# Use of semiconductor nanocrystals to encode microbeads for multiplexed analysis of biological samples

Mikhail A Berestovoy, Regina S Bilan, Victor Krivenkov, Igor Nabiev, Alyona Sukhanova

► To cite this version:

Mikhail A Berestovoy, Regina S Bilan, Victor Krivenkov, Igor Nabiev, Alyona Sukhanova. Use of semiconductor nanocrystals to encode microbeads for multiplexed analysis of biological samples. Journal of Physics: Conference Series, 2017, International Symposium Physics, Engineering and Technologies for Bio-Medicine, 784, pp.012012. 10.1088/1742-6596/784/1/012012. hal-03036049

HAL Id: hal-03036049

https://hal.science/hal-03036049

Submitted on 2 Dec 2020

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
PAPER • OPEN ACCESS

# Use of semiconductor nanocrystals to encode microbeads for multiplexed analysis of biological samples

To cite this article: Mikhail A Berestovoy et al 2017 *J. Phys.: Conf. Ser.* **784** 012012

View the [article online](#) for updates and enhancements.

## Related content

- Thomas-Fermi model of electronic screening in semiconductor nanocrystals
  D. Ninno, F. Trani, G. Cantele et al.

- Spectral Fingerprints of Clusters of Microlasers in Aqueous Phase
  Michael Himmelhaus

- Collagen Micro-Flow Channels as an for *In vitro Blood-Brain Barrier Model*
  Katsuya Shibata, Hideyuki Terazono, Akihiro Hattori et al.

<figure><img src="image_2.png" /></figure>

IOP ebooks™

Bringing together innovative digital publishing with leading authors from the global scientific community.

Start exploring the collection-download the first chapter of every title for free.
# Use of semiconductor nanocrystals to encode microbeads for multiplexed analysis of biological samples

Mikhail A Berestovoy¹#, Regina S Bilan¹#, Victor Krivenkov¹, Igor Nabiev¹,² and Alyona Sukhanova¹,²*

¹Laboratory of Nano-Bioengineering, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Moscow, Russian Federation,

²Laboratoire de Recherche en Nanosciences, LRN - EA4682, Université de Reims Champagne-Ardenne, Reims, France.

*These authors contributed equally to the study.

E-mail: alyona.sukhanova@univ-reims.fr

**Abstract.** Microbeads encoded with semiconductor quantum dots (QDs) are suitable tools for multiplexed analyses of various biological markers using flow cytometry. We have prepared a panel of microbeads encoded with QDs of different colors emitting with different luminescence intensities using the layer-by-layer deposition technique, which consists in layering of alternately charged polyelectrolytes and negatively charged QDs onto the surface of microbeads. This method allows QDs to be separated with one or several polymer layers in order to prevent Förster resonance energy transfer (FRET) and the resultant quenching of QD fluorescence in multicolor microbeads.

## 1. Introduction

In recent years, interest in optically encoded microbeads has been growing due to their potential applications in medical diagnostics [1]. Microbeads can be encoded with either organic fluorophores or semiconductor quantum dots (QDs) [2–6]. The use of microbeads encoded with organic fluorophores with different fluorescence maxima requires complex equipment with multiple excitation lasers for decoding, which complicates the analysis and increases the cost of instrumentation. QDs constitute a new class of fluorophores that have a number of advantages over routinely used fluorescent organic dyes, such as a high brightness, resistance to photobleaching, a wide excitation spectrum, and a narrow emission spectrum (Figure 1) [7, 8]. The unique optical characteristics of QDs make it possible to use them in multiplexed analyses, as well as in multicolor imaging [9], because QDs of different colors can be simultaneously excited using a single radiation source, whereas their fluorescence peaks can be effectively separated and detected in different channels of a flow cytometer. Therefore, multiplexed analysis by means of flow cytometry using QD-encoded microbeads is easy to perform and does not require sophisticated equipment.

<figure><img src="image_3.png" /></figure>
<figure><img src="image_4.png" /><figcaption>**Figure 1.** Fluorescent semiconductor nanocrystals of different sizes simultaneously excited using a single light source (http://lnbe.mephi.ru/ru).</figcaption></figure>

A number of approaches have been designed for engineering QD-encoded microparticles: embedding of QDs into the microbeads during the manufacturing [3], incorporation of QDs into pores of swollen microbeads, [2, 4], doping of mesoporous microbeads with QDs [5], the concentration-controlled flow-focusing technique [6], and layer-by-layer deposition [10]. By using several colors of QDs and several intensity levels, it is theoretically possible to create thousands or even millions of individual optical codes [2].

In this study, we have prepared a panel of microbeads encoded with QDs of different colors at different luminescence intensity levels using the layer-by-layer deposition technique, which consists in layering of alternately charged polyelectrolytes and negatively charged QDs onto the surface of microbeads. We established the number of QDs that was adsorbed onto the microbeads and investigated some physicochemical aspects of electrostatic adsorption of water-soluble negatively charged QDs onto a positively charged microbead surface. Fluorescence lifetime measurements were used for investigation of FRET between QDs in the solution and within QD-encoded microbeads. The technique of optical encoding developed in this study makes it possible to fabricate various multicolor microbead populations for multiplexed flow-cytometry analysis.

## 2. Materials and Methods

### 2.1 Preparation and characterization of water-soluble QDs

CdSe/ZnS core/shell QDs [7] with fluorescence maxima at 508, 590, and 640 nm and CdSe/ZnS/CdS/ZnS multishell QDs [9] were synthesized and kindly provided by Dr. Pavel Samokhvalov (Laboratory of Nano-Bioengineering, Moscow Engineering Physics Institute, Moscow, Russia). Originally water-insoluble QDs coated with trioctylphosphine oxide (TOPO) were solubilized by replacing TOPO with D,L-cysteine [11] and subsequently replacing the cysteine with derivatives of polyethylene glycol containing thiol and carboxyl terminal groups (SH-(PEG)₁₂-COOH, Thermo Fisher Scientific, USA) as described earlier [12]. The QD concentrations were determined from their extinction spectra at the positions of the first excitonic maxima [13]. The concentration of multishell QDs was estimated from the experimental values of molar extinction coefficient and molecular weight (100,000 g/(mol·cm) and 92,600 g/mol, respectively) (data not shown). The hydrodynamic sizes of water-soluble QDs were determined by dynamic light scattering measurements using a Zetasizer NanoZS analyzer (Malvern, UK).

### 2.2 Preparation of QD-encoded microbeads

Optical encoding of microbeads with QDs was performed using the adapted procedure of layer-by-layer deposition of alternately charged polymer layers and water-soluble QDs described in our
previous studies (Figure 2) [14, 15]. According to the adapted protocol, 3·10⁷ carboxylated melamine resin microbeads with a diameter of 4.08 µm (Microparticles GmbH, Berlin, Germany) were suspended in 0.5 ml of ultrapure water and mixed with 0.5 ml of 2 mg/ml poly(allylamine hydrochloride) (PAH, Mw = 15,000 Da, Sigma-Aldrich, USA) dissolved in 0.5 M NaCl. The suspension was sonicated and incubated while shaking for 20 min; then, the microbeads were washed from excess polymer by triple centrifugation (2000g for 5 min) and resuspension in ultrapure water. For deposition of the next polymer layer, the microbeads were resuspended in 0.5 ml of ultrapure water and mixed with 0.5 ml of 2 mg/ml poly(sodium 4-styrensulfonate) (PSS, Mw = 70,000 Da, Sigma-Aldrich, USA) dissolved in 0.5 M NaCl. As with the first layer, the suspension was sonicated and incubated while shaking for 20 min, and the microbeads were washed by triple centrifugation and resuspension in ultrapure water. The procedure of polymer deposition and washing was repeated until five alternately charged polymer layers were formed on the microbead surface, the outer layer consisting of positively charged PAH. Then, the microbeads were resuspended in 100 µl of ultrapure water, and various amounts (from 0.4 to 146 µg) of negatively charged water-soluble QDs were added while stirring the suspension. The mixture was incubated while shaking for 20 min, after which the microbeads were washed by three cycles of centrifugation and resuspension. For preparation of single-color microbeads, the next stage was the deposition of five layers of alternately charged polymers, as described above. In the case of two- or three-color microbeads, the deposition of QDs of different colors was alternated with deposition of positively charged PAH layers, after which five alternately charged polymer layers were deposited. The resultant encoded microbeads were stored at 4°C in the dark.

<figure><img src="image_5.png" /><figcaption>**Figure 2.** The method of layer-by-layer deposition [10] was used to obtain a population of microbeads encoded with QDs with different fluorescence peaks and fluorescence intensities: the surface of microbeads was successively coated with layers of differently charged polyelectrolytes and negatively charged QDs.</figcaption></figure>

## 2.3 Analysis of photoluminescence properties

The fluorescence spectra of all samples were measured using an Infinite 200 PRO multimode reader (TECAN, Switzerland). The fluorescence decay times of QDs and QD-encoded microbeads were measured by means of a specially designed experimental setup. All the samples were excited with the use of a Tsunami pulse laser (Spectra Physics) (wavelength, 395 nm; pulse duration, 300 fs; pulse repetition rate, 8 MHz; pulse energy, 0.5 nJ). The photoluminescent signal from a sample was collected with an optical condenser and supplied to a monochromator, which was adjusted to the photoluminescence maxima of QDs. The signal from the detector (an avalanche photodiode) was analyzed using a PicoHarp time-correlated single photon counting (TCSPC) system (PicoQuant) with a set resolution of 256 ps.

## 2.4 Flow cytometry
QD-encoded microbeads were analyzed with the use of a FACSCanto flow cytometer (Becton Dickinson, USA). The three-color spectral code of the microbeads was excited with a blue laser (488 nm), and the fluorescence intensity was analyzed in three channels: FITC (530/30 nm), PE (575/25 nm), and PerCP (695/40 nm). The data were processed using the FACSDiva software (Becton Dickinson, USA).

## 2.5 Fluorescence microscopy

For studying the fluorescence of the QD-encoded microbeads, we used a Carl Zeiss Axio Scope A1 fluorescent microscope (Carl Zeiss, Germany). Before the experiment, QD-encoded microbead samples were mixed with a 20% glycerol solution and fixed on microscope slides. Imaging of the specimens was performed with the use of two optical filters, FITC (excitation wavelength, 495 nm; emission wavelength, 520 nm) and Alexa Fluor 568 (excitation wavelength, 568 nm; emission wavelength, 593 nm), and a Zeiss N-achroplan 40×/0.65 Ph2 lens. Image processing was performed using the ZEN2012 SP1 software (blue edition) (Carl Zeiss, Germany).

## 3. Results and Discussion

The layer-by-layer deposition technique for optical encoding of microbeads consists in applying layers of alternately charged polyelectrolytes and negatively charged QDs on the surface of microbeads. Polystyrene sulfonate (PSS) and polyallylamine (PAH) contain sulfo and amino groups ensuring the formation of multiple salt bonds between the polymers. For layering the polymers, preliminarily carboxylated microbeads are incubated with PAH to form a positively charged polymer layer on their surface. Then, excess PAH is removed from the solution, and negatively charged PSS is added. The layering is repeated until five polymer layers, the outer layer consisting of PAH, are formed. Then, the microbeads are incubated in the presence of negatively charged QDs carrying carboxyl groups on their surface. The QDs are electrostatically adsorbed onto the microbeads and form their optical code. Finally, five additional polymer layers are deposited onto the microbeads to give them stability.

Populations of monicolor microbeads encoded with QDs with fluorescence maxima at 508, 590, and 640 nm were studied in detail using flow cytometry. The range of fluorescence was analyzed in different channels of the flow cytometer (Figure 3). Fluorescence of microbeads encoded with QDs was excited using a single light source (a laser with a wavelength of 488 nm). Microbeads encoded with QDs had a high level of florescence and were detected at a high resolution.

<figure><img src="image_6.png" /><figcaption>**Figure 3.** Histograms of populations of microbeads encoded with QDs of different colors. The range of fluorescence analyzed in different channels of the flow cytometer.</figcaption></figure>
We estimated the maximum number of adsorbed QDs on the surface of microbeads. For this purpose, we compared the absorbance spectra of QDs in the stock solution and in the supernatant after incubation with microbeads. From the values of molecular weight and emission maximum of QDs, we calculated that number of QDs adsorbed on the surface of a single microbead, 4.08 µm in diameter, is $1.8-2 \cdot 10^6$.

We performed fluorescence lifetime measurements of QDs in the solution and the same QDs adsorbed on microbeads. The photoluminescence decays of QDs emitting at 508 nm ($QDs_{508}$) in the solution and those adsorbed on microbeads are shown in Figure 4. The decay was significantly faster for QDs adsorbed on microbeads than for QDs in the solution. Specifically, adsorption onto microbeads shortened the decay time of $QD_{508}$ fluorescence from 16.1 to 5.1 ns. This may have been accounted for by FRET between QDs [16] or specific influence of PAH, which interacts with functional groups on the QD shell surface.

<figure><img src="image_7.png" /><figcaption>**Figure 4.** Fluorescence lifetime of $QDs_{508}$ in the solution and those adsorbed on microbeads.</figcaption></figure>

In multi-color QD-encoded microbeads, distance-dependent optical effects, such as FRET and photon reabsorption, may occur, affecting the resultant relative levels of the QD fluorescence intensity [6]. A way to reduce these optical effects is to spatially separate QDs of different colors, so that the distance between them is larger than the Förster energy transfer radius (5–8 nm for QDs) [17]. Furthermore, homo-FRET within a monochromatic QD population may occur due to distribution of QD sizes within the population and, hence, broadening of their fluorescence peak [16]. An overlap between the absorbance and emission spectra of the QD population leads to quenching of the blue side and enhancement of the red side of the photoluminescence peak, causing a red shift of the photoluminescence spectrum.

In order to prevent FRET between two QD populations, we spatially separated them with one or several polymer layers during the encoding process. We prepared single-color microbeads encoded with $QDs_{508}$ (1) and two types of bicolor microbeads encoded with $QDs_{508}$ and $QDs_{590}$ that are spatially separated from each other by one (2) or three (3) polymer layers. The decay times of the samples were measured upon excitation at 508 nm (Table 1). All the three samples were characterized by comparable decay times of about 8 ns, which were almost independent of the number of polymer layers between two types of QDs and were considerably shorter than that in the $QD_{508}$ solution (16 ns). If there were to be FRET, the decay times in cases (2) and (3) would be shorter than in case (1). However, reduction of decay time was not observed in these samples, which confirms the absence of
FRET. This result has allowed us to use an effective strategy of FRET prevention in preparing multi-color microbeads with a hundred of optical codes.

<table><caption>**Table 1.** The average decay time ($t_{avr}$) values for QDs$_{508}$ in a solution, single-color microbeads encoded with QDs$_{565}$, and two types of bicolor microbeads encoded with QDs$_{508}$ and QDs$_{590}$ spatially separated by one and three polymer layers, respectively.</caption><thead><tr><th rowspan="2">Sample</th><th rowspan="2">QDs<sub>508</sub><br>in<br>solution</th><th rowspan="2">Single-color<br>QD<sub>508</sub>-encoded<br>microbeads</th><th colspan="2">Bicolor microbeads encoded with<br>QDs<sub>508</sub> and QDs<sub>590</sub> separated by:</th></tr><tr><th>one polymer<br>layer</th><th>three polymer<br>layers</th></tr></thead><tbody><tr><td>t<sub>avr</sub>, ns</td><td>16.0</td><td>7.35</td><td>7.86</td><td>9.5</td></tr></tbody></table>

The populations of QD-encoded microbeads have been studied in detail using fluorescence microscopy. QD-encoded microbead samples were mixed with 1% glycerol and fixed on microscope slides. Imaging of the specimens was performed with the use of two optical filters, FITC (excitation wavelength, 495 nm; emission wavelength, 520 nm) and Alexa Fluor 568 (excitation wavelength, 568 nm; emission wavelength, 593 nm), and a Zeiss N-achroplan 40×/0.65 Ph2 lens. The microbeads had a high brightness and were easily discerned under the microscope (Figure 5).

<figure><img src="image_8.png" /><figcaption>**Figure 5.** Typical fluorescence microscopy images of microbeads of different sizes encoded with (A) QDs$_{508}$ and (B) QDs$_{590}$. All the images were taken at a magnification of 40×.</figcaption></figure>

## 4. Conclusions

In this study, we have investigated some physicochemical aspects of electrostatic adsorption of negatively charged QDs on a positively charged microbead surface. In particular, we have estimated the maximal number of QDs that may be adsorbed in a single stage on the surface of a single microbead. We have also developed a technique of multistage QD adsorption for preparation of a panel of QD-encoded microbead populations with a wide range of fluorescence intensities. Using fluorescence lifetime measurements, we have found that the layer-by-layer deposition technique prevents FRET between QDs of different colors adsorbed at different stages.

The layer-by-layer technique for optical encoding of polymer microbeads with water-soluble QDs developed in this study makes it possible to obtain microbead populations for multiplexed analysis of biological markers using flow cytometry.
Acknowledgments

This study was supported by the Federal Targeted Program for Research and Development of the Ministry of Education and Science of the Russian Federation (grant no. 14.578.21.0054, contract no. RFMEFI57814X0054).

References

[1] Dunbar S A 2006 Clin. Chim. Acta 363 71

[2] Han M, Gao X, Su J Z and Nie S 2001 Nat. Biotechnol. 19 631

[3] Wang G, Leng Y, Dou H, Wang L, Li W, Wang X, Sun K, Shen L, Yuan X, Li J, Sun K, Han J, Xiao H and Li Y 2013 ACS Nano 7 471

[4] Cao Y C, Huang Z L, Liu T C, Wang H Q, Zhu X X, Wang Z, Zhao Y D, Liu M X and Luo Q M 2006 Anal. Biochem. 351 193

[5] Gao X and Nie S 2004 Anal. Chem. 76 2406

[6] Fournier-Bidoz S, Jennings T L, Klostranec J M, Fung W, Rhee A, Li D and Chan W C 2008 Angew. Chem. Int. Edit. 47 5577

[7] Baranov A V, Rakovich Y P, Donegan J F, Perova T S, Moore R A, Talapin D V, Rogach A L, Masumoto Y and Nabiev I 2003 Phys. Rev. B 68 165306

[8] Samokhvalov P, Linkov P, Michel J, Molinari M and Nabiev I 2014 Proc. SPIE of Colloidal Nanoparticles for Biomedical Applications 8955 89550S

[9] Sukhanova A and Nabiev I 2008 Crit. Rev. Oncol. Hematol. 68 39

[10] Susha A S, Caruso F, Rogach A L, Sukhorukov G B, Kornowski A, Möhwald H, Giersig M, Eychmüller A and Weller H 2000 Colloid. Surfaces A 163 39

[11] Sukhanova A, Venteo L, Devy J, Artemyev M, Oleinikov V, Pluot M and Nabiev I 2002 Lab. Invest. 82 1259

[12] Sukhanova A, Even-Desrumeaux K, Kisserli A, Tabary T, Reveil B, Millot J M, Chames P, Baty D, Artemyev M, Oleinikov V, Pluot M, Cohen J H and Nabiev I 2012 Nanomed. Nanotechnol. 8 516

[13] Yu W W, Qu L, Guo W and Peng X 2003 Chem. Mater. 15 2854

[14] Brazhnik K, Sokolova Z, Baryshnikova M, Bilan R, Efimov A, Nabiev I and Sukhanova A 2015 Nanomed. Nanotechnol. 11 1065

[15] Sukhanova A, Susha A S, Bek A, Mayilo S, Rogach A L, Feldmann J, Oleinikov V, Reveil B, Donvito B, Cohen J H and Nabiev I 2007 Nano Lett. 7 2322

[16] Chou K F and Dennis A M 2015 Sensors-Basel 15 13288

[17] Mićić O I, Jones K M, Cahill A and Nozik A J 1998 J. Phys. Chem. B 102 9791