Programmable periodicity of quantum dot arrays with DNA origami nanotubes

Abstract

To fabricate quantum dot arrays with programmable periodicity, functionalized DNA origami nanotubes were developed. Selected DNA staple strands were biotin-labeled to form periodic binding sites for streptavidin-conjugated quantum dots. Successful formation of arrays with periods of 43 and 71 nm demonstrates precise, programmable, large-scale nanoparticle patterning; however, limitations in array periodicity were also observed. Statistical analysis of AFM images revealed evidence for steric hindrance or site bridging that limited the minimum array periodicity.

Figure 1

Schematics, AFM images at low magnification (upper) and high magnification (lower), and cross-sectional (upper) and axial (lower) height profiles of functionalized DNA origami nanotubes with nine biotin binding sites with (a−e) no attached nanoparticles; (f−j) attached streptavidin; and (k−o) attached streptavidin-conjugated quantum dots. The dashed lines in the high-magnification AFM images indicate the location of the cross-sectional profiles. Axial profiles represent the average of multiple profiles across the width of the nanotube (see Supporting Information S6).

Figure 2

High-magnification AFM images of streptavidin-conjugated quantum dots attached to functionalized DNA origami nanotubes with (a) 5 binding sites, 71 nm period; (b) 9 binding sites, 43 nm period; (c) 15 binding sites, 29 nm period; and (d) 29 binding sites, 14 nm period. All scale bars are 100 nm. Note (c) and (d) have fewer attached quantum dots than available binding sites. In addition, the diameter of quantum dots varies between images because of variation in tip radii between scans.

Figure 3

Histograms (bars) and calculated binomial distributions (lines) for the number of attached quantum dots for DNA nanotubes with (a) 5, (b) 9, (c) 15, and (d) 29 biotin binding sites. Data for each histogram were compiled from AFM image analysis for over 225 separate nanotubes, with the exact number, N, shown for each histogram. The average attachment probabilities, p, used to generate the calculated binomial distributions are indicated for each case.

Figure 4

Histograms (bars) and calculated geometric distributions (lines) for nearest-neighbor (N-N) separation of bound quantum dot pairs for DNA nanotubes with (a) 5, (b) 9, (c) 15, and (d) 29 biotin binding sites. The numbers of separations, N, measured for each case are provided in the figures, along with the average attachment probabilities, p. N-N separation of zero indicates two nearest neighbors with a separation less than one-half of a period.