Network Topology-directed Design of Molecular CPU for Cell-like Dynamic Information Processing

Overview

Journal Sci Adv

Specialties Biology
Science

Date 2022 Aug 10

PMID 35947658

Authors

Dan Wang

Yani Yang

Fengming Chen

Yifan Lyu

Weihong Tan

Affiliations

Soon will be listed here.

Abstract

Natural cells (NCs) can automatically and continuously respond to fluctuant external information and distinguish meaningful stimuli from weak noise depending on their powerful genetic and protein networks. We herein report a network topology-directed design of dynamic molecular processing system (DMPS) as a molecular central processing unit that powers an artificial cell (AC) able to process fluctuant information in its immediate environment similar to NCs. By constructing a mixed cell community, ACs and NCs have synchronous response to fluctuant extracellular stimuli under physiological condition and in a blood vessel-mimic circulation system. We also show that fluctuant bioinformation released by NCs can be received and processed by ACs. The molecular design of DMPS-powered AC is expected to allow a profound understanding of biological systems, advance the construction of intelligent molecular systems, and promote more elegant bioengineering applications.

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References

Dauphin-Ducharme P, Yang K, Arroyo-Curras N, Ploense K, Zhang Y, Gerson J . Electrochemical Aptamer-Based Sensors for Improved Therapeutic Drug Monitoring and High-Precision, Feedback-Controlled Drug Delivery. ACS Sens. 2019; 4(10):2832-2837. PMC: 6886665. DOI: 10.1021/acssensors.9b01616. View

Ouyang Y, Zhang P, Willner I . Dissipative biocatalytic cascades and gated transient biocatalytic cascades driven by nucleic acid networks. Sci Adv. 2022; 8(18):eabn3534. PMC: 9075803. DOI: 10.1126/sciadv.abn3534. View

Wang Z, Detomasi T, Chang C . A dual-fluorophore sensor approach for ratiometric fluorescence imaging of potassium in living cells. Chem Sci. 2021; 12(5):1720-1729. PMC: 8179100. DOI: 10.1039/d0sc03844j. View

Krishnan S, Ziegler D, Arnaut V, Martin T, Kapsner K, Henneberg K . Molecular transport through large-diameter DNA nanopores. Nat Commun. 2016; 7:12787. PMC: 5036142. DOI: 10.1038/ncomms12787. View

Lanphere C, Offenbartl-Stiegert D, Dorey A, Pugh G, Georgiou E, Xing Y . Design, assembly, and characterization of membrane-spanning DNA nanopores. Nat Protoc. 2020; 16(1):86-130. DOI: 10.1038/s41596-020-0331-7. View

Gobbo P, Tian L, Kumar B, Turvey S, Cattelan M, Patil A . Catalytic processing in ruthenium-based polyoxometalate coacervate protocells. Nat Commun. 2020; 11(1):41. PMC: 6941959. DOI: 10.1038/s41467-019-13759-1. View

Li S, Jiang Q, Liu S, Zhang Y, Tian Y, Song C . A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo. Nat Biotechnol. 2018; 36(3):258-264. DOI: 10.1038/nbt.4071. View

Dey S, Dorey A, Abraham L, Xing Y, Zhang I, Zhang F . A reversibly gated protein-transporting membrane channel made of DNA. Nat Commun. 2022; 13(1):2271. PMC: 9051096. DOI: 10.1038/s41467-022-28522-2. View

Omidvar M, Zdarta J, Sigurdardottir S, Pinelo M . Mimicking natural strategies to create multi-environment enzymatic reactors: From natural cell compartments to artificial polyelectrolyte reactors. Biotechnol Adv. 2021; 54:107798. DOI: 10.1016/j.biotechadv.2021.107798. View

10.

Vermesh O, Aalipour A, Ge T, Saenz Y, Guo Y, Alam I . An intravascular magnetic wire for the high-throughput retrieval of circulating tumour cells in vivo. Nat Biomed Eng. 2018; 2(9):696-705. PMC: 6261517. DOI: 10.1038/s41551-018-0257-3. View

11.

Peng R, Xu L, Wang H, Lyu Y, Wang D, Bi C . DNA-based artificial molecular signaling system that mimics basic elements of reception and response. Nat Commun. 2020; 11(1):978. PMC: 7033183. DOI: 10.1038/s41467-020-14739-6. View

12.

Simmel F, Yurke B, Singh H . Principles and Applications of Nucleic Acid Strand Displacement Reactions. Chem Rev. 2019; 119(10):6326-6369. DOI: 10.1021/acs.chemrev.8b00580. View

13.

Liu S, Zhang Y, Li M, Xiong L, Zhang Z, Yang X . Enzyme-mediated nitric oxide production in vasoactive erythrocyte membrane-enclosed coacervate protocells. Nat Chem. 2020; 12(12):1165-1173. DOI: 10.1038/s41557-020-00585-y. View

14.

Burns J, Seifert A, Fertig N, Howorka S . A biomimetic DNA-based channel for the ligand-controlled transport of charged molecular cargo across a biological membrane. Nat Nanotechnol. 2016; 11(2):152-6. DOI: 10.1038/nnano.2015.279. View

15.

Rateitschak K, Wolkenhauer O . Thresholds in transient dynamics of signal transduction pathways. J Theor Biol. 2010; 264(2):334-46. DOI: 10.1016/j.jtbi.2010.02.001. View

16.

Wang X, Tian L, Ren Y, Zhao Z, Du H, Zhang Z . Chemical Information Exchange in Organized Protocells and Natural Cell Assemblies with Controllable Spatial Positions. Small. 2020; 16(27):e1906394. DOI: 10.1002/smll.201906394. View

17.

Ohtsuka K, Sato S, Sato Y, Sota K, Ohzawa S, Matsuda T . Fluorescence imaging of potassium ions in living cells using a fluorescent probe based on a thrombin binding aptamer-peptide conjugate. Chem Commun (Camb). 2012; 48(39):4740-2. DOI: 10.1039/c2cc30536d. View

18.

Hadorn M, Boenzli E, Sorensen K, Lucrezia D, Hanczyc M, Yomo T . Defined DNA-mediated assemblies of gene-expressing giant unilamellar vesicles. Langmuir. 2013; 29(49):15309-19. DOI: 10.1021/la402621r. View

19.

Zhang Y, Chen Y, Yang X, He X, Li M, Liu S . Giant Coacervate Vesicles As an Integrated Approach to Cytomimetic Modeling. J Am Chem Soc. 2021; 143(7):2866-2874. DOI: 10.1021/jacs.0c12494. View

20.

Liu J, Li F, Wang Y, Pan L, Lin P, Zhang B . A sensitive and specific nanosensor for monitoring extracellular potassium levels in the brain. Nat Nanotechnol. 2020; 15(4):321-330. DOI: 10.1038/s41565-020-0634-4. View