Qdot synthesis and "loops-trains-tails" update

December 7, 2017

by Abhilasha "Abby" Dehankar

Quantum dot synthesis

TOP assisted SILAR (Xu, J. M.; Ruchala, P.; Ebenstain, Y.; Li, J. J.; Weiss, S., Stable, Compact, Bright Biofunctional Quantum Dots with Improved Peptide Coating. Journal of Physical Chemistry B 2012, 116 (36), 11370-11378.)
TOP assisted SILAR (Xu, J. M.; Ruchala, P.; Ebenstain, Y.; Li, J. J.; Weiss, S., Stable,
Compact, Bright Biofunctional Quantum Dots with Improved Peptide Coating.
Journal of Physical Chemistry B 2012, 116 (36), 11370-11378. )

Previously, ~4 monolayers of Zinc Sulfide (ZnS) shell was developed on the CdSe cores. These QDs were not stable against ligand exchange to pyridine. Therefore, to increase the robustness of these particles, it was decided to develop additional (~10-15) ZnS monolayers. Unlike previous trials, recent effort to synthesize multiple ZnS layers, did not depict the decrease in CdSe core size on first TOP activation (Refer to figure: TOP assisted SILAR). Furthermore, addition of just two layers clearly indicated formation of two population sizes. Thus, this trial could not achieve the desired CdSe/ZnS QDs. Following figure consists of the Fluorescence and Absorption spectrum of CdSe cores and 2 ZnS monolayer coated QDs. The growth of two fluorescence peak for CdSe/ZnS as compared to a single peak for CdSe cores represents inefficient bimodal growth. The absorbance peak widening for CdSe/ZnS also hints towards presence of multiple trap states. Therefore, future efforts would be directed towards better understanding the synthesis flaws through deeper literature search and re-trial of synthesis.

Absorption and Emission spectrum of CdSe core and CdSe/ZnS QDs
Fluorescence (Left) and Absorption (Right) spectrum of CdSe core and CdSe-2ZnS monolayer QDs
Aqueous transfer
Aqueous transfer of QDs (Hao, J. J.; Zhou, J.; Zhang, C. Y., A tri-n-octylphosphine-assisted successive
ionic layer adsorption and reaction method to synthesize multilayered core-shell CdSe-ZnS quantum dots
with extremely high quantum yield. Chemical Communications 2013, 49 (56), 6346-6348 )

Biocompatible QDs and DNA conjugation:

Loops-trains-tails procedure is being used for making organic QDs biocompatible. The pathway for aqueous transfer of QDs is illustrated in the diagram above. Previous trials for exchanging the native ligands of QDs with pyridine was extremely inefficient as observed from precipitation of QDs over time as well incomplete dissolution. As a result, ligand exhchange with the compact peptide (phytochelatin-3, PC3) also did not produce desired results. Therefore, experiments in this reporting period focused mostly on optimization of pyridine ligand exchange. Amongst all the tested procedures, ligand exchange using hot pyridine (80C) provided best results. 

In the aqueous transfer process, QDs in pyridine are mixed with excess PC3 dissolved in water and the ligand exchange is triggered by addition of a base (tetramethyl ammonium hydroxide). During the current reporting period, experiments for aqueous transfer did not show complete dissolution of QDs in water and was accompanied by sedimentation over time. Literature indicates that following four factors greatly influence a robust PC3 coating:

  1. Amount of TMAOH (Tetramethyl ammonium hydroxide)
  2. Ionic strength of the buffer
  3. pH of the buffer
  4. Length of peptide (PC is available in 2-4)

Moving ahead, factors influencing the ligand exchange to PC3 would be investigated.

QD-micelles-DNA hinge
Left: QD-micelle at DNA hinge conjugation site, Right: DNA hinge-
micelle conjugated, yellow circles are successful conjugations

Furthermore, DNA conjugation was tested on QD encapsulating micelles and MPA-coated QDs as a control to  simultaneously optimize the future steps loops-trains-tails biocompatible QDs. Since, all these particles are carboxyl group terminated after aqueous transfer, a standard EDC-sulfo NHS chemistry would be used for DNA conjugation. This process involves buffer exchange of carboxyl terminated QDs to low (pH~5)/physiological pH (pH~7) buffers. MPA-coated QDs as opposed to PC3-coated QDs, cannot survive low pH (~5). Therefore, these QDs cannot provide a good control for our experiments.

Micelle encapsulated QDs on the other hand are extremely robust to all required pH conditions and were conjugated to DNA. Post DNA conjugation, they were tested with DNA origami hinges for specific binding which would determine a successful conjugation. As shown in the figure below, the conjugation site for the micelle is supposed to be at the lower arm of the DNA hinge. Although many specific bindings were observed (yellow circles structures), the trial turned out to be inconclusive becayse of follwoing reasons:

  1. Steric hindrance of micelle to hinge (big size of micelles)
  2. Non-specific interactions of polymer in micelles with DNA overhangs at different sites. 
  3. Amount of DNA available per micelle.

As a result, micelle also did not provide a good control. Therefore, future experiments for DNA conjugation optimization would focus mostly on either smaller micelles or PC3 coated QDs.