No abstract

The field of DNA nanoscience has demonstrated many exquisite DNA nanostructures and intricate DNA nanodevices. However, the operation of each step of prior demonstrated DNA nanodevices requires the diffusion of DNA strands, and the speed of these devices is limited by diffusion kinetics. Here we demonstrate chains of localized DNA hybridization reactions on the surface of a self-assembled DNA origami rectangle. The localization design for our DNA nanodevices does not rely on the diffusion of DNA strands for each step, thus providing faster reaction kinetics. The locality also provides considerable increased scalability, since localized components of the devices can be reused in other locations. A variety of techniques, including atomic force microscopy, total internal reflection fluorescence, and ensemble fluorescence spectroscopy, are used to confirm the occurrence of localized DNA hybridization reactions on the surface of DNA origami. There are many potential biological applications for our localized DNA nanodevices, and the localization design is extensible to applications involving DNA nanodevices operating on other molecular surfaces, such as those of the cell.

DNA circuits have been widely used to develop biological computing devices because of their high programmability and versatility. Here, we propose an architecture for the systematic construction of DNA circuits for analog computation based on DNA strand displacement. The elementary gates in our architecture include addition, subtraction, and multiplication gates. The input and output of these gates are analog, which means that they are directly represented by the concentrations of the input and output DNA strands, respectively, without requiring a threshold for converting to Boolean signals. We provide detailed domain designs and kinetic simulations of the gates to demonstrate their expected performance. On the basis of these gates, we describe how DNA circuits to compute polynomial functions of inputs can be built. Using Taylor Series and Newton Iteration methods, functions beyond the scope of polynomials can also be computed by DNA circuits built upon our architecture.

DNA devices have been shown to be capable of evaluating Boolean logic. Several robust designs for DNA circuits have been demonstrated. Some prior DNA-based circuits are use-once circuits since the gate motifs of the DNA circuits get permanently destroyed as a side effect of the computation, and hence cannot respond correctly to subsequent changes in inputs. Other DNA-based circuits use a large reservoir of buffered gates to replace the working gates of the circuit and can be used to drive a finite number of computation cycles. In many applications of DNA circuits, the inputs are inherently asynchronous, and this necessitates that the DNA circuits be asynchronous: the output must always be correct regardless of differences in the arrival time of inputs. This paper demonstrates: 1) renewable DNA circuits, which can be manually reverted to their original state by addition of DNA strands, and 2) time-responsive DNA circuits, where if the inputs change over time, the DNA circuit can recompute the output correctly based on the new inputs, that are manually added after the system has been reset. The properties of renewable, asynchronous, and time-responsiveness appear to be central to molecular-scale systems; for example, self-regulation in cellular organisms.

DNA is a highly programmable biomolecule and has been used to construct biological circuits for different purposes. An important development of DNA circuits is to process the information on receptors on cell membranes. In this Communication, we introduce an architecture to program localized DNA-based biomolecular reaction networks on cancer cell membranes. Based on our architecture, various types of reaction networks have been experimentally demonstrated, from simple linear cascades to reaction networks of complex structures. These localized DNA-based reaction networks can be used for medical applications such as cancer cell detection. Compared to prior work on DNA circuits for evaluating cell membrane receptors, the DNA circuits made by our architecture have several major advantages including simpler design, lower leak, lower cost, and higher signal-to-background ratio.