research paper of dna computing

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Recent advances in DNA computing

For immediate release, acs news service weekly presspac: november 17, 2021.

DNA molecules encode the instructions for life itself. They make up the genes responsible for everything from hair color to disease risk. And as if that weren’t enough, DNA can also perform calculations and compute! The molecules are fully programmable and can perform calculations very quickly in parallel, making them ideal for complex and time-consuming operations. Below are some recent papers published in ACS journals that report on innovations in DNA computing. 

“Advances in Applications of Molecular Logic Gates” ACS Omega Nov. 6, 2021 This review discusses recent advances in molecular logic gates, including those that incorporate DNA. The researchers describe how the gates are being used to monitor water quality, test food safety, and diagnose and treat diseases.  

“CRISPR-Powered DNA Computing and Digital Display” ACS Synthetic Biology Oct. 27, 2021 In this paper, the researchers developed a microfluidic chip with CRISPR reactions freeze-dried onto it that can perform and display the results of several different types of mathematical calculations, such as obtaining the square root of a number. They say the chip could someday be used to encrypt and conceal messages.

“Programmable DNAzyme Computing for Specific  In Vivo  Imaging: Intracellular Stimulus-Unlocked Target Sensing and Signal Amplification” Analytical Chemistry Aug. 27, 2021 Some biomarkers of cancer are present in both healthy and tumor tissues, just at slightly different levels. To distinguish these types of cells in living mice, the authors of this paper used programmable DNAzyme computing, which also could image the tumors, making them visible with fluorescent light.

“DNA Computing: NOT Logic Gates See the Light” ACS Synthetic Biology June 18, 2021 Researchers have used DNA to perform Boolean “AND” and “OR” functions, but it’s been difficult to construct “NOT” gates, in which the absence of an input is converted into an output. And premature execution of a “NOT” function can produce erroneous results. So, for greater control, this group created a novel photoactivatable “NOT” gate that responds to microRNA sequences.

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[The current status and future prospects of DNA computing]

Affiliations.

• 1 Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China.
• 2 State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, China.
• PMID: 33973429
• DOI: 10.13345/j.cjb.200408

Abstract in English, Chinese

As the demand for high-performance computing continues to grow, traditional computing models are facing unprecedented challenges. Among the many emerging computing technologies, DNA computing has attracted much attention due to its low energy consumption and parallelism. The DNA circuit, which is the basis for DNA computing, is an important technology for the regulation and processing of the molecular information. This review highlights the basic principles of DNA computing, summarizes the latest research progress, and concludes with a discussion of the challenges of DNA computing. Such integrated molecular computing systems are expected to be widely used in the fields of aerospace, information security and defense system.

随着高性能计算需求的不断增长，传统计算模式面临着前所未有的巨大挑战。在众多新兴计算技术中，DNA计算系统以其低能耗、并行化等特点而广受关注。DNA电路 (DNA circuit) 是实现DNA计算的基础，也是该领域重要的分子信息调控和处理技术。文中重点介绍了DNA计算的基本原理，并总结了最新的研究进展，最后讨论了基于DNA计算所面临的挑战。此类集成的分子计算系统有望广泛应用于航空航天、信息安全及国防建设等领域。.

Keywords: DNA chip; DNA circuit; DNA computing; DNA strand replacement technology; gene circuit.

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Journal of Materials Chemistry B

Advancements in dna computing: exploring dna logic systems and their biomedical applications.

DNA computing is regarded as one of the most promising candidates for the next generation of molecular computers, utilizing DNA to execute Boolean logic operations. In recent decades, DNA computing has garnered widespread attention due to its powerful programmable and parallel computing capabilities, demonstrating significant potential in intelligent biological analysis. This review summarizes the latest advancements in DNA logic systems and their biomedical applications. Firstly, it introduces recent DNA logic systems based on various materials such as functional DNA sequences, nanomaterials, and three-dimensional DNA nanostructures. The material innovations driving DNA computing have been summarized, highlighting novel molecular reactions and analytical performance metrics like efficiency, sensitivity, and selectivity. Subsequently, it outlines the biomedical applications of DNA computing-based multi-biomarker analysis in cellular imaging, clinical diagnosis, and disease treatment. Additionally, it discusses the existing challenges and future research directions for the development of DNA computing.

• This article is part of the themed collections: Journal of Materials Chemistry B Emerging Investigators 2024 and Journal of Materials Chemistry B Recent Review Articles

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Y. Zhao, X. Li, Y. Zhou, X. Tian, Y. Miao, J. Wang, L. Huang and F. Meng, J. Mater. Chem. B , 2024, Accepted Manuscript , DOI: 10.1039/D4TB00936C

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DNA Computing

New Computing Paradigms

• © 1998
• Gheorghe Păun 0 ,
• Grzegorz Rozenberg 1 ,
• Arto Salomaa 2

Institute of Mathematics of Romanian Academy, Bucharest, Romania Research Group on Natural Computing, Department of Computer Science and Artificial Intelligence, Sevilla University, Sevilla, Spain

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Leiden Institute of Advanced Computer Science, University of Leiden, Leiden, The Netherlands

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• The first book about DNA computing, a revolutionary new paradigm with great promise
• On massively parallel molecular computing using DNA
• Extremely well known and prolific authors
• An introductory text with views on fundamental theory

Part of the book series: Texts in Theoretical Computer Science. An EATCS Series (TTCS)

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On Design and Analysis of Chemical Reaction Network Algorithms

Looking for Computers in the Biological Cell. After Twenty Years

The Biomolecular Computation Paradigm: A Survey in Massive Biological Computation

• Berechenbarkeit
• Berechnungsmodelle
• DNA computing
• DNA-Rechnen
• Paralleles Rechnen
• Watson-Crick-Komplementarität
• formal language

Table of contents (12 chapters)

Front matter, introduction: dna computing in a nutshell.

• Gheorghe Păun, Grzegorz Rozenberg, Arto Salomaa

Background and Motivation

Dna: its structure and processing, beginnings of molecular computing, mathematical theory, introduction to formal language theory, sticker systems, watson—crick automata, insertion-deletion systems, splicing systems, universality by finite h systems, splicing circular strings, distributed h systems, splicing revisited, back matter, authors and affiliations, institute of mathematics of romanian academy, bucharest, romania.

Gheorghe Păun

Research Group on Natural Computing, Department of Computer Science and Artificial Intelligence, Sevilla University, Sevilla, Spain

Grzegorz Rozenberg

Arto Salomaa

Bibliographic Information

Book Title : DNA Computing

Book Subtitle : New Computing Paradigms

Authors : Gheorghe Păun, Grzegorz Rozenberg, Arto Salomaa

Series Title : Texts in Theoretical Computer Science. An EATCS Series

DOI : https://doi.org/10.1007/978-3-662-03563-4

Publisher : Springer Berlin, Heidelberg

eBook Packages : Springer Book Archive

Copyright Information : Springer-Verlag Berlin Heidelberg 1998

Hardcover ISBN : 978-3-540-64196-4 Published: 15 September 1998

Softcover ISBN : 978-3-642-08388-4 Published: 07 December 2010

eBook ISBN : 978-3-662-03563-4 Published: 09 March 2013

Series ISSN : 1862-4499

Series E-ISSN : 1862-4502

Edition Number : 1

Number of Pages : IX, 400

Topics : Theory of Computation , Computation by Abstract Devices , Mathematical Logic and Formal Languages , Biotechnology , Microbiology

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• Review Article
• Published: 12 June 2012

Biomolecular computing systems: principles, progress and potential

• Yaakov Benenson 1  

Nature Reviews Genetics volume  13 ,  pages 455–468 ( 2012 ) Cite this article

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• Computational biology and bioinformatics
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The notion of computation is none other than a systematic way of processing information, and thus computation is central to the function of biological systems, as it is crucial for complex man-made machinery.

Whereas biological computing is ubiquitous in living systems, the capacity to engineer new biological computing systems will open the way to an unprecedented level of rational control over living matter that can be used in all areas of biological engineering and medicine

Current engineering effort is split between biochemical systems that function in carefully constituted settings and biological systems that operate in living cells or cell ensembles. The two approaches are complementary because biochemical systems show what is possible in principle, whereas biological systems must deal with the complexity of the host and thus are at this point simpler and smaller in scale.

The construction of molecular computing systems has been inspired by known theoretical models of computation, such as state machines and logic and analogue circuits. Each model is best suited for a different class of tasks.

The logic circuits model has spawned a large number of implementations both in the test tube and in living cells, with the basic building blocks comprising DNA oligomers in the test tube and re-engineered regulatory switches in living cells. Recent achievements include neural-like network with associative memory made of DNA switches, a trainable ribozyme-based molecular network, a number of distributed logic gates in bacteria and yeast and a cell-type classifier for cancer cell detection and destruction.

Molecular systems inspired by state machines were implemented with both biochemical and biological approaches, resulting in molecular finite automaton and recombinase-based counter.

The task of information processing, or computation, can be performed by natural and man-made 'devices'. Man-made computers are made from silicon chips, whereas natural 'computers', such as the brain, use cells and molecules. Computation also occurs on a much smaller scale in regulatory and signalling pathways in individual cells and even within single biomolecules. Indeed, much of what we recognize as life results from the remarkable capacity of biological building blocks to compute in highly sophisticated ways. Rational design and engineering of biological computing systems can greatly enhance our ability to study and to control biological systems. Potential applications include tissue engineering and regeneration and medical treatments. This Review introduces key concepts and discusses recent progress that has been made in biomolecular computing.

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Pathways to cellular supremacy in biocomputing

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Acknowledgements

The author's research is funded by ETH Zurich, a US National Institutes of Health and National Cancer Institute grant (5R01CA155320) and a European Research Council starting grant. He wishes to thank F. Rudolf for discussions.

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A unit of information that is processed by a computing system, or a collection of all such units.

A unit of information that is produced as a result of computation, or a collection of all such units.

A specific relationship between the inputs and the outputs of computation expressed as a mathematical function or as a computation procedure (program); it can be formally described as a collection of all pairs ([inputs], [outputs]), where [inputs] is a specific combination of legitimate inputs, and [outputs] is a result of computation for this combination.

Specific approaches towards implementing information-processing tasks; they are usually required to be universal.

A design framework that enables construction of molecular systems that are capable of implementing desired input–output mappings between molecular inputs and outputs or a specific implementation of such a system.

A molecular computer that does not require external interference apart from initializing the computer components and (optionally) the inputs.

A set of engineered genes that can be implanted into a living cell and, following their expression, can form functional biological networks comprising these genes and their products (RNA and protein).

Mappings between multiple inputs and a single output, where both the inputs and the output can only take values of zero and one (or false and true).

Specific arrangements of logic gates that can compute specific logic functions.

A collection of gate types that can be used to compute any logic function.

Gates of a single type that can be used to implement any conceivable logic function.

A standard way of expressing logic functions that can be used to represent any logic function.

Arrangements of gates that compute continuous-value functions, such as multiplication.

A class of models of computation that comprise a tape of symbols as data storage and a controller that scans the tape, reads and writes symbols and modifies its own state based on specific transition rules.

A class of state machines that process strings from left to right. The controller scans symbols one by one, changing the state at each step, depending on the current state, according to the rule <current state>, <current symbol> <next state> (and move to the next symbol).

A set of coupled chemical processes that do not reach equilibrium for extended periods of time and instead exhibit oscillations or other dynamic features

A computer architecture that uses multiple stand-alone computing units that interact with each other to accomplish a common computational task.

An extreme case of distributed computing with very large number of simple computing units that can move in space and only interact locally.

An abstract gate embodying some features of neuron cells, which calculates a weighted sum of the inputs and generates an output of one when this sum is above a certain threshold.

A small computational unit that implements a fixed logic function such as AND between one or two, but sometimes more, inputs.

A chemical process whereby a single-stranded DNA oligonucleotide replaces the shorter of two strands in a partially double-stranded DNA duplex. This starts with the oligonucleotide binding to the single-stranded section (the 'toehold') and goes to completion because the new duplex has a higher thermodynamic stability.

A class of artificial neural networks in which the individual 'neurons' mutually excite and inhibit each other. The network can be trained with specific input sets (patterns) such that each pattern corresponds to a steady state. After the network has been trained, any new input pattern will cause the network to convert to the state that is closest to this pattern, implementing memory by association.

Physical processes or computations whose outputs do not affect the inputs.

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Benenson, Y. Biomolecular computing systems: principles, progress and potential. Nat Rev Genet 13 , 455–468 (2012). https://doi.org/10.1038/nrg3197

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Published : 12 June 2012

Issue Date : July 2012

DOI : https://doi.org/10.1038/nrg3197

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