Optical and electronic measurement of DNA Origami-based detectors
Abstract
DNA origami provides the ability to engineer structures of arbitrary 3D geometry at length scales from 5 nanometers to 100 nanometers. Of particular interest are reconfigurable origami de- vices, whose shape and function can be switched upon binding of other molecules. One important class of such devices are origami-based detectors of other target molecules, ranging from small molecules such as antibiotics, to DNA and protein biomarkers of disease. Such detectors exhibit an ~open state~ in which the target molecule is unbound, and the detector is flexible, and a ~closed state~ in which the target molecule binds and rigidly fixes both halves of the detector together. Previously reported detectors have taken the form of scissor-like structures (whose dynamics could only be measured via laborious atomic force microscopy) and FRET-based based sensors (which must be measured with relatively bulky and expensive optical equipment). Under a pending ONR award we have proposed to develop Venus flytrap-shaped origami sensors, whose state changes from open to closed can be sensed electronically, either via electrochemical measurements on gold electrodes or capacitive measurements on graphene. Should either method work, the system should be able to be miniaturized to a cellphone-sized device suitable for point-of-care treatment, and detection should be able to be multiplexed, so that a single disposable chip can detect hundreds of different analytes (such as disease biomarkers). The pending ONR award has funds for two aspects of the project: (1) design and synthesis of origami-based sensors and (2) a commercial electronic instrument for capacitive measurements on graphene. Under the current DURIP proposal we seek to acquire two additional instruments, which will work together with the graphene-based instrument in a unified feedback-based workflow, to greatly accelerate the development of origami-based detectors. The first requested instrument is a potentiostat, for performing electrochemical analysis of origami detectors on gold electrodes. This instrument is complementary to the instrument for capacitive analysis, as the mechanism of sensing is completely different and we propose to compare the sensitivity of the two methods. Importantly, electrochemical measurement promises significant advantages: it is less sensitive to spurious signals from nonspecifically adsorbed molecules on the sensor surface, and thus has greater potential for real-time measurement of a diagnostic markers in a patient. The second instrument is a super-resolution microscope which will enable us to do fast design and test iterations on both the origami detectors, and the materials systems used for electronic detection. While our eventual goal is all-electronic detection, debugging origami-based detectors in an electronic setting is very difficult as it is impossible to directly see which origami devices are functional, and which are stuck open or closed. Because we will be testing origami sensors on a variety of surfaces that have only rarely been used with origami (gold and graphene) and we will be modifying each of these surfaces with several different chemistries for both adhering the detectors and providing passivation to prevent nonspecific binding, we will have to re-observe the yield of functional origami detectors, and re-evaluate nonspecific binding constantly during detector development. Only a super-resolution optical method, as provided by the requested microscope, will be sufficient for daily design-test cycles. Both instruments will help serve the goals of other DNA origami-related DoD, NSF, NIH, and HFSP funded projects at Caltech and both instruments will be extensively used in a combined undergraduate/graduate class entitled ~Design and Construction of Programmable Molecular Systems~ which introduces students to cutting edge experimental methods in DNA nanotechnology. APPROVED FOR PUBLIC RELEASE.
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- May 24, 2019
- Source ID
- N000141912341
Entities
People
- Paul W. K. Rothemund
Organizations
- California Institute of Technology
- Office of Naval Research
- United States Navy