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. 2015 Dec 8;6:10089.
doi: 10.1038/ncomms10089.

A DNA-based System for Selecting and Displaying the Combined Result of Two Input Variables

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Free PMC article

A DNA-based System for Selecting and Displaying the Combined Result of Two Input Variables

Huajie Liu et al. Nat Commun. .
Free PMC article

Abstract

Oligonucleotide-based technologies for biosensing or bio-regulation produce huge amounts of rich high-dimensional information. There is a consequent need for flexible means to combine diverse pieces of such information to form useful derivative outputs, and to display those immediately. Here we demonstrate this capability in a DNA-based system that takes two input numbers, represented in DNA strands, and returns the result of their multiplication, writing this as a number in a display. Unlike a conventional calculator, this system operates by selecting the result from a library of solutions rather than through logic operations. The multiplicative example demonstrated here illustrates a much more general capability--to generate a unique output for any distinct pair of DNA inputs. The system thereby functions as a lookup table and could be a key component in future, more powerful data-processing systems for diagnostics and sensing.

Figures

Figure 1
Figure 1. Illustration of the steps involved in the multiplication.
Two input DNA strands X and Y (for example, 1 and 2) are converted into a digital presentation of the result.
Figure 2
Figure 2. Illustration of the steps involved in the multiplication.
(a) Illustration of the steps involved in the process from the input hybridization, capture on MB, result selection and translator selection. (b) Native PAGE analysis of the hybridization processes involved in the process.
Figure 3
Figure 3. Selection of a result from arbitrary input sequences X and Y.
(a) Illustration of the steps involved in the process from the input hybridization with the capture–linker and MBs, and result selection. (b) Native PAGE analysis of the hybridization processes involved in the formation of the input complex. (c) Native PAGE analysis of the hybridization processes involved in the selection of the correct result strand in a four-way junction.
Figure 4
Figure 4. Illustration of the selection of translator strands and immobilization on a seven-segmented display.
The result `2' complex captured on magnetic beads is mixed with the translator library resulting in selection of the strands required to display 2 in the seven-segmented display. R: Contrast agent for imaging such as a dye or magnetic bead.
Figure 5
Figure 5. Displaying the results of multiplication reactions on seven-segmented displays.
(a) The design of the first DNA chip used to display the results. The values of inputs X and Y are printed with Cy3, an operator of ‘ × ' and a line are printed with Cy5-labelled strands. Host strands are printed on the output area for digital display of calculated results. (b) The recognition between host and translated result. (c) Fluorescent images by a plate reader of the chip before and after the result–translator complex was added. (d) The results of a series of multiplications imaged by a plate reader. (e) Displaying the result by immobilization of the result–translator complex connected to MBs on a DNA chip. The right-hand panel shows a photo and its magnification of the result of the 1 × 2 multiplication. (f) Immobilization of the unlabelled result–translator complex on V-shaped patterns on DNA origami and imaging of the output numbers of three multiplications using AFM. Scale bars, 500 nm.

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