity for target detection [21]. Wide excitation and narrow emission spectra of QDs facilitate the simultaneous study of multiple probes. The use of QDs in multilabeling has been described for immunohistochemistry [22] and immunoassay [19,23]. QD-DNA conjugates [24,25] were obtained using the ligand exchange [26,27], streptavidin-biotin interaction [28] or EDC/NHS chemistry [29,30]. For the last twenty years the most popular QDs to apply in a (bio) chemical assay have been synthesized at a high temperature in organic solvents. These organic dispersed QDs need a water solubilization sand following multistep conjugation [16,31e34]. The most widely used hydrophilization approaches are a cap-layer exchange (for

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example with 3-mercaptopropionic acid [16] or dihydrolipoic acid [35]), encapsulation into polymer microspheres [36] or liposomes, and silanization [31,37]. These processes are multistep and complex; QDs obtained via the last two approaches are shelled with a thick hydrophilization layer. As mentioned above, miRNAs are small analytes, as well as single strand oligonucleotide sequences which are used as components of QD-DNA conjugates. Traditional QDs prepared via the conventional synthetic routes with thick protecting shells could influence hybridization processes or strand displacement. Additionally, a thick protecting layer of such QDs leads to a low efficiency of energy transfer to or from QD probes due to a relatively large separation distance between the energy donor and acceptor [38,39]. Last years some developments in synthesis and application of stable high-luminescent water-soluble QDs were published. Application of such QDs in (bio) chemical assay does not require any additional hydrophilization step(s). To the moment several surveys related to the QDs' application in miRNA assay were published. Russ Algar at al. presented an overview of various nanoparticles (including QDs) for DNA detection [40]. QDs' application for miRNA detection was summarized as parts of the reviews on optical or luminescence nanoparticle-based methods for the detection of miRNAs [21,41,42]. A review of the use of QDs for miRNA detection was published by the authors recently [43]. The presented study is the first one focused on the application of waterdispersed QDs for miRNA detection. The review speaks about the synthesis of water dispersed QDs and DNA-templated QDs and provides a systematical description of the methods based on watersoluble QDs for miRNA detection. 2. Water-dispersed luminescent QDs The increase of interest to apply of water-dispersed luminescent QDs in the assay is related with breaking of several new one-step and/or one-pot synthetic strategies to obtain stable bright QDs directly in water media. Oligonucleotide-functionalization of these QDs is usually realized via the traditional bioconjugation chemistry using DNA molecules with a 50 or 30 -end modified with amine, thiol or carboxyl groups. The most widely used water dispersed QDs for miRNA detection are CdTe nanocrystals, synthesized using different Te precursors. CdTe QDs capped with 3-mercaptopropionic acid (MPA) as stabilizing agent were synthesized using CdCl2 and air-stable Na2TeO3 as the Te source [44]. During the reaction NaBH4 reduces TeO2 3 to Te2, and the fresh Te2 reacts with Cd2þ to form CdTe nanocrystals with an average size of 3 nm [45]. The CdTe QDs were further conjugated with doxorubicin using EDC. The obtained conjugate could intercalate into the base pairs of the hybrid duplexes. Electrochemiluminescent (ECL) signal of these QDs was applied to monitor miRNAs from human prostate carcinoma (22Rv1) cell lysates [44]. Cheng et al. [46] worked with the CdTe QDs synthesized using the electrolysis method with a Te rod as a working electrode and meso-2,3- dimercaptosuccinic acid as a stabilizer [47]. Quenching of the ECL signal of these QDs by the Au nanoclusters (NCs) via ECL resonance energy transfer, ERET was sensitive to the presence of a model miRNA [46]. CdTe-QDs, stabilized with Nacetyl-L-cysteine, with the maximum fluorescence emission at 710 nm and the hydrodynamic size of 10 nm were synthesized by Shen et al. [48] using freshly prepared NaHTe as the Te source. This NaHTe was obtained via the reaction of tellurium powder with an excessive amount of sodium borohydride in water. Then, H2Te gas which was generated by the addition of H2SO4 was conducted into the solution containing N-acetyl-L-cysteine and CdCl2. To obtain QDs the reaction mixture was autoclaved.

To obtain QDs with a high quantum yield (QY) (up to 75%) Su et al. [26] used the core/shell CdTe/CdS structure. For CdTe core synthesis freshly prepared NaHTe solution was added to a CdCl2 solution in the presence of MPA. The mixture was subjected to a microway irradiation. For shelling, CdTe cores were added to a solution containing CdCl2, Na2S and MPA. Afterward, the surfacebound short-chain MPA molecules were substituted by thiolated DNA, and the probe was used as the energy donor in the pair with €rster resonance energy an organic quencher (BHQ2 dye) for the Fo transfer (FRET)-based detection of miRNA-21 in serum [26]. The ECL energy transfer between the thioglycolic acid capped CdSe QDs (the size of 3 nm) and the gold nanoparticles (Au NPs) was used for the DNA damage detection [49]. The oligonucleotideencapsulated Ag nanoclusters acted as the energy acceptor of the CdS QDs ECL, which leads to an effective ERET. The CdS QDs were prepared by mixing Cd(NO3)2 and Na2S in water, and heating the mixture at 70 C for 3 h [50]. Cd-free non-toxic MoS2 QDs was used as the source of the cathodic ECL with Ag-PAMAM NCs serving as the bifunctional tags for quenching and enhancing ECL of MoS2-reduced graphene oxide composites. MoS2 QDs with a diameter of 4.3 nm were synthesized using the hydrothermal method from a solution containing sodium molybdate and L-cysteine. With the change of excitation wavelength from 350 to 420 nm, the PL of MoS2 QDs shows a red shifting with the strongest emission at 442 nm under the excitation wavelength of 380 nm [51]. The QDs were applied for the detection of miRNA-21 in human serum. The near-infrared Ag2S QDs (the QY of 27%) was used by Miao et al. [52] in a DNA logic gate platform for miRNA diagnostics. The QDs were synthesized by adding Na2S solution to the mixture of cysteine and AgNO3 and heating the solution at 100 C for 4 h. The DNA e Ag2S QDs conjugates were obtained by coupling the Ag2S QDs with DNA probes at the presence of carboxyl group activation solution (EDC/NHS). The higher QY for Ag-based QDs was archived for the QDs containing AgInS (AIS) cores and AIS/ZnS core/shell structures. These QDs were produced by a precipitation technique. Up to 10e11 fractions of the size-selected QDs emitting in a broad color range from deep-red to bluish-green were isolated with the PLQY of ~47% and the size of ~2e3.5 nm [53]. The copper-doping of AIS QDs shifts the PL bands into the near IR spectral range from around 630 nme780 nm and therefore promotes the application of such QDs in biosensing. Decreasing of Cu inducing PL intensity was recovered by the deposition of a ZnS shell with the highest QY of 15% [54]. 3. Water-dispersed luminescent QDs with DNA as a template The new direction in the QD preparation is the DNA-templated synthesis of QDs, which was pioneered by the Kelley group in 2009 [55]. In 2018 the application of these QDs for DNA sensing was carefully reviewed by Wang et al. [38]. DNA-templated QDs are prepared via a one-step approach using DNA molecule as a template for the direct QD growth. Size and emission of the QDs could be tuned by using different DNA sequences or three-dimensional structures of RNA molecules [56,57]. DNA-QDs exhibit a high biocompatibility and low cytotoxicity, ensuring their applicability for biosensing and bioimaging [55,58]. A chimeric DNA molecule containing a phosphorothioate domain (ps) and a phosphate domain (po) is used as a template (Fig. 1) [38]. QDs are preferentially associated with the ps domain due to the high affinity of sulfur atom towards metal ions. The po domain remains free for biotargeting. Such scheme defines DNA-QD ratio in conjugate and does not contain any additional conjugation step. The DNA-QD ratio of 1:1 (monovalency) is preferable for controlled assembly and biological targeting. He et al. [57] using gel

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electrophoresis showed DNA-QDs contains 89% monovalent QDs and 11% bivalent QDs. Polyvalent DNA-QD probes could be constructed by DNA chemistry, for example via a co-polymerization of DNA-QDs and DNA aptamers [613]. Heterobivalent DNA-QDs were constructed using a po-ps-poDNA template for QD synthesis [59]. Different design of DNA-templated QD structures are presented in Fig. 1. An example of the synthesis of QD-aptamer polymers is presented in Fig. 2. For the DNA-templated CdTe QDs synthesis He at al [61]. and Li et al. [60] mixed CdCl2 and L-glutathione with freshly prepared NaHTe, and then added a chimeric DNA template solution. The small thiol-containing molecules (L-glutathione) were introduced as co-ligands to passivate the unoccupied surface of the metal atoms, and therefore to improve the stability and QY of the nanoparticles [38]. The reaction was conducted at 100 C. The QDs possess the absorption peak at 572 nm and the emission peak at 623 nm with the QY of 18% [58]. The synthesized CdTe QDs of 3.8 nm were used as energy donors in the FRET-based detection of miRNA-21 in total RNA extracted from HeLa, MCF-7, MDA-MB-231, and HEK-293 cells [57]. 4. Methods for detection of miRNA using water-dispersed QDs Two types of water-dispersed QDs luminescence e photoluminescence and electrochemiluminescence are used miRNA detection (Fig. 3). 4.1. Methods based on the QD photoluminescence measurement A DNA logic gate platform for miRNA detection is a simple heterogeneous analytical technique based on enzyme-free toehold exchange-mediated strand displacements [52]. The principle of measurement is given in Fig. 4. Near-infrared PL from the Ag2S QDs

199

was chosen as a signal output. The obtained signal is reversely proportional to the analyte concentration. The measured linear range was 1016 e 1011 M. A novel rotary biosensor based on v-free F0F1-ATPase and the pH-sensitive CdTe QDs for miRNA detection was developed [60]. Detection of miRNAs was based on the proton flux change induced by light-driven rotation of chromatophore. The hybridization reaction was indicated by changes in the PL intensity of QDs. The method was sensitive enough to detect miRNAs in 10 MCF-7 human breast cancer cells. 4.2. Methods based on FRET €rster (or fluorescence) resonance energy transfer (FRET) is a Fo non-radiative energy transfer from an excited donor chromophore (D) to an acceptor chromophore (A) in the ground state. The principal conditions for FRET are: (i) the energy of the electronically excited state of D must be higher than a possible energy level of A; (ii) D emission and A absorption must overlap; (iii) D and A should be in close proximity to each other (ca. 1e20 nm) [20,43]. For FRET miRNA detection, QDs can be used both as an energy donor and as an energy acceptor. The DNA-conjugated QDs were used as energy donors in a combination with the organic quencher BHQ2 labeled DNA sequences (energy acceptor) [26]. As FRET is very sensitive to the distance between D and A, in the absence of a target miRNA, the quencher-labeled DNA has almost no influence on the QDs PL in a solution. With the addition of the target miRNA, the “sandwich” hybrid was formed, the distance between energy donor and acceptor decreased and so QDs PL was quenched by BHQ2 via FRET (Fig. 5). The developed technique was able to detect miRNA-21 in 2% serum with the LOD of 100 fM. To increase the sensitivity of FRET-based detection different enhancement strategies could be applied. For the catalytic FRETbased detection of low-abundance miRNA molecules in live

Fig. 1. Schematic illustration of a DNA-templated QDs and its derivatives. (a) Chemical structure of a phosphorothioate linkage and a phosphate linkage of a chimeric DNA template for a QD synthesis. (b) Binding of a DNA-QD with a complementary DNA target or a specific protein target. (c) Schematic illustration of DNA-QD derivatives including a heterobivalent DNA-QD, a polyvalent DNA-QD, a ternary QDs assembly, and a GNP-QDs assembly. Reprinted from Ref. [38].

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Fig. 2. Schematic illustration of QD-aptamer polymers. (a) Preparation of a DNA-templated QD monomer and an aptamer monomer by hybridizing the DNA-QD and aptamer through overhangs. (b) Copolymerization of the QD monomer and the aptamer monomer into a QD aptamer polymer through the DNA-programmed hybridization chain reaction. Reprinted from Ref. [58].

Fig. 3. Methods for mi-RNA detection using water dispersed luminescent QDs.

cancer cells an Au NP - QD complex was constructed [57]. In this complex QDs act as energy donors, Au NPs - as energy acceptors. In the absence of a target miRNA the QDs PL is quenched by the Au NP located in a close proximity. In this strategy the target miRNA

serves as a catalyst for sequential disassembling of the multiple QDs from the centered Au NP through the entropy-driven DNA strand displacement reaction (Fig. 6). In the first strand displacement reaction the target miRNA binds to the end toehold, and displaces the

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Fig. 4. The principle of the Ag2S QDs-based NIR PL detection of miRNA. Reprinted from Ref. [52].

DNA-QD from the DNA linker. In the second strand displacement reaction the fuel DNA binds to the middle toehold, and displaces both the DNA - Au NP and the miRNA from the DNA linker. The released miRNA further participates in the next round of the displacements. The displacement of the DNA-QD results in the increasing distance between Au NP and QD, no FRET is possible, and the QDs PL is recovered [57]. Another FRET indicated the strand displacement reaction-based system is described by Luo et al. [61]. The authors developed a microRNA-catalyzed drug release system based on the DNAprogrammed Au NP - QD complex. A trace amount of the target miRNA-21 could specifically catalyze the two-step strand displacement reaction of the doxorubicin-loaded Au NP - QDs complex. As result the QDs PL enhanced providing a reliable feedback on the microRNA presence (Fig. 7). Authors showed this catalytic reaction could precede both in fixed cells and live cells with miRNA-21 overexpression. In cells the bound doxorubicin molecules could be efficiently released and translocated to cell nuclei. The Au NP e QDs - doxorubicin complex represents a promising platform for the accurate and effective cancer cell treatment, combining the miRNA-21 overexpression detection and the target drug release [61].

4.3. Methods based on ECL Chemiluminescence triggered by electrochemical processes (electrogenerated chemiluminescence, ECL), has emerged as a powerful signal generation mechanism due to its advantages, such as no need of any external light source, low background signal and high sensitivity [62,63]. The Bard group first employed QDs as an ECL label, which could generate an efficient and stable ECL signal during the potential cycling or pulsing [64,65]. As an example, the ECL system of a semiconductor nanocrystal/K2S2O8 and/or dissolved oxygen as an oxidizing agent could be mentioned. In this case the nanocrystals immobilized on an electrode surface would be reduced (CdS) by a charge injection, while the co-reactant S2O2 would be reduced to the strong oxidant SO 8 4 , and then  CdS could react with SO 4 giving the broad ECL emission peaked at ca. 500 nm [52]. The signal acquisition is accomplished by a chemical modification of the capture probes with QDs [66], or the formation of a QDs-containing film on the electrode surface [67]. ECL detection of miRNA was also reported in the assay formats, where the analytical signal depends on an amount of QDs. In this sensor CdTe QDs were conjugated with doxorubicin. The thiolated DNA probes are self-assembled onto the gold electrodes. The

Fig. 5. Schematic representation of the FRET-based nanosensor. The QDs-labeled DNA acts as an energy donor, the BHQ2-DNA e as an acceptor. Reprinted from Ref. [26].

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Fig. 6. Au NP - QDs nanoassembly for the catalytic FRET-based sensing of a miRNA. The miRNA molecule serves as a catalyst to disassemble the QDs from the Au NP with the aid of fuel DNA strands. Reprinted from Ref. [57].

Fig. 7. Mechanisms of the catalytic reaction programmed by the two-step strand displacement reactions. Reprinted from Ref. [61].

sensing surface was further incubated in a buffer solution containing the target miRNA to form the double-stranded duplexes. The doxorubicin-conjugated QDs were able to intercalate into the DNA/RNA hybrids (Fig. 8), resulting in the amplified ECL emission

due to their reactions with S2O2 8 or/and the dissolved oxygen. This increase in the ECL intensity is proportional to the amount of QDs which related to the concentration of the target miRNA in samples. This sensor does not require any labeling or conjugation [68].

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Fig. 8. Schematic representation of the ECL sensor Dox-QDs amplification platform. Reprinted from Ref. [68].

4.4. Methods based on ERET Electrochemiluminescence resonance energy transfer (ERET) is a non-radiative energy transfer from an excited donor chromophore, which came to the exited state via electrochemical reaction to an acceptor in the ground state, which has no excitation source and no interference from the scattering light. As any energy transfer process, ERET is distance-dependent. After the discovery of ERET in 2009 [69], ECL quenching has been demonstrated as an effective tool in biosensing [50]. As other energy transfer processes, ERET is sensitive to the distance between D and A. Similar to FRET the basic requirements for an efficient ERET are spectral overlapping of the ECL spectrum of D and the absorption spectrum of A as well as their space proximity [50]. ERET suppose heterogeneous electrode based assay format. In typical ERET procedure semiconductor NCs play a donor role and were attached to an electrode (glass carbon electrode [50]) surface together with molecular beacons. If these beacons contained a quencher (acceptor), in the presence of the target miRNA (and additionally labeled or not oligonucleotides) the beacon straightened up, increasing the distance between D and A, and thus decreasing the ERET probability. If no quencher was attached to the beacon, it bound to the oligonucleotide, added to the sample before the miRNA detection. The labeled with the quencher oligonucleotide and the target miRNA took part in the beacon hybridization. The hairpin structure opened up, and then the quencher appeared

to be in a close proximity to CdS NCs on the electrode surface. Upon the hybridization of 1.0 nM of the target miRNA the quenching efficiency of 88.2% for the ECL intensity was observed [50]. The same authors also demonstrated that Ag NCs have the dual ECL quenching effects. Ag NCs could not only quench the ECL emissions from CdS NCs by ERET, but also catalyze the electro-reduction reaction of K2S2O8 making ECL co-reactant greatly consumed near the electrode surface and thus leading to the obvious decrease in ECL intensity. Cheng et al. [46] used the CdTe nanocrystals as ERET donors and Au NCs - as acceptors. The CdTe nanocrystals were attached to the modified electrode surface where the hairpin DNA e Au NCs composite was also bound. The close proximity and strong interaction between the CdTe nanocrystals and the Au NCs led to the ECL quenching. MiRNA, if present, hybridized with the hairpin DNA (Fig. 9, bottom), the ECL emission signal was increased, but was still weak due to the ERET effect between the CdTe nanocrystals and the Au NCs at the relatively short distance. After the addition of the assistant DNA, the ligase could selectively ligate both of them on the strand of the hairpin DNA to form the long DNAeRNA heteroduplexes (Fig. 9, top). The long distance increased the ECL signal due to the inhibition of the ERET [46]. The distance-dependence of the ECL energy transfer between CdSe QDs as donor and Au NPs as acceptor was also used for control of DNA damage [51]. The table summarizes the selected photoluminescent QD-based assays for miRNA detection (Table 1).

Fig. 9. Schematic representation of the ERET-based nanosensors. CdTe QDs act as energy donor, DNA conjugated Au NC - as acceptor. Reprinted from Ref. [46].

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Table 1 Examples of mi-RNA detection using water-dispersed quantum dots. Method

QD type/size (nm)/lem (nm)

Capping agent

miRNA

Signal appearing

LOD

Linear range

Format

Real sample

Ref

PL

Ag2S/2/802

L-cysteine

miR-20a

12  1015 M

1016 to 1011 M

heta

no

[52]

PL

CdTe//535

multiplex logic gate platform light-driven rotation of d-free F0F1-ATPase BHQ2 as a quencher Dox-QDs intercalated into DNA/RNA hybrids

1.2  1018 mol

het

no

[60]

10 10 M 5.5 1015 M

1.2  1018 to 1.2  1013 mol 1015 to 108 M 1014 to 1.2 1012 M

hom het

[26] [68]

0.2  1015 M

1015 to 1010 M

hetss

serum, 2% Human prostate carcinoma cells 22Rv1, cervical cancer cells Hela serum no

[46] [50]

mir-145 b

FRET ECL

CdTe/CdS/3/580 CdTe/3.1

MPA MPA

ECL/ERET

MoS2/4.3/442

L-cysteine

ERET ERET a b c d

CdTe/5 CdS

DMSA

d

miRNA-21 miR-429 miR-200b let-7d miRNA-21 3 mi-RNAs model

Ag-PAMAM NCs as bifunctional tags Au NCs as a quencher Ag NCs as bifunctional tags

15

21.7  10

15

M

13

7

10 to 10 M 1014 to 1010 M

c

het het

[51]

het e heterogeneous. hom e homogeneous. MPA e 3-mercaptopropionic acid. DMSA - meso-2,3- dimercaptosuccinic acid.

5. Conclusions

Acknowledgments

Successful detection with miRNAs is likely to boost cancer diagnosis and prognosis in the future. Therefore, the method of miRNA detection requires high specificity and sensitivity with the potential of multiplexing. To address this analytical conundrum, advanced nano-materials with surface modifications have emerged as the methods of choice. However, several attempts in this particular area of research have not yet surpassed the proofof-principle stage. Moreover, most of these analytical methods have used fully synthetic or spiked samples to devise the assay technologies, such as quantitative RT-PCR, northern blotting, and microarrays, which are not ideal. Critical assessment of sample quality and usage of stringent controls often interferes with these types of assay validations. Nanotechnology-based methodologies explored for miRNA detection can be categorized broadly into three major groups: methods involving nanoparticles in solution, nanostructured surfaces, and a combination of nanomaterials with solid support. The majority of these is optical methods and involves Au NPs, Ag NCs, carbonaceous nano-materials or QDs. Altogether, water-dispersed QDs show significant promise as a new class of optical probes possessing high brightness, stability, and potential for multiplexing. Following unique characteristics of these QDs led to their application as PL label [70]:

The work was supported by the Russian Ministry of Science and Education, project 4.1063.2017/4.6; Russian Foundation for Basic Research, Indo-Russian Collaborative Project 17-53-49002.

- High PL QY and high resistance to photobleaching. - Large effective Stokes shifts (up to hundreds of nanometers). - Broad absorption spectra with large one-photon (ε ¼ 104e107 M1 cm1) absorption cross-sections. - Multiplexing capability. - Nanoscale scaffold for chemistry and functionalization. Over time, heavy-atom-free QDs were introduced and their properties matched or superseded those of CdSe-based core/shell structures. The alternatives to multistep procedures appeared by achieving semiconductor nanocrystal synthesis directly in water. Synthesis of nucleic acid templated QDs revokes even the necessity for QD bioconjugation. As an additional benefit, the small size of water-dispersed QDs minimizes their influence on the conjugated reagent properties. Therefore, water-dispersed QDs open up a new array of highly sensitive and intelligent sensing of a broad range of small biomolecules, including miRNAs and this could be the basis for the development of new QD based methods [71,72].

References [1] L. He, G.J. Hannon, MicroRNAs: small RNAs with a big role in gene regulation, Nat. Rev. Genet. 5 (2004) 522e531. [2] D.P. Bartel, C.Z. Chen, Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs, Nat. Rev. Genet. 5 (2004) 396e400. [3] M.V. Iorio, M. Ferracin, C.G. Liu, A. Veronese, R. Spizzo, S. Sabbioni, E. Magri, nard, J.P. Palazzo, A. Rosenberg, M. Pedriali, M. Fabbri, M. Campiglio, S. Me P. Musiani, S. Volinia, I. Nenci, G.A. Calin, P. Querzoli, M. Negrini, C.M. Croce, MicroRNA gene expression deregulation in human breast cancer, Cancer Res. 65 (2005) 7065e7070. [4] M. Ha, V.N. Kim, Regulation of microRNA biogenesis, Nat. Rev. Mol. Cell Biol. 15 (2014) 509e524. [5] R.C. Lee, R.L. Feinbaum, V. Ambros, The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14, Cell 75 (1993) 843e854. [6] B. Wightman, I. Ha, G. Ruvkun, Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans, Cell 75 (1993) 855e862. [7] A. Kozomara, S. Griffiths-Jones, MiR base: annotating high confidence MicroRNAs using deep sequencing data, Nucleic Acids Res. 42 (2014) D68eD73. [8] C. Blenkiron, L.D. Goldstein, N.P. Thorne, I. Spiteri, S.F. Chin, M.J. Dunning, , N.L. Barbosa-Morais, A.E. Teschendorff, A.R. Green, I.O. Ellis, S. Tavare C. Caldas, E.A. Miska, MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype, Genome Biol. 8 (2007) R214. [9] A.W. Wark, H.J. Lee, R.M. Corn, Multiplexed detection methods for profiling microRNA expression in biological samples, Angew. Chem. Int. Ed. 47 (2008) 644e652. [10] T. Tian, J. Wang, X. Zhou, A review: microRNA detection methods, Org. Biomol. Chem. 13 (2015) 2226e2238. [11] A. Banerjee, T. Pons, N. Lequeux, B. Dubertret, Quantum dotseDNA bioconjugates: synthesis to applications, Interface Focus 6 (2016) 20160064. [12] A. Banerjee, C. Grazon, B. Nadal, T. Pons, Y. Krishnan, B. Dubertret, Fast, efficient and stable conjugation of multiple DNA strands on colloidal quantum dots, Bioconjug. Chem. 26 (2015) 1582e1589. [13] H. Deng, Q. Liu, X. Wang, R. Huang, H. Liu, Q. Lin, X. Zhou, D. Xing, Quantum dots-labeled strip biosensor for rapid and sensitive detection of microRNA based on target-recycled nonenzymatic amplification strategy, Biosens. Bioelectron. 87 (2017) 931e940. [14] L. Fan, H. Qi, J. Teng, B. Su, H. Chen, C. Wang, Q. Xia, Identification of serum miRNAs by nano-quantum dots microarray as diagnostic biomarkers for early detection of non-small cell lung cancer, Tumor Biol. 37 (2016) 7777e7784. [15] X. Qiu, N. Hildebrandt, Rapid and multiplexed MicroRNA diagnostic assay € rster resonance energy transfer, ACS Nano 9 (8) using quantum, dot-based fo (2015) 8449e8457. [16] W.C. Chan, S. Nie, Quantum dot bioconjugates for ultrasensitive nonisotopic detection, Science 281 (1998) 2016e2018. [17] J.K. Jaiswal, H. Mattoussi, J.M. Mauro, S.M. Simon, Long-term multiple color imaging of live cells using quantum dot bioconjugates, Nat. Biotechnol. 21 (2003) 47e51.

O.A. Goryacheva et al. / Trends in Analytical Chemistry 111 (2019) 197e205 [18] I.Y. Goryacheva, P. Lenain, S. De Saeger, Nanosized labels for rapid immunotests: new trends and developments, Trends Anal. Chem. 46 (2013) 30e46. [19] N.V. Beloglazova, E.S. Speranskaya, A. Wu, Z. Wang, M. Sanders, V. Goftman, D. Zhang, I.Yu. Goryacheva, S. De Saeger, Novel multiplex fluorescent immunoassays based on quantum dot nanolabels for mycotoxins determination, Biosens. Bioelectron. 62 (2014) 59e65. [20] O.A. Goryacheva, N.V. Beloglazova, A.M. Vostrikova, M.V. Pozharov, €rster resonance A.M. Sobolev, I. Yu, Goryacheva Lanthanide-to-quantum dot Fo energy transfer (FRET): application for immunoassay, Talanta 164 (2017) 377e385. [21] M. La, L. Liu, B.B. Zhou, Nanomaterials-based fluorimetric methods for microRNAs detection, Materials 8 (2015) 2809e2829. [22] M. Stroh, J.P. Zimmer, D.G. Duda, T.S. Levchenko, K.S. Cohen, E.B. Brown, D.T. Scadden, V.P. Torchilin, M.G. Bawendi, D. Fukumura, R. K Jain, Quantum dots spectrally distinguish multiple species within the tumor milieu in vivo, Nat. Med. 11 (2005) 678e682. [23] N.V. Beloglazova, A. Foubert, A. Gordienko, M.D. Tessier, T. Aubert, E. Drijvers, I. Goryacheva, Z. Hens, S. De Saeger, Sensitive QD@SiO2-based immunoassay for triplex determination of cereal-borne mycotoxins, Talanta 160 (2016) 66e71. [24] J.H. Kim, D. Morikis, M. Ozkan, Adaptation of inorganic quantum dots for stable molecular beacons, Sensor. Actuator. B Chem. 102 (2004) 315e319. [25] F. Patolsky, R. Gill, Y. Weizmann, T. Mokari, U. Banin, I. Willner, Lighting-up the dynamics of telomerization and DNA replication by CdSeeZnS quantum dots, J. Am. Chem. Soc. 125 (2003) 13918e13919. [26] S. Su, J. Fan, B. Xue, L. Yuwen, X. Liu, D. Pan, C. Fan, L. Wang, DNA-conjugated quantum dot nanoprobe for high-sensitivityfluorescent detection of DNA and micro-RNA, ACS Appl. Mater. Interfaces 6 (2014) 1152e1157. [27] D. Zhou, J.D. Piper, C. Abell, D. Klenerman, D.J. Kang, L. Ying, Fluorescence resonance energy transfer between a quantum dot donor and a dye acceptor attached to DNA, Chem. Commun. 38 (2005) 4807e4809. [28] J. Sharma, Y. Ke, C. Lin, R. Chhabra, Q. Wang, J. Nangreave, Y. Liu, H. Yan, DNAtile-directed self-assembly of quantum dots into two-dimensional nanopatterns, Angew. Chem. Int. Ed. 47 (2008) 5157e5159. [29] J. Lee, S.U. Moon, Y.S. Lee, B.A. Ali, A.A. Al-Khedhairy, D. Ali, J. Ahmed, A.M. Al Salem, S. Kim, Quantum dot-based molecular beacon to monitor intracellular microRNAs, Sensors 15 (2015) 12872e12883. [30] D. Zhou, L. Ying, X. Hong, E.A. Hall, C. Abell, D. Klenerman, A compact functional quantum Dot-DNA conjugate: preparation, hybridization, and specific label-free DNA detection, Langmuir 24 (2008) 1659e1664. [31] M. Bruchez, M. Moronne, P. Gin, S. Weiss, A.P. Alivisatos, Semiconductor nanocrystals as fluorescent biological labels, Science 281 (1998) 2013e2016. [32] I.L. Medintz, H.T. Uyeda, E.R. Goldman, H. Mattoussi, Quantum dot bioconjugates for imaging, labeling and sensing, Nat. Mater. 4 (2005) 435e446. [33] J. Zhou, Y. Yang, C.Y. Zhang, Toward biocompatible semiconductor quantum dots: from biosynthesis and bioconjugation to biomedical application, Chem. Rev. 115 (2015) 11669e11717. [34] A. Foubert, N.V. Beloglazova, A. Rajkovic, B. Sas, A. Madder, I.Y. Goryacheva, S. De Saeger, Bioconjugation of quantum dots: review & impact on future application, Trends Anal. Chem. 83 (2016) 31e48. [35] A.R. Clapp, E.R. Goldman, H. Mattoussi, Capping of CdSeeZnS quantum dots with DHLA and subsequent conjugation with proteins, Nat. Protoc. 1 (2006) 1258e1266. [36] E.S. Speranskaya, N.V. Beloglazova, P. Lenain, S. De Saeger, Z. Wang, S. Zhang, Z. Hens, D. Knopp, D. V Potapkin, I.Y. Goryacheva, Polymer-coated fluorescent CdSe-based quantum dots for application in immunoassay, Biosens. Bioelectron. 53 (2014) 225e231. [37] V.V. Goftman, T. Aubert, R. Van Deun, N.V. Beloglazova, Z. Hens, S. De Saeger, I.Y. Goryacheva, Synthesis, modification, bioconjugation of silica coated fluorescent quantum dots and their application for mycotoxin detection, Biosens. Bioelectron. 79 (2016) 476e481. [38] G. Wang, Z. Li, N. Ma, Next-generation DNA-functionalized quantum dots as biological sensors, ACS Chem. Biol. 13 (2018) 1705e1713. [39] N. Hildebrandt, C.M. Spillmann, W.R. Algar, T. Pons, M.H. Stewart, E. Oh, K. Susumu, S.A. Diaz, J.B. Delehanty, I.L. Medintz, Energy transfer with semiconductor quantum dot bioconjugates: a versatile platform for biosensing, energy harvesting, and other developing applications, Chem. Rev. 117 (2017) 536e711. [40] W. Russ Algar, M. Massey, U.J. Krull, The application of quantum dots, gold nanoparticles and molecular switches to optical nucleic-acid diagnostics, Trends Anal. Chem. 28 (2009) 292e306. [41] A.A. Jamali, M. Pourhassan-Moghaddam, J. Ezzati, N. Dolatabadi, Y. Omidi, Nanomaterials on the road to miRNA detection with optical and electrochemical nanobiosensors, Trends Anal. Chem. 55 (2014) 24e42. [42] J. Zhang, D. Cui, Nanoparticle-based optical detection of MicroRNA, Nano Biomed. Eng. 5 (2013) 1e10. [43] O.A. Goryacheva, P.K. Mishra, I.Y. Goryacheva, Luminescent quantum dots for miRNA detection, Talanta 179 (2018) 456e465. [44] Y. Chen, B.Y. Jiang, Y. Xiang, Y.Q. Chai, R. Yuan, Aptamer-based highly sensitive electrochemiluminescent detection of thrombin via nanoparticle layer-bylayer assembled amplification labels, Chem. Commun. 47 (2011) 7758e7760. [45] H. Bao, E. Wang, S. Dong, One-pot synthesis of CdTe nanocrystals and shape control of luminescent CdTeecystine nanocomposites, Small 2 (2006) 476e480. [46] Y. Cheng, J. Lei, Y. Chen, H. Ju, Highly selective detection of micro RNA based on distance-dependent electrochemiluminescence resonance energy transfer

[47]

[48]

[49]

[50]

[51]

[52]

[53]

[54]

[55]

[56]

[57]

[58]

[59]

[60] [61]

[62] [63]

[64]

[65]

[66]

[67]

[68]

[69]

[70]

[71]

[72]

205

between CdTe nanocrystals and Au nanoclusters Biosens, Bioelectron 51 (2014) 431e436. C.W. Ge, M. Xu, J. Liu, J.P. Lei, H.X. Ju, Facile synthesis and application of highly luminescent CdTe quantum dots with an electrogenerated precursor, Chem. Commun. 4 (2008) 450e452. Y. Shen, N. Zhang, Y. Sun, W.W. Zhao, D. Ye, J.J. Xu, H.Y. Chen, Activatable QDbased near-infrared fluorescence probe for sensitive detection and imaging of DNA, ACS Appl. Mater. Interfaces 9 (2017) 25107e25113. L. Lu, J. Wu, M. Li, T. Kang, S. Cheng, Detection of DNA damage by exploiting the distance dependence of the electrochemiluminescence energy transfer between quantum dots and gold nanoparticles, Microchim. Acta 182 (2015) 233e239. Y.Y. Zhang, Q.M. Feng, J.J. Xu, H.Y. Chen, Silver nanoclusters for high-efficiency quenching of CdS nanocrystals electrochemisluminescence and sensitive detection of microRNA, ACS Appl. Mater. Interfaces 7 (2015) 26307e26314. J.T. Cao, F.R. Liu, F. Hou, J. Peng, S.W. Ren, Y.M. Liu, Cathodic electrochemiluminescence behaviour of MoS2 quantum dots and its biosensing for microRNA-21, Analyst 143 (2018) 3702e3707. P. Miao, Y. Tang, B. Wang, F. Meng, Near-infrared Ag2S quantum dots-based DNA logic gate platform for miRNA diagnostics, Anal. Chem. 88 (2016) 7567e7573. A. Raevskaya, V. Lesnyak, D. Haubold, V. Dzhagan, O. Stroyuk, N. Gaponik, D.R.T. Zahn, A. Eychmüller, A fine size selection of brightly luminescent watersoluble AgInS and AgInS/ZnS quantum dots, J. Phys. Chem. C 121 (2017) 9032e9042. A. Raevskaya, O. Rozovik, A. Novikova, O. Selyshchev, O. Stroyuk, V. Dzhagan, I. Goryacheva, N. Gaponik, D.R.T. Zahnd, A. Eychmuller, Luminescence and photoelectrochemical properties of size-selected aqueous copper-doped AgeIneS quantum dots, RSC Adv. 8 (2018) 7550e7557. N. Ma, E.H. Sargent, S.O. Kelley, One-step DNA-programmed growth of luminescent and biofunctionalized nanocrystals, Nat. Nanotechnol. 4 (2009) 121e125. G. Tikhomirov, S. Hoogland, P.E. Lee, A. Fischer, E.H. Sargent, S.O. Kelley, DNAbased programming of quantum dot valency, self-assembly and luminescence, Nat. Nanotechnol. 6 (2011) 485e490. X. He, T. Zeng, Z. Li, G. Wang, N. Ma, Catalytic molecular imaging of MicroRNA in living cells by DNA-programmed nanoparticle disassembly, Angew. Chem. Int. Ed. 55 (2016) 3073e3076. Z. Li, X. He, X. Luo, L. Wang, N. Ma, DNA-programmed quantum dot polymerization for ultrasensitive molecular imaging of cancer cells, Anal. Chem. 88 (2016) 9355e9358. W. Wei, X. He, N. Ma, DNA-templated assembly of a heterobivalent quantum dot nanoprobe for extra- and intracellular dual-targeting and imaging of live cancer cells, Angew. Chem. Int. Ed. 53 (2014) 5573e5577. J.Y. Liao, J.Q. Yin, J.C. Yue, A novel biosensor to detect micro RNAs rapidly, Journal of Sensors (2009) 6. Article ID 671896. X. Luo, Z. Li, G. Wang, X. He, X. Shen, Q. Sun, L. Wang, R. Yue, N. Ma, MicroRNAcatalyzed cancer therapeutics based on DNA-programmed nanoparticle complex, ACS Appl. Mater. Interfaces 9 (2017) 33624e33631. M.M. Richter, Electrochemiluminescence (ECL), Chem. Rev. 104 (2004) 3003e3036. P. Wu, X. Hou, J.-J. Xu, H.-Y. Chen, Electrochemically generated versus photoexcited luminescence from semiconductor nanomaterials: bridging the valley between two worlds, Chem. Rev. 114 (2014) 11027e11059. Z. Ding, B.M. Quinn, S.K. Haram, L.E. Pell, B.A. Korgel, A.J. Bard, Electrochemistry and electrogenerated chemiluminescence from silicon nanocrystal quantum dots, Science 296 (2002) 1293e1297. G. Jie, B. Liu, H. Pan, J.-J. Zhu, H.-Y. Chen, CdS nanocrystal-based electrochemiluminescence biosensor for the detection of low-density lipoprotein by increasing sensitivity with gold nanoparticle amplification, Anal. Chem. 79 (2007) 5574e5581. H.P. Huang, J.J. Zhu, DNA aptamer-based QDs electrochemiluminescence biosensor for the detection of thrombin, Biosens. Bioelectron. 25 (2009) 927e930. J. Wang, Y. Shan, W.W. Zhao, J.J. Xu, H.Y. Chen, Gold nanoparticle enhanced electrochemiluminescence of CdS thin films for ultrasensitive thrombin detection, Anal. Chem. 83 (2011) 4004e4011. Y. Chen, Y. Xiang, R. Yuan, Y. Chai, Intercalation of quantum dots as the new signal acquisition and amplification platform for sensitive electrochemiluminescent detection of microRNA, Anal. Chim. Acta 891 (2015) 130e135. Y. Shan, J.-J. Xu, H.-Y. Chen, Distance-dependent quenching and enhancing of electrochemiluminescence from a CdS:Mn nanocrystal film by Au nanoparticles for highly sensitive detection of DNA, Chem. Commun. 8 (2009) 905e907. I.Y. Goryacheva, E.S. Speranskaya, V.V. Goftman, D. Tang, S. De Saeger, Synthesis and bioanalytical applications of nanostructures multiloaded with quantum dots, Trends Anal. Chem. 66 (2015) 53e62. K. Zhang, S. Lv, Z. Lin, D. Tang, CdS:Mn quantum dot-functionalized g-C3N4 nanohybrids as signal-generation tags for photoelectrochemical immunoassay of prostate specific antigen coupling DNAzyme concatamer with enzymatic biocatalytic precipitation, Biosens. Bioelectron. 95 (2017) 34e40. Z. Qiu, J. Shu, Y. He, Z. Lin, K. Zhang, S. Lv, D. Tang, CdTe/CdSe quantum dotbased fluorescent aptasensor with hemin/G-quadruplex DNzyme for sensitive detection of lysozyme using rolling circle amplification and strand hybridization, Biosens. Bioelectron. 87 (2017) 18e24.