A Circuit Simplification Mechanism Based on DNA Combinatorial Strands Displacement

• Autorzy: Niu Ying , Han Feng , Zhang Xuncai , Zhou Zheng

Identyfikatory

DOI

10.3233/FI-2019-1765

• Języki publikacji: EN

Abstrakty

EN

DNA strand displacement technology has been widely used in the field of molecular computing. In the traditional strand displacement circuits, the DNA strands of the toehold domain and the branch migration domain are connected by covalent bonds, while the toehold domain and the branch migration domain of the combinatorial strand displacement are located in different single-stranded DNA (ssDNA), and the flexible combinations of the two domains are realized by the hybridization of the linking domains. It has obvious advantages in the design of multi-input circuits. In this paper, the AND gate, OR gate and XOR gate are constructed by the combinatorial strand displacement mechanism. On this basis, the half-adder and encoder circuit are constructed. The Visual DSD simulation results show that when the DNA molecular signal strands are input, the desired DNA molecular signal strands are output by the specific intermolecular hybridization reaction and the intermolecular strand displacement reaction, which proves the validity and feasibility of the logic circuit.

Słowa kluczowe

EN

combinatorial strand displacement; DNA reaction network; encoder circuit; logic circuit; visual DSD

• Wydawca: IOS Press
• Czasopismo: Fundamenta Informaticae
• Rocznik: 2019
• Tom: Vol. 164, nr 2-3
• Strony: 243--257
• Opis fizyczny: Bibliogr. 30 poz., rys., tab., wykr.

Twórcy

autor

Niu Ying

• College of Electrical and Electronic Engineering, Zhengzhou University of Light Industry, Zhengzhou, China

autor

Han Feng

• College of Electrical and Electronic Engineering, Zhengzhou University of Light Industry, Zhengzhou, China

autor

Zhang Xuncai

• College of Electrical and Electronic Engineering, Zhengzhou University of Light Industry, Zhengzhou, China

autor

Zhou Zheng

• College of Electrical and Electronic Engineering, Zhengzhou University of Light Industry, Zhengzhou, China

Bibliografia

• [1] Mao C, Labean TH, Relf JH. Logical computation using algorithmic self-assembly of DNA triplecrossover molecules. Nature. 2000;407(6803):493-496. doi:10.1038/35035038.
• [2] Penchovsky R, Breaker RR. Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nature Biotechnology. 2005;23(11):1424-1433. dio:10.1038/nbt1155.
• [3] Benenson Y, Gil B, Bendor U, Adar R, Shapiro E. An autonomous molecular computer for logical control of gene expression. Nature. 2004;429(6990):423-429. dio:10.1038/nature02551.
• [4] Zhang DY, Winfree E. Control of DNA strand displacement kinetics using toehold exchange. Journal of the American Chemical Society. 2009;131(47):17303-17314. dio:10.1021/ja906987s.
• [5] Zhang DY, Seelig G. Dynamic DNA nanotechnology using strand-displacement reactions. Nature Chemistry. 2011;3(2):103-113. doi: 10.1038/nchem.957.
• [6] Genot AJ, Zhan DY, Bath J, Turberfield AJ. Remote toehold: a mechanism for flexible control of DNA hybridization kinetics. Journal of the American Chemical Society. 2011;113(7):2177-2182. dio:10.1021/ja1073239.
• [7] Qian L, Winfree E. A simple DNA gate motif for synthesizing large-scale circuits. International Workshop on DNA-Based Computers. 2008;5347(62):70-89. dio:10.1007/2F978-3-642-03076-5-7.
• [8] Qian L, Winfree E, Bruck J. Neural network computation with DNA strand displacement cascades. Nature. 2011;475(7356):368-372. doi:10.1038/nature10262.
• [9] Zhang C, Li N. Molecular logic computing model based on DNA self-assembly strand branch migration. Chinese Science Bulletin. 2013;58(1):32-38. dio:10.1007/s11434-012-5498-z.
• [10] Zhang X, Zhou Z, Niu Y. An Image Encryption Method Based on the Feistel Network and Dynamic DNA Encoding. IEEE Photonics Journal. 2018;10(4), Article Sequence Number:3901014. dio:10.1109/JPHOT.2018.2859257.
• [11] Pan LQ, Wang ZY, Li YF, Xu F, Zhang Q, Zhang C. Nicking enzyme-controlled toehold regulation for DNA logic circuits. Nanoscale.2017;9:18223-18228. dio:10.1039/C7NR06484E.
• [12] Shi X, Wang Z, Deng C. A novel bio-sensor based on DNA strand displacement. Plos One. 2014; 9(10):e108856. dio:10.1371/journal.
• [13] Stano NM, Jeong YJ, DonmezI, Tummalapalli P, Levin MK, Patel SS. DNA synthesis provides the driving force to accelerate DNA unwinding by a helicase. Nature, 2005; 435(7040):370-373. dio: 10.1038/nature03615.
• [14] Song T, Garg S, Mokhtar R. Analog computation by DNA strand displacement circuits. Acs Synthetic Biology. 2016; 5(8):898-912. dio:10.1021/acssynbio.6b00144.
• [15] Zhang C, Yang J, Xu J. Molecular logic computing model based on self-assembly of DNA nanoparticles. Chinese Science Bulletin. 2011;56(33):3566-3571. dio:10.1007/s11434-011-4725-3.
• [16] Li W, Zhang F, Yan H, Liu, Y. DNA based arithmetic function: a half adder based on DNA strand displacement. Nanoscale. 2016;8(6):3775-3784. dio:10.1039/c5nr08497k.
• [17] Zhang X, Zhou Z, Wang X, Cui G, Niu Y. A half-subtractor logic circuit based on the DNA double hairpin structure. Journal of Nanoelectronics and Optoelectronics. 2018;13(8):1153-1166.
• [18] Genot AJ, Bath J, Turberfield AJ. Combinatorial displacement of DNA strands: application to matrix multiplication and weighted sums. Angewandte Chemie International Edition. 2013;125(4):1227-1230. dio:10.1002/anie.201206201.
• [19] Zhang X, Niu Y, Shen C, Cui G. Fluorescence resonance energy transfer-based photonic circuits using single-stranded tile self-assembly and DNA strand displacement. Journal of Nanoscience and Nanotechnology. 2017;17(2):10531060. dio: 10.1166/jnn.2017.12656.
• [20] Yang J, Song Z, Liu S, Zhang Q, Zhang C. Dynamically arranging gold nanoparticles on DNA origami for molecular logic gates. Acs Applied Materials and Interfaces. 2016;8(34):22451-22456. dio:10.1021/acsami.6b04992.
• [21] Elbaz J, Yin P, Voigt CA. Genetic encoding of DNA nanostructures and their self-assembly in living bacteria. Nature Communications. 2016;7:11179. doi: 10.1038/ncomms11179.
• [22] Sawlekar R, Montefusco F, Kulkarni VV. Implementing nonlinear feedback controllers using DNA strand displacement reactions. IEEE Transactions on Nanobioscience. 2016;15(5):443-454. doi:10.1109/TNB.2016.2560764.
• [23] Mateiu L, Rannala B. Inferring complex DNA substitution processes on phylogenies using uniformization and data augmentation. Systematic Biology. 2006;55(2):259-269. doi:10.1080/10635150500541599.
• [24] Li W, Yang Y, Yan H. Three-input majority logic gate and multiple input logic circuit based on DNA strand displacement. Nano Letters. 2013;13(6):2980. doi:10.1021/nl4016107.
• [25] Alexandru M, Banu V, Vellvehi M, Godignon P, Milln J. Design of digital electronics for high temperature using basic logic gates made of 4H-SiC MESFETs. Materials Science Forum. 2011;711:104-108. doi:10.4028/www.scientific.net/MSF.711.104.
• [26] Thachuk C, Winfree E, Soloveichik D. Leakless DNA strand displacement systems. International Conference on DNA Computing and Molecular Programming. 2015;9211:133-153. doi:10.1007/978-3-319-21999-8_9.
• [27] Soloveichik D, Seelig G, Winfree E. DNA as a universal substrate for chemical kinetics. Proceedings of the National Academy of Sciences of the United States of America. 2010,107(12):5393-5398. doi:10.1073/pnas.0909380107.
• [28] Pennisi E. Genomics. ENCODE project writes eulogy for junk DNA. Science. 2012;337(6099):1159-1161. doi:10.1126/science.337.6099.1159.
• [29] Zhang X, Wang Y, Cui G, Niu Y, Xu J. Application of a novel IWO to the design of encoding sequences for DNA computing. Computers and Mathematics with Applications. 2009;57(11):2001-2008. doi:10.1016/j.camwa.2008.10.038.
• [30] Lakin MR, Simon Y, Filippo P, Emmott S, Phillips A. Visual DSD: a design and analysis tool for DNA strand displacement systems. Bioinformatics. Bioinformatics, 2011; 27(22):3211-3213. doi:10.1093/bioinformatics/btr543.

Uwagi

Opracowanie rekordu w ramach umowy 509/P-DUN/2018 ze środków MNiSW przeznaczonych na działalność upowszechniającą naukę (2019).