Toward DNA-embedded Quantum Dots: Take VI

November 7, 2018

by Kil Ho Lee



So far, we demonstrated successful ligand exchange that replaces organic ligands (i.e. octadecylamine) with aqueous ligand (3-MPA). QDs coated with 3-MPA are stable in aqueous solution, which is required to further modify QD surface with single-stranded DNA (ssDNA). As discussed in my previous blog posts, the “DNA embedding” procedure requires the deposition of the additional shell of core/shell QDs. Specifically, embedding ssDNA on the surface of CdSe(core)/ZnS(shell) QDs requires the formation of additional ZnS layer for one end of ssDNA to be “embedded”. The deposition of additional ZnS layer can be achieved by adding free Zn ions and thiol (-SH)-modified ssDNA into a solution containing QDs at elevated temperature (90 °C).

In the last blog post, the attempts to embed DNA on QD surface showed some promising results, including the fluorescence emission red-shift. Furthering our analysis, in this report, the embedding procedure was repeated using Cyanine Dye (Cy5)-modified ssDNA. Specifically, the thiol-modified (5’ end) ssDNA terminated with Cy5 fluorescence dye (3’ end) was used to modify the surface of QDs. QDs emit green fluorescence (550 nm) and Cy5 emits red fluorescence (~660 nm). Therefore, two different fluorescence signals would be emitted from QDs with DNA successfully embedded on the surface.


In this experiment, DNA embedding procedure was performed in the same way described in the previous blog post (Toward DNA-embedded Quantum Dots: TakeV).

After the embedding procedure, excess DNA was removed using the centrifugal filter devices (3 times). 

Below summarizes the sample types analyzed using a fluorometer

For Aqueous QD (control), the fluorescence curve was obtained by exciting QDs with 350 nm wavelength (Figure 1a). For Cy5 DNA (control), the fluorescence curve(s) was obtained using 600 nm wavelengths (Figure 1b).

Figure 1. Fluorescence spectra of (a) aqueous QDs in water, and (b) Cy5 DNA after centrifugal filtration steps

For Cy5-modified DNA embedded QD, the fluorescence curve(s) was obtained first using 350 nm wavelength, followed by 590, 600, 610 nm wavelength (Figure 2). 

Figure 2. Fluorescence spectra of Cy5-modified DNA embedded QD: (a) QD emission, and (b) Cy5 emission  

After the embedding procedure, QD emission was slightly red-shifted (550 nm to 560 nm). Figure 1b shows the fluorescence intensity of the aqueous solution collected from the centrifugal filter. Because Cy5-modified DNA is easily washed through the filter, the fluorescence emission from Cy5 was not observed.

Examining Cy5-modified DNA embedded QDs for Cy5 fluorescence signal, the red fluorescence emission near 660 nm was detected. This result suggested that DNA embedding was indeed successful.

However, the fluorescence intensity for Cy5 from QD surface was too low. Further optimization is required to embedded more DNA on QD surface.