Discerning single molecule interactions of DNA and quantum dots

Measurements of interactions between nanoparticles and DNA at the molecular level offer insight for the rationale design of nano-complexes for biomedical imaging and sensing. In this issue of Biotechnology Journal, Li et al. details a study of atomic force microscopy-enabled single molecule imaging of quantum dots and DNA for exploring their underlying binding mechanisms. Originated by the motivation to study materials’ behavior at the molecular scale [1], semiconductor quantum dots (QDs), which straddle the line between condensed matter and atomic physics, are among the most exciting and ubiquitous discoveries that have arisen from the nanotechnology field [2]. In a QD, all three dimensions of the crystal are limited to less than the exciton radius of the material and this quantum confinement effect gives rise to the well-documented properties of quantum dots, including size-tunable emission spectra, broad absorption spectra, narrow and symmetric emission spectra, high brightness and extremely stable photoluminescence [3, 4]. These extraordinary optical properties have rendered QDs a highly promising replacement to conventional organic dyes in molecular and cell and imaging and biosensing [5, 6]. Another fast-growing arena that benefits from the development of QDs is single molecule detection (SMD). The high extinction coefficient and quantum yield of QDs enable the robust detection of single nanoparticle labels by simple fluorescence microscopy for the study of single molecule dynamics. Unlike ensemble analysis, which measures averaged fluorescence properties, single molecule technologies interrogate individual molecules and provide statistical information on entire target populations. By incorporating novel signal transduction strategies, such as fluorescence resonance energy transfer (FRET)-based probes [7], QDs have been applied to single molecule detection of DNA/RNA targets [7] and intracellular trafficking [8]. Although ultrahigh sensitivity can be achieved, to date the detailed couplings between biomolecules and QDs have not thoroughly been investigated. This is in part due to the limited spatial resolution of the optical detection methods predominately employed in current studies of QD-DNA nano-complexes. In this issue of Biotechnology Journal, Li and co-workers report the interrogation of QD and DNA interactions at the single molecule level using atomic force microscopy (AFM) (Fig. 1). DNA molecules are immobilized on mica in the presence of cations, which serve as a counter ion on the DNA backbone to promote absorption to the negatively-charged mica. In this study, binding of a ~ 4 kbp plasmid DNA to QDs conjugated with poly-diallydimethylammonium chloride (PDDA) is chosen as a model where molecular bindings are favored by both electrostatic and van der Waals interactions. High resolution AFM imaging reveals multiple binding mechanisms, including: QD binding to DNA backbones, DNA wrapping around a QD, QD-mediated DNA looping, and DNA bridging by a QD, which are difficult to resolve by conventional optical measurements. Such comprehensive observation of multifaceted bio-conjugation provides insight to the rational design of DNA-QD nano-complexes for a variety of applications in medical imaging, diagnostics and gene delivery. The observed conformational change of DNA, induced by QD binding, provides information essential to the study of genotoxicity of QDs and other types of nanoparticles. Figure 1 Imaging of interactions between DNA and quantum dots by AFM