Quantum Dot DNA Bioconjugates: Attachment Chemistry Strongly Influences the Resulting Composite Architecture

Abstract

The unique properties provided by hybrid semiconductor quantum dot- (QD) bioconjugates continue to stimulate interest for many applications ranging from biosensing to energy harvesting. Understanding both the structure and function of these composite materials is an important component in their development. Here, we compare the architecture that results from using two common self-assembly chemistries to attach DNA to QDs. DNA modified to display either a terminal biotin or an oligohistidine peptidyl sequence was assembled to streptavidin/amphiphilic polymer- or PEG-functionalized QDs, respectively. A series of complementary acceptor dye-labeled DNA were hybridized to different positions on the DNA in each QD configuration and the separation distances between the QD donor and each dye-acceptor probed with Förster resonance energy transfer (FRET). The polyhistidine self-assembly yielded QD-DNA bioconjugates where predicted and experimental separation distances matched reasonably well. Although displaying efficient FRET, data from QD-DNA bioconjugates assembled using biotin-streptavidin chemistry did not match any predicted separation distances. Modeling based upon known QD and DNA structures along with the linkage chemistry and FRET-derived distances was used to simulate each QD-DNA structure and provide insight into the underlying architecture. Although displaying some rotational freedom, the DNA modified with the polyhistidine assembles to the QD with its structure extended out from the QD-PEG surface as predicted. In contrast, the random orientation of streptavidin on the QD surface resulted in DNA with a wide variety of possible orientations relative to the QD which cannot be controlled during assembly. These results suggest that if a particular QD-biocomposite structure is desired, for example, random versus oriented, the type of bioconjugation chemistry utilized will be a key influencing factor.

Quantum Dots in Bioanalysis: A Review of Applications across Various Platforms for Fluorescence Spectroscopy and Imaging

“…This strategy permits a moderate level of control over the number of biomolecules assembled per QD (conjugate valence) and their orientations; however, there are limitations associated with the heterogeneous attachment of the streptavidin to the underlying QD coating. 103 To date, the bioconjugate method that has provided the best overall control is self-assembly between polyhistidine-appended biomolecules and the ZnS shell of ligandcoated QDs ( Fig. 3vii; nanomolar dissociation constants), thereby providing excellent control over conjugate valence and orientation.…”

Quantum dots–DNA bioconjugates: synthesis to applications

“…Conjugation of proteins with near neutral isoelectric points ( pIs) often reduces electrophoretic migration of QDs [89]. Contrarily, conjugation of DNA generally increases anodic migration, which is also affected by the length and number of DNA conjugated [76,79,90].…”

Materials for FRET Analysis: Beyond Traditional Dye–Dye Combinations

“…Loss of biomolecular activity is to be expected if the recognition site of the biomolecule is positioned in close proximity to the surface [30]. In a study of QD-DNA bioconjugates, Boeneman et al found that the attachment chemistry strongly influenced the orientation of DNA on a QD-poly(ethylene glycol) (PEG) surface [36]. His-tag-modified DNA attached directly to the QD surface resulted in a structure that, as predicted, extended out from the surface.…”

“…However, given their NM nature, additional issues (also discussed in Section 6.2), such as the influence of the surface ligand on bioconjugation reactions and subsequent biomolecular interactions and how the attachment chemistry influences the NM stability and biomolecule orientation, should be considered for QDs [30,[33][34][35][36]515].…”