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DNA Nanotech

In collaboration with Professors Bernie Yurke, Will Hughes, Wan Kuang, Jeunghoon Lee, Elton Graugnard and Bill Knowlton, DNA as an engineering material is being used in a variety of ways as highlighted in the projects below.

Nucleic Acid Memory (NAM)

In collaboration with Will Hughes,  Reza M. Zadegan, Victor Zhirnov (SRC), George Church (Harvard) and Micron Technology, Inc. DNA is being used to to store digital data in DNA.

With the ever increasing volume of digital information, it is estimated that the global memory demand will exceed the projected silicon supply by 2040. Critical factors for the information and  communication industries are the scaling and energetics of information storage materials. One mechanism to expedite materials discovery for memory applications is to consider unconventional sources that have unique characteristics unavailable in other material systems. Nucleic acids, for example DNA, chemically encode information with a base-4 quaternary code (A,T,C,G). Nucleic Acid Memory (NAM) is a potential alternative to silicon based memory because its volumetric density is 1000 times greater and its energy of operation is 100M times less than flash memory – the industry standard. Rapid progress in DNA synthesis and sequencing has enabled reading and writing of arbitrary digital formats.Although ~100% recovery of encoded information has been demonstrated, the existing algorithms are not universal nor do they compensate for naturally occurring defects. Defects, including the loss of individual bases (letters) and complete sequences (words), are expected during NAM writing (synthesis), reading (sequencing), and storage. Our objective is to develop efficient and stable error correction algorithms for DNA that: (1) compensate for naturally occurring defects, and (2) account for synthesis constraints such as GC content and sequence repetition. This study is in pursuit of non-biological and nonvolatile NAM applications.

COLLABORATIONS:

FUNDING:

  • SRC STARnet- FAME 2015
  • Micron (2015)

Quantum DNA (qDNA)

Learn More about the qDNA Research Group

The Quantum DNA (qDNA) research area is a collaboration among Drs. Bill Knowlton, Bernie Yurke, Jeunghoon Lee, Lan Li, Ryan Pensack, Paul Davis, Wan Kuang, and Elton Graugnard. This collaboration spans multiple departments and colleges at Boise State and in combination forms the Quantum DNA Research Group. Dr. Li also leads the Materials Theory and Modeling Group at Boise State, which provides expertise and capabilities complementary to the collaboration. The Quantum DNA Research Group is itself organized into five research teams: (1) Dye Synthesis (led by Dr. Olga Mass, (2) DNA Construct Synthesis (led by Prof. Lee), (2) Ultrafast Spectroscopy (led by Drs. Pensack and Davis), (3) Single Molecule Characterization (led by Profs. Wan and Graugnard), and (5) Theory and Simulation (led by Prof. Li). Prof. Knowlton and Dr. Yurke co-lead the group.

The qDNA research area pioneers the use of deoxyribonucleic acid (DNA)—the building block of life on our planet—as a programmable, self-assembling architecture to organize dye molecules for quantum information systems (QIS). In particular, the qDNA research group has shown DNA self-assembly to be a viable platform for arranging and controlling the organization of dye aggregates to enable exciton delocalization. Exciton delocalization is the mechanism of energy transfer between dyes, in which an exciton is a bound electron-electron hole pair created when a dye is excited by a photon of light. Delocalization indicates that the exciton is not limited to one location and can move between dyes. Exciton delocalization and its electronic coherence between dyes and aggregates of dyes are mediated by several key parameters. We postulate, and have shown theoretically, that certain combinations of these parameters give rise to optically- accessible, entangled many-exciton states that can be tuned by tailoring the dye aggregate structure. Successful experimental demonstration of the preceding can result in defining design rules for a pathway to create, measure, and control quantum entanglement, a fundamental challenge in QIS. One of the long-term goals of the research group is to achieve room- temperature, molecular-excitonic quantum computing based on the rational design—that is using physical models to predict how a molecules structure will affect its behavior—of excitonic quantum gates. Most other quantum computing approaches may be more mature than this approach; however, they require extreme environments (e.g., extremely low temperatures, dry environments, external fields), and top-down approaches to fabricate constructs.

Professional Staff

Students

Graduate Students

Undergraduate Students

Collaboration

  • Boise State’s Nanoscale Materials and Device Group
  • California State University, Chico
  • Integrated DNA Technologies
  • Naval Research Laboratory
  • New York University
  • Princeton University
  • SETA BioMedicals
  • Southern Utah University
  • Temple University

Funding

  • Department of Energy, Idaho National Laboratory, Laboratory Directed Research and
    Development (sub-contract: July 2017−April 2020)
  • National Science Foundation’s Integrated NSF Support Promoting Interdisciplinary Research
    and Education (INSPIRE) (August 2017−July 2021)
  •  Department of Energy’s Established Program to Stimulate Competitive Research (DOE
    EPSCoR) (Phase 1: August 2019−August 2021)
  • Department of the Navy, Office of Naval Research (August 2019−August 2022)

DNA Reaction Networks

From an engineering perspective, DNA is to catalytic amplifiers as silicon is to transistors. As modular components, DNA amplifiers can be interconnected to perform complex calculations chemically much the same way that transistors can be combined to perform calculations electronically. When engineered into a detection system, DNA can amplify miRNAs, perform calculations on the amplified signal, and generate an observable output, analogous to the results of a disposable pregnancy test. As miRNAs are linked to over 180 diseases, including cardiovascular, neurological, muscular, sexually transmitted, obesogenic, and diabetic diseases, the proposed research is significant because of its implications on human health. Our proposed detection system consists of four programmable DNA reaction network modules, illustrated in Fig. 1 with components color-coded by function.

Figure 1 - DNA amplifier

FIGURE 1. DNA reaction network engineered to detect disease-related miRNAs. Translator (a): This reaction network is engineered to detect a target miRNA. The miRNA triggers a chain reaction in which a fuel strand releases both the original miRNA and an output DNA strand. Output strands are released only if both fuel and miRNA are present. Cross-Catalytic Amplifier (b): This system of coupled reaction networks amplifies the output strand of the translator to make the miRNA presence more apparent. The translator output initiates a second chain reaction that results in exponential growth of signal strands. Fluorescent Reporter (c) and Colorimetric Reporter (d): The reporters in these two modules react with signal strands from the amplifier to produce easily observable optical signals that provide a positive/negative indication for disease.


DNA Origami for Optoelectronic Applications

The ability to precisely pattern nanoparticles is essential for realizing the potential of nanoelectronic and nanoplasmonic devices. Over the last decade, DNA oligonucleotides have been programmed to aggregate, crystallize, and self-assemble into spatially discrete assemblies and linear arrays. DNA nanotechnology offers a compelling approach towards programmable nanoparticle patterning. By implementing basic design rules, DNA can be used to form complex nanostructures using the methods of either tiled DNA motifs or DNA origami. When functionalized, these nanostructures can serve as two- and three-dimensional nanoparticle scaffolds.

Presented here is our method of fabricating nanoparticle arrays with controlled periodicity using three-dimensional, six-helix DNA origami nanotubes. DNA origami nanotubes of predetermined dimensions were used to precisely arrange nanoparticles by incorporating binding sites along the axis of the nanotube using biotin-labeled staple strands. The unique sequence of each staple strand permits precise spatial control and modular design of periodic or aperiodic binding sites. The three-dimensional DNA origami nanotubes provide a rigid structure for nanoparticle attachment in solution.

Figure 2 DNA AFM example

FIGURE 2. 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 9 biotin binding sites with: (a-e) no attached nanoparticles; (f-j) attached streptavidin; (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.


Collaborations:

Funding: