DNA-Based Excitonic AND Logic Gate

Department of Enrollment

Materials Science

Faculty Mentor Name

William B. Knowlton

Report Date


Document Type

Student Presentation


Scaffolded DNA Origami1 has been utilized as a ‘nanobreadboard,’ and decorated with nanoparticles (e.g. organic dyes, inorganic quantum dots and metallic nanoparticles) to engineer near-field optoelectronic devices. Successfully fabricated DNA origami-based excitonic devices include waveguides2-5, switches6, and logic gates7-9.

Recently, an alternative approach to scaffolded DNA origami, termed ‘molecular canvases’, has been introduced that uses short single-stranded DNA motifs (~16-42 bps) to fabricate two- and three-dimensional nanostructures10-12. DNA motifs can be viewed as ‘molecular pixels/voxels’ and constituently selected to reconfigure the shape and size of the canvas. Similar to DNA origami, molecular canvas self-assembly is a one-step process that offers programmability afforded by DNA, however, without the aid of a long single-stranded scaffold. Molecular canvas structures can be utilized as nanobreadboards with programmable sub-diffraction resolution positioning of nanoparticles. Augmenting certain single-stranded DNA motifs with strand extensions, called ‘sticky-ends’ (~20-25 bps), enables nanoparticle attachment to occur via strand hybridization13 and allows dynamic device operations to be performed. Though the molecular canvas offers reconfigurability and modularity, it has yet to be utilized as a nanobreadboard for device applications.

Constructing single-module devices utilizing molecular canvases is the first step towards developing self-ordering modular devices. In Figure 1(a), we present a 16 nm X 28 nm two-dimensional molecular canvas composed of 28 short DNA strands used as a nanobreadboard for the attachment of fluorescent dyes (FAM, TAMRA, and Cy5)11. Figure 1(b,c) demonstrates programmable reconfigurability of the structure shape and size as provided by the molecular canvas. AND logic operations and excitonic waveguides (e.g. photonic wires) are demonstrated through proximate positioning of four dyes onto nanobreadboards. The input and output dyes (named F and C, respectively) are attached directly onto nanobreadboards. Two intermediary dyes (T1 and T2) are attached to independent strands such that logic operations can be performed via strand hybridization. Attachment of all four dyes yields an energy waveguide resulting in photonic emission that is easily detected. As depicted in the truth table in Fig. 1(d), a ‘1’ truth value corresponds only to the attachment of both T1 and T2 in which the ON-OFF threshold is surpassed. Spectral data, such as that shown in Fig. 1(e), is obtained by exciting the input dye (F) with 450 nm wavelength photons and monitoring fluorescent emission over a range of wavelengths. Excitonic energy transfer from F to T1 & T2 and from T1 & T2 to C corresponds to spectral peaks at 579 nm and 661 nm, respectively. Logic operations are expressed by exciting F with 450 nm wavelength photons and examining fluorescent emission wavelengths from C at only 668 nm. Figure 1(f, g) demonstrates the attachment of T1 and T2 independently to define an ON-OFF threshold. Hence, we have validated the use of a molecular canvas as a nanobreadboard and demonstrated a near-field AND logic device that can be extended to fabricate near-field logic devices of greater complexity via a modular approach.


This project was supported in part by: (1) NSF Grant No. CCF 0855212, (2) NSF IDR No. 1014922, (3) NIH Grant No. P20 RR016454, (4) NIH Grant No. K25GM093233, (5) W.M. Keck Foundation Award, (6) DARPA Contract No. N66001-01-C-80345, and (6) Micron MSE PhD Fellowship. We also thank the students and staff within the Nanoscale Materials & Device Research Group (nano.boisestate.edu).


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