The authors would like to thank Dr. Hong Yi at the Emory University Integrated Microscopy Core for electron microscopy imaging. This work was sponsored by NIH grants (PN2EY018244, R01 CA108468, U54CA119338, and 1K99CA154006-01).

The following synthesis procedures involve standard air-free techniques and the use of a vacuum/inert gas manifold; detailed methodology can be found in references 10 and 11. MSDS for all potentially toxic and flammable substances should be consulted before use and all flammable and/or air-labile compounds should be aliquoted into septum-sealed vials in a glove box or glove bag.
1. Synthesis of Mercury Cadmium Selenide (HgxCd1-xSe) Quantum Dot Cores
<ol>
 <li>Prepare a 0.4 M solution of selenium in trioctylphosphine (TOP). Add selenium (0.316 g, 4 mmol) to a 50 ml 3-necked flask, then evacuate and fill with argon using a Schlenk line. Under air-free conditions (dry nitrogen or argon atmosphere), add 10 ml TOP and heat to 100 &deg;C while stirring for 1 hr to yield a clear, colorless solution. Cool the solution to room temperature and set the flask aside.</li>
 <li>To a 250 ml 3-necked flask, add cadmium oxide (CdO 0.0770 g, 0.6 mmol), tetradecylphosphonic acid (TDPA, 0.3674 g, 1.32 mmol), and octadecene (ODE, 27.6 ml), and evacuate the solution using a Schlenk line while stirring. Increase the temperature to 100 &deg;C and evacuate for an additional 15 min to remove low-boiling point impurities.</li>
 <li>Under argon or nitrogen gas, heat the mixture to 300 &deg;C for 1 hr to fully dissolve the CdO. The solution will change from a reddish color to clear and colorless. Cool the solution to room temperature.</li>
 <li>Add hexadecylamine (HDA, 7.0 g) to the cadmium solution, heat to 70 &deg;C, and evacuate. Once a constant pressure is attained, increase the temperature to 100-110 &deg;C and reflux the solution for 30 min. Switch the Schlenk line valve to inert gas and insert the thermocouple directly into the solution.</li>
 <li>Under air-free conditions, add diphenylphosphine (DPP, 100 &mu;l) to the solution and increase the temperature to 310 &deg;C. Remove 7.5 ml of the 0.4 M TOP-Se solution (3 mmol selenium) in a disposable plastic syringe attached to a 16 gauge needle.</li>
 <li>Once the temperature equilibrates at 310 &deg;C, set the temperature controller to 0 &deg;C and swiftly inject the TOP-Se solution directly into the cadmium solution. The solution will change from colorless to yellow-orange and the temperature will quickly drop and increase again to ~280 &deg;C. After 1 min of reaction, remove the flask from the heating mantle and quickly cool with a stream of air until the temperature is less than 200 &deg;C.</li>
 <li>When the temperature reaches ~40 &deg;C, dilute with 30 ml hexane; most of the remaining cadmium precursor will settle out of solution. Remove this precipitate by centrifugation (5,000 x g, 10 min).</li>
 <li>In each of six 50 ml polypropylene conical centrifuge tube, dilute 12 ml of the crude nanocrystal solution with 40 ml acetone, centrifuge (5,000 x g for 10 min), and carefully decant and discard the supernatant.</li>
 <li>Dissolve the nanocrystal pellets in hexane (25 ml total volume). Extract this solution 3 times with an equal volume of methanol, retaining the top phase. For the third extraction, the volume of methanol may be adjusted to ~15 ml to obtain a concentrated hexane solution of pure CdSe QDs at roughly 200 &mu;M. The typical yield of this reaction is 3 &mu;mol of CdSe nanocrystals with a diameter of 2.3 nm (50-60% reaction yield).</li>
 <li>Determine the nanocrystal diameter and concentration by measuring the UV-Vis absorption spectrum and consulting the size-fitting chart of Mulvaney and coworkers 12 and the extinction correlations of Bawendi and coworkers 13. See Appendix for details.</li>
 <li>Mercury cation exchange: the nanocrystals may be partially exchanged with mercury to red-shift the absorption and fluorescence emission. Mix the following together in order in a 20 ml glass vial with stirbar (this reaction may be scaled as desired): 3 ml hexane, 2 ml chloroform, 1 ml 200 &mu;M CdSe QD solution (200 nmol), 15 &mu;l oleylamine (OLA), and 500 &mu;l of a 0.1 M solution of Hg(OT)2 in chloroform. Mercury octanethioate (HgOT2) may be prepared by reacting mercury acetate and octanethiol in methanol (see appendix). As the cation exchange reaction proceeds, the extent of red-shift may be monitored with UV-Vis absorption spectrophotometry. After the desired absorption band has been attained, measure the absorption of the nanocrystal solution at 350 nm and determine the new extinction coefficient, assuming that the nanocrystal concentration has not changed (30.7 &mu;M in this example). Quench the reaction by removing the unreacted mercury: add 5 ml decane, 10 ml hexane, and 7 ml methanol and extract the solution, keeping the top phase containing the nanocrystals. Extract twice more with hexane and methanol, and adjust the volume of methanol so that the top phase is ~7 ml. If the phases are slow to separate, the solution may be centrifuged (5,000 x g, 10 min). Add 100 &mu;l TOP, 100 &mu;l OLA, and 100 &mu;l oleic acid to the nanocrystals followed by 40 ml acetone to induce precipitation. Collect the nanocrystals via centrifugation and disperse in 3 ml hexane. Centrifuge again to remove insoluble components and determine the nanocrystal concentration again, using the new extinction coefficient at 350 nm. Allow the nanocrystal solution to age for at least 24 hr at room temperature before proceeding to the next step.</li>
</ol>
2. Growth of Cadmium Zinc Sulfide (CdyZn1-yS) Shell
<ol>
 <li>Prepare 0.1 M shell precursor solutions in 50 ml 3-necked flasks. Cadmium precursor: cadmium acetate hydrate (230.5 mg, 1 mmol) and 10 ml oleylamine (OLA). Zinc precursor: zinc acetate (183.5 mg, 1 mmol) and 10 ml OLA. Sulfur precursor: sulfur (32.1 mg, 1 mmol) and 10 ml ODE. Under vacuum, heat each solution to reflux for 1 hr to yield clear solutions, and then charge with argon. The sulfur solution may be cooled to room temperature, but the cadmium and zinc precursors are maintained at approximately 50 &deg;C. Calculations of shell precursor quantities can be found in reference 14.</li>
 <li>Add to a 3-necked flask: HgxCd1-xSe QDs (120 nmol, 2.3 nm diameter), ODE (2 ml), and trioctylphosphine oxide (TOPO, 250 mg). Evacuate off the hexane at room temperature using the Schlenk line. Increase the temperature to 100 &deg;C and reflux for 15 min. Change the Schlenk line valve to argon or nitrogen gas and insert the thermocouple in the nanocrystal solution.</li>
 <li>Increase the temperature to 120 &deg;C, add 0.5 monolayers of sulfur precursor solution (140 &mu;l), and allow the reaction to proceed for 15 min. Small aliquots (&lt;50 &mu;l) may be removed using a glass syringe to monitor the progress of the reaction using fluorescence and/or UV-Vis absorption spectrophotometry. Increase the temperature to 140 &deg;C, add 0.5 monolayers of cadmium precursor solution (140 &mu;l), and allow the reaction to proceed for 15 min. Add 500 &mu;l anhydrous OLA to the reaction solution.</li>
 <li>At 160 &deg;C add 0.5 monolayers of sulfur precursor solution (220 &mu;l) followed by an equal quantity of zinc precursor solution at 170 &deg;C with 15 min between each addition. Then at 180 &deg;C add 0.25 monolayers of sulfur precursor solution (150 &mu;l) and zinc precursor solution in 15 min intervals.</li>
 <li>Cool the solution to room temperature and again calculate a new extinction coefficient for these particles using a UV-Vis spectrum, assuming that the number of nanocrystals has not changed (120 nmol in 3.8 ml reaction solution). Store the reaction solution as a crude mixture in a freezer; the nanocrystals may be thawed and purified as needed using the same method described in sections 1.8 and 1.9.</li>
 <li>The nanocrystals may be characterized using electron microscopy, UV-Vis absorption spectroscopy, and fluorescence spectroscopy. Quantum yield may be calculated absolutely using an integrating sphere or relatively in comparison to a known standard using the methods of reference 15.</li>
</ol>
3. Phase Transfer
<ol>
 <li>Add purified core/shell HgxCd1-xSe/CdyZn1-yS QDs (5 ml, 20 &mu;M) to a 50 ml 3-necked flask and remove the hexane under a high vacuum to yield a dry film. Fill the flask with argon, add anhydrous pyridine (3 ml) to the nanoparticle film and heat the slurry to 80 &deg;C. Over the course of 1-2 hr the nanoparticles will fully dissolve.</li>
 <li>Add 1-thioglycerol (1 ml) to the solution and stir at 80 &deg;C for 2 hr. Then cool the solution to room temperature and add triethylamine (0.5 ml) to deprotonate thioglycerol. Stir for 30 min. The solution may become cloudy after the addition of triethylamine due to the poor solubility of polar nanocrystals in this solvent mixture.</li>
 <li>Transfer the QD solution into a 50 ml conical centrifuge tube containing a mixture of 20 ml hexane and 20 ml acetone, and mix well. Isolate the precipitated nanocrystals via centrifugation (5,000 x g, 10 min), and wash the pellet with acetone.</li>
 <li>Dissolve the QD pellet in DMSO (5 ml) with bath sonication, and then centrifuge (7,000 x g, 10 min) to remove possible aggregates. Determine the nanoparticle concentration from a UV-Vis absorption spectrum. This solution of pure QDs should be used within 3 hr, as the surface thiols can slowly oxidize under ambient conditions in air.</li>
 <li>Dilute the QD solution to 10 &mu;M or less with DMSO and transfer to a 50 ml flask. Prepare a 5 mg/ml solution of thiolated polyacrylic acid (synthesis described in Appendix) in DMSO. Add the polymer solution (0.15 mg polymer per nmol QDs) dropwise to the QD solution while stirring and degas the solution at room temperature for 5 min.</li>
 <li>Purge the QD/polymer solution with argon and heat to 80 &deg;C for 90 min. Then cool the solution to room temperature and dropwise add an equal volume of 50 mM sodium borate, pH 8. Stir for 10 min.</li>
 <li>Purify the QDs via dialysis (20 kDa cutoff) in 50 mM sodium borate, pH 8, and then concentrate the particles using a centrifugal filter (10 kDa cutoff). Determine the concentration from a UV-Vis absorption spectrum.</li>
</ol>
4. PEG Coating
<ol>
 <li>In a 4 ml glass vial with stirbar, mix 1 nmol QDs in borate buffer with a 40,000 x molar excess of 750 Da monoamino-polyethylene glycol (30 mg, 40 &mu;mol). If a specific chemical functionality is to be added to the nanocrystals (e.g. hydrazide or maleimide), it may be introduced by replacing a fraction of the amino-PEG with a heterobifunctional amino-PEG (30% mole fraction typically works well). Dilute the nanocrystal solution to 1 &mu;M with borate buffer. This reaction may be scaled as desired.</li>
 <li>Prepare a fresh solution of DMTMM (20 mg, 72 &mu;mol) in DMSO (144 &mu;l). This solution can be briefly heated under a stream of warm tap-water or submerged in a bath sonicator to fully dissolve the DMTMM. Quickly add a 25,000 x molar excess of this 0.5 M DMTMM solution (50 &mu;l) to the QD solution and stir at room temperature for 30 min.</li>
 <li>Repeat step 4.2 four more times to saturate the nanocrystal surface with PEG. Finally, add 200 &mu;l 1 M Tris buffer to quench the reaction and purify the nanocrystals using dialysis, centrifugal filters, or ultracentrifugation.</li>
 <li>The nanocrystals may be analyzed for monodispersity, hydrodynamic size, and surface charge using liquid chromatography, agarose gel electrophoresis, and fluorescence microscopy. To determine hydrodynamic size and size distribution using an automated liquid chromatography system (GE AKTAprime Plus), use a Superose 6 column, a flow rate of 0.5 ml/min with PBS buffer eluent, and absorption detection at 260 or 280 nm. Compare nanoparticle elution times with those of molecular weight standards. For agarose gel electrophoresis, prepare a 0.5% agarose gel in 50 mM sodium borate buffer (pH 8.5) or 50 mM sodium phosphate buffer (pH 7.4), mix 1 &mu;M samples with 10% glycerol and load into wells, and run at 100 V for 30 min. Image the nanocrystals in the gel using a UV hand wand or UV transilluminator and for fluorescence excitation. To image the nanocrystals at the single molecule level using fluorescence microscopy, dilute the particles to 0.2 nM in 10 mM phosphate buffer, drop 2.5 &mu;l of the solution on a glass coverslip, and carefully place a second coverslip on top of the liquid bead to spread a film between the coverslips. Image the surface-bound particles using a high numerical aperture objective (ideally at least 1.40) in either epifluorescence or TIRF mode with excitation at wavelengths between 400-580 nm and an electron-multiplying CCD camera. Exact imaging parameters will vary between microscopy setup.</li>
</ol>

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No conflicts of interest declared.

Compared to conventional CdSe quantum dots, ternary alloy HgxCd1-xSe nanocrystals can be tuned in size and fluorescence wavelength independently. The size is first selected during the synthesis of CdSe nanocrystal cores, and the fluorescence wavelength is chosen in a secondary mercury cation exchange step, which does not substantially alter the nanocrystal size 9. It is important to allow the purified HgxCd1-xSe nanocrystals to incubate at room temperature fo...

<table border="1">
 <tbody>
 <tr>
 <td>Name of the reagent</td>
 <td>Company</td>
 <td>Catalogue number</td>
 <td>Comments (optional)</td>
 </tr>
 <tr>
 <td>Selenium</td>
 <td>Sigma-Aldrich</td>
 <td>229865</td>
 <td></td>
 </tr>
 <tr>
 <td>Tri-n-octylphosphine</td>
 <td>Strem</td>
 <td>15-6655</td>
 <td>97% pure, unstable in air</td>
 </tr>
 <tr>
 <td>Cadmium oxide</td>
 <td>Sigma-Aldrich</td>
 <td>202894</td>
 <td>Highly toxic: use caution </td>
 </tr>
 <tr>
 <td>Tetradecylphosphonic acid</td>
 <td>PCI Synthesis</td>
 <td>4671-75-4</td>
 <td></td>
 </tr>
 <tr>
 <td>Octadecene</td>
 <td>Alfa Aesar</td>
 <td>L11004</td>
 <td>Technical grade</td>
 </tr>
 <tr>
 <td>Hexadecylamine</td>
 <td>Sigma-Aldrich</td>
 <td>H7408</td>
 <td></td>
 </tr>
 <tr>
 <td>Diphenylphosphine</td>
 <td>Sigma-Aldrich</td>
 <td>252964</td>
 <td>Pyrophoric</td>
 </tr>
 <tr>
 <td>Mercury acetate</td>
 <td>Sigma-Aldrich</td>
 <td>456012</td>
 <td>Highly toxic: use caution</td>
 </tr>
 <tr>
 <td>1-Octanethiol</td>
 <td>Sigma-Aldrich</td>
 <td>471836</td>
 <td>Strong odor</td>
 </tr>
 <tr>
 <td>Oleic acid</td>
 <td>Sigma-Aldrich</td>
 <td>W281506</td>
 <td></td>
 </tr>
 <tr>
 <td>Zinc acetate </td>
 <td>Alfa Aesar</td>
 <td>35792</td>
 <td></td>
 </tr>
 <tr>
 <td>Cadmium acetate hydrate</td>
 <td>Sigma-Aldrich</td>
 <td>229490</td>
 <td>Highly toxic: use caution</td>
 </tr>
 <tr>
 <td>Oleylamine</td>
 <td>Fisher Scientific</td>
 <td>AC12954</td>
 <td>Unstable in air</td>
 </tr>
 <tr>
 <td>Sulfur</td>
 <td>Sigma-Aldrich</td>
 <td>344621</td>
 <td></td>
 </tr>
 <tr>
 <td>Trioctylphosphine oxide</td>
 <td>Strem</td>
 <td>15-6661</td>
 <td>99%</td>
 </tr>
 <tr>
 <td>Pyridine</td>
 <td>VWR</td>
 <td>EM-PX2012-6</td>
 <td>Anhydrous</td>
 </tr>
 <tr>
 <td>Thioglycerol</td>
 <td>Sigma-Aldrich</td>
 <td>M1753</td>
 <td>Strong odor</td>
 </tr>
 <tr>
 <td>Triethylamine</td>
 <td>Sigma-Aldrich</td>
 <td>471283</td>
 <td>Anhydrous</td>
 </tr>
 <tr>
 <td>Dialysis tubing</td>
 <td>Spectrum Labs</td>
 <td>131342</td>
 <td>20 kDa cutoff</td>
 </tr>
 <tr>
 <td>Centrifugal filter</td>
 <td>Millipore</td>
 <td>UFC801024</td>
 <td>10 kDa cutoff</td>
 </tr>
 <tr>
 <td>Monoamino-PEG</td>
 <td>Rapp Polymere</td>
 <td>12 750-2</td>
 <td>750 Da</td>
 </tr>
 <tr>
 <td>DMTMM, 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride hydrate</td>
 <td>Alfa Aesar</td>
 <td>H26333</td>
 <td></td>
 </tr>
 <tr>
 <td>AKTAprime Plus Chromatography System</td>
 <td>GE HealthCare</td>
 <td></td>
 <td></td>
 </tr>
 <tr>
 <td>Superose 6 10/300 GL chromatography column</td>
 <td>GE HealthCare</td>
 <td>17-5172-01</td>
 <td></td>
 </tr>
 <tr>
 <td>Agarose, OmniPur</td>
 <td>VWR</td>
 <td>EM-2120</td>
 <td></td>
 </tr>
 <tr>
 <td></td>
 <td></td>
 <td></td>
 <td>Appendix
Synthesis of mercury octanethiolate: Slowly add a methanol solution of mercury acetate (1 eq.) to a stirring solution of 1-octanethiol (3 eq.) and potassium hydroxide (3 eq.) in methanol at room temperature. Isolate the mercury(II) octanethiolate precipitate via filtration, wash two times with methanol and once with ether, and then dry under vacuum.
Synthesis of multidentate polymer: Dissolve polyacrylic acid (1 g, 1,773 Da) in 25 ml dimethylformamide (DMF) in a 150 ml three-necked flask and bubble with argon for 30 min. Add an anhydrous solution of cysteamine (374 mg, 4.87 mmol) in 10 ml DMF. At room temperature with vigorous stirring, slowly add anhydrous diisopropylcarbodiimide (DIC, 736 mg, 5.83 mmol) over 30 min, followed by triethylamine (170 &mu;l, 1.22 mmol), and allow the reaction to proceed for 72 hr at 60 &deg;C. Add mercaptoethanol (501 mg, 6.41 mmol) to quench the reaction, and stir for 2 hr at room temperature. Remove DMF via rotary evaporation and isolate the polymer with the addition of a 2:1 mixture of ice-cold acetone:chloroform, followed by centrifugation. Dissolve the polymer in ~5 ml anhydrous DMF, filter, precipitate again with diethyl ether, and repeat. Dry the product under vacuum and store under argon.
Determination of CdSe core diameter: From the UV-Vis absorption spectrum determine the wavelength of the first exciton peak (&lambda;, in nm), which is the longest-wavelength peak (e.g. roughly 498 nm for CdSe in Figure 2a), and use the sizing curve of Mulvaney and coworkers 12:
<img src="/files/ftp_upload/4236/4236eq1.jpg" alt="Equation 1" />
Determination of CdSe nanocrystal concentration: From a background-subtracted UV-Vis spectrum of an optically clear solution of CdSe nanocrystals, determine the absorption at 350 nm wavelength. Serial dilutions can be used to determine if the optical absorption is within the linear range of Beer's Law. The nanocrystal concentration (QD, in M) can be determined by plugging in the nanocrystal diameter (D, in nm), the optical absorption value (A3sa), and the cuvette path length (l, in cm) into the following equation from the empirical correlation of Bawendi and coworkers 13:
<img src="/files/ftp_upload/4236/4236eq2.jpg" alt="Equation 2" /></td>
 </tr>
 </tbody>
</table>

compact quantum dots for single-molecule imaging

Single-molecule imaging is an important tool for understanding the mechanisms of biomolecular function and for visualizing the spatial and temporal heterogeneity of molecular behaviors that underlie cellular biology 1-4. To image an individual molecule of interest, it is typically conjugated to a fluorescent tag (dye, protein, bead, or quantum dot) and observed with epifluorescence or total internal reflection fluorescence (TIRF) microscopy. While dyes and fluorescent proteins have been the mainstay of fluorescence imaging for decades, their fluorescence is unstable under high photon fluxes necessary to observe individual molecules, yielding only a few seconds of observation before complete loss of signal. Latex beads and dye-labeled beads provide improved signal stability but at the expense of drastically larger hydrodynamic size, which can deleteriously alter the diffusion and behavior of the molecule under study.
Quantum dots (QDs) offer a balance between these two problematic regimes. These nanoparticles are composed of semiconductor materials and can be engineered with a hydrodynamically compact size with exceptional resistance to photodegradation 5. Thus in recent years QDs have been instrumental in enabling long-term observation of complex macromolecular behavior on the single molecule level. However these particles have still been found to exhibit impaired diffusion in crowded molecular environments such as the cellular cytoplasm and the neuronal synaptic cleft, where their sizes are still too large 4,6,7.
Recently we have engineered the cores and surface coatings of QDs for minimized hydrodynamic size, while balancing offsets to colloidal stability, photostability, brightness, and nonspecific binding that have hindered the utility of compact QDs in the past 8,9. The goal of this article is to demonstrate the synthesis, modification, and characterization of these optimized nanocrystals, composed of an alloyed HgxCd1-xSe core coated with an insulating CdyZn1-yS shell, further coated with a multidentate polymer ligand modified with short polyethylene glycol (PEG) chains (Figure 1). Compared with conventional CdSe nanocrystals, HgxCd1-xSe alloys offer greater quantum yields of fluorescence, fluorescence at red and near-infrared wavelengths for enhanced signal-to-noise in cells, and excitation at non-cytotoxic visible wavelengths. Multidentate polymer coatings bind to the nanocrystal surface in a closed and flat conformation to minimize hydrodynamic size, and PEG neutralizes the surface charge to minimize nonspecific binding to cells and biomolecules. The end result is a brightly fluorescent nanocrystal with emission between 550-800 nm and a total hydrodynamic size near 12 nm. This is in the same size range as many soluble globular proteins in cells, and substantially smaller than conventional PEGylated QDs (25-35 nm).

Figure 2 depicts representative absorption and fluorescence spectra for CdSe nanocrystals, HgxCd1-xSe nanocrystals after cation exchange, and HgxCd1-xSe/CdyZn1-yS nanocrystals after shell growth. The core CdSe nanocrystals have a quantum yield of fluorescence near 15% (including long-wavelength deep-trap emission) but this efficiency drops to less than 1% after mercury exchange, likely due to charge carrier traps introduced through surface...

Watch this Scientific Journal Video about Compact Quantum Dots for Single-molecule Imaging at JoVE.com

Compact Quantum Dots for Single-molecule Imaging

We describe the preparation of colloidal quantum dots with minimized hydrodynamic size for single-molecule fluorescence imaging. Compared to conventional quantum dots, these nanoparticles are similar in size to globular proteins and are optimized for single-molecule brightness, stability against photodegradation, and resistance to nonspecific binding to proteins and cells.

Single-molecule imaging is an important tool for  understanding the mechanisms of biomolecular function and for visualizing the  spatial and temporal ...

compact-quantum-dots-for-single-molecule-imaging

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18.0K Views.  Emory University. We describe the preparation of colloidal quantum dots with minimized hydrodynamic size for single-molecule fluorescence imaging. Compared to conventional quantum dots, these nanoparticles are similar in size to globular proteins and are optimized for single-molecule brightness, stability against photodegradation, and resistance to nonspecific binding to proteins and cells.