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McCaskill JS. From quasispecies to quasispaces: coding and cooperation in chemical and electronic systems. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:459-478. [PMID: 29500529 DOI: 10.1007/s00249-018-1284-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/15/2018] [Accepted: 02/14/2018] [Indexed: 10/17/2022]
Abstract
This contribution addresses the physical roles of spatial structures, either externally imposed or generated through self-assembly, either passive or active, on the physical chemistry of evolution. Starting with simple diffusion in closed capillaries, a one-dimensional space, it covers eight aspects of experimental and theoretical research into the interaction of evolution with spatial structures: in various dimensions, including hitherto unexplored ones, spanning from externally defined physical spaces to actively tailored spaces, assembled by the evolving components themselves. As such, it contains some original research by the author as well as tracing how other insights grew over three decades out of the mentorship of Manfred Eigen in the 1980s. Much of the early interest in spatial structures centres on its role in stabilizing higher order cooperative structures involving the coevolution of different molecules, as the genetic coding system exemplifies. Modern nanotechnology enables the design and construction of genetically encoded variants of smart components that can actively control both the proliferation of molecules and the structuring of space. A key role for this article is to show the continuity in this line of enquiry, beginning with quasispecies and projecting to autonomous microparticles with electronic genomes able to form programmable quasispaces.
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Affiliation(s)
- John S McCaskill
- Microsystems Chemistry and BioIT, Ruhr-Universität Bochum, Bochum, Germany. .,European Centre for Living Technology, Ca' Foscari Universitas, Venice, Italy.
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Noort DV, Tang Z, Landweber LF. Fully Controllable Microfluidics for Molecular Computers. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.jala.2004.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Automation will be a necessary step for the success of molecular computing. Here we have applied microfluidic technology to DNA computers, with a sample application towards solving Boolean logic problems.
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Affiliation(s)
- Danny van Noort
- School of Computer Science and Engineering, Seoul National University, Seoul, Korea
| | - Zhongliang Tang
- Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
| | - Laura F. Landweber
- Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
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Wang J, Huang Y. Design and Implementation of a Microfluidic Half Adder Chip Based on Double-Stranded DNA. IEEE Trans Nanobioscience 2014; 13:146-51. [DOI: 10.1109/tnb.2014.2311792] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Penchovsky R. Programmable and automated bead-based microfluidics for versatile DNA microarrays under isothermal conditions. LAB ON A CHIP 2013; 13:2370-2380. [PMID: 23645132 DOI: 10.1039/c3lc50208b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Advances in modern genomic research depend heavily on applications of various devices for automated high- or ultra-throughput arrays. Micro- and nanofluidics offer possibilities for miniaturization and integration of many different arrays onto a single device. Therefore, such devices are becoming a platform of choice for developing analytical instruments for modern biotechnology. This paper presents an implementation of a bead-based microfluidic platform for fully automated and programmable DNA microarrays. The devices are designed to work under isothermal conditions as DNA immobilization and hybridization transfer are performed under steady temperature using reversible pH alterations of reaction solutions. This offers the possibility for integration of more selection modules onto a single chip compared to maintaining a temperature gradient. This novel technology allows integration of many modules on a single reusable chip reducing the application cost. The method takes advantage of demonstrated high-speed DNA hybridization kinetics and denaturation on beads under flow conditions, high-fidelity of DNA hybridization, and small sample volumes are needed. The microfluidic devices are applied for a single nucleotide polymorphism analysis and DNA sequencing by synthesis without the need for fluorescent removal step. Apart from that, the microfluidic platform presented is applicable to many areas of modern biotechnology, including biosensor devices, DNA hybridization microarrays, molecular computation, on-chip nucleic acid selection, high-throughput screening of chemical libraries for drug discovery.
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Affiliation(s)
- Robert Penchovsky
- Department of Genetics, Faculty of Biology, Sofia University St. Kliment Ohridski, Sofia, Bulgaria.
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Lee SH, van Noort D, Yang KA, Lee IH, Zhang BT, Park TH. Biomolecular theorem proving on a chip: a novel microfluidic solution to a classical logic problem. LAB ON A CHIP 2012; 12:1841-1848. [PMID: 22441410 DOI: 10.1039/c2lc20677c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Biomolecules inside a microfluidic system can be used to solve computational problems, such as theorem proving, which is an important class of logical reasoning problems. In this article, the Boolean variables (literals) were represented using single-stranded DNA molecules, and theorem proving was performed by the hybridization and ligation of these variables into a double-stranded "solution" DNA. Then, a novel sequential reaction mixing method in a microfluidic chip was designed to solve a theorem proving problem, where a reaction loop and three additional chambers were integrated and controlled by pneumatic valves. DNA hybridization, ligation, toehold-mediated DNA strand displacement, exonuclease I digestion, and fluorescence detection of the double-stranded DNA were sequentially performed using this platform. Depending on the computational result, detection of the correct answer was demonstrated based on the presence of a fluorescence signal. This result is the first demonstration that microfluidics can be used to facilitate DNA-based logical inference.
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Affiliation(s)
- Seung Hwan Lee
- School of Chemical and Biological Engineering, Bio-MAX Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-744, Korea
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Wagler PF, Tangen U, Maeke T, McCaskill JS. Field programmable chemistry: integrated chemical and electronic processing of informational molecules towards electronic chemical cells. Biosystems 2012; 109:2-17. [PMID: 22309763 DOI: 10.1016/j.biosystems.2012.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Accepted: 01/09/2012] [Indexed: 12/13/2022]
Abstract
The topic addressed is that of combining self-constructing chemical systems with electronic computation to form unconventional embedded computation systems performing complex nano-scale chemical tasks autonomously. The hybrid route to complex programmable chemistry, and ultimately to artificial cells based on novel chemistry, requires a solution of the two-way massively parallel coupling problem between digital electronics and chemical systems. We present a chemical microprocessor technology and show how it can provide a generic programmable platform for complex molecular processing tasks in Field Programmable Chemistry, including steps towards the grand challenge of constructing the first electronic chemical cells. Field programmable chemistry employs a massively parallel field of electrodes, under the control of latched voltages, which are used to modulate chemical activity. We implement such a field programmable chemistry which links to chemistry in rather generic, two-phase microfluidic channel networks that are separated into weakly coupled domains. Electric fields, produced by the high-density array of electrodes embedded in the channel floors, are used to control the transport of chemicals across the hydrodynamic barriers separating domains. In the absence of electric fields, separate microfluidic domains are essentially independent with only slow diffusional interchange of chemicals. Electronic chemical cells, based on chemical microprocessors, exploit a spatially resolved sandwich structure in which the electronic and chemical systems are locally coupled through homogeneous fine-grained actuation and sensor networks and play symmetric and complementary roles. We describe how these systems are fabricated, experimentally test their basic functionality, simulate their potential (e.g. for feed forward digital electrophoretic (FFDE) separation) and outline the application to building electronic chemical cells.
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Jeng DJF, Kim I, Watada J. Bio-soft computing with fixed-length DNA to a group control optimization problem. Soft comput 2007. [DOI: 10.1007/s00500-007-0202-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Liu JQ, Shimohara K. Molecular Computation and Evolutionary Wetware: A Cutting-Edge Technology for Artificial Life and Nanobiotechnologies. ACTA ACUST UNITED AC 2007. [DOI: 10.1109/tsmcc.2006.887011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Cost GJ, Cozzarelli NR. Directed assembly of DNA molecules via simultaneous ligation and digestion. Biotechniques 2007; 42:84, 86-9. [PMID: 17269489 DOI: 10.2144/000112283] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA ligation is a routine laboratory practice, yet the yield of the desired product is often very low due to competing off-pathway reactions. The sensitivity of subsequent manipulations (e.g., selection via bacterial transformation) often obviates the need for a high yield of correctly ligated products. However the ability to perform high-yield, preparative-scale DNA ligations would benefit a number of downstream applications ranging from standard molecular cloning to biophysics and DNA computing. We describe here a ligation technique that specifically converts off-pathway ligation products back into substrate. We term this second-chance strategy enzymatic ligation assisted by nucleases (ELAN) and demonstrate the ordered assembly of four DNA fragments via simultaneous ligation and digestion in the presence of eight restriction enzymes. Use of ELAN increased the yield of the desired product by more than 30-fold.
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Affiliation(s)
- Gregory J Cost
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA.
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García-Arnau M, Manrique D, Rodríguez-Patón A, Sosík P. A P system and a constructive membrane-inspired DNA algorithm for solving the Maximum Clique Problem. Biosystems 2007; 90:687-97. [PMID: 17418940 DOI: 10.1016/j.biosystems.2007.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2006] [Revised: 12/22/2006] [Accepted: 02/20/2007] [Indexed: 10/23/2022]
Abstract
We present a P system with replicated rewriting to solve the Maximum Clique Problem for a graph. Strings representing cliques are built gradually. This involves the use of inhibitors that control the space of all generated solutions to the problem. Calculating the maximum clique for a graph is a highly relevant issue not only on purely computational grounds, but also because of its relationship to fundamental problems in genomics. We propose to implement the designed P system by means of a DNA algorithm. This algorithm is then compared with two standard papers that addressed the same problem and its DNA implementation in the past. This comparison is carried out on the basis of a series of computational and physical parameters. Our solution features a significantly lower cost in terms of time, the number and size of strands, as well as the simplicity of the biological implementation.
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Affiliation(s)
- Marc García-Arnau
- Departamento Inteligencia Artificial, Universidad Politécnica de Madrid (UPM), Boadilla del Monte s/n, 28660 Madrid, Spain.
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Tangen U, Wagler PF, Chemnitz S, Goranovic G, Maeke T, McCaskill JS. An Electronically Controlled Microfluidic Approach towards Artificial Cells. ACTA ACUST UNITED AC 2006. [DOI: 10.1159/000094187] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Grover WH, Mathies RA. An integrated microfluidic processor for single nucleotide polymorphism-based DNA computing. LAB ON A CHIP 2005; 5:1033-40. [PMID: 16175257 DOI: 10.1039/b505840f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
An integrated microfluidic processor is developed that performs molecular computations using single nucleotide polymorphisms (SNPs) as binary bits. A complete population of fluorescein-labeled DNA "answers" is synthesized containing three distinct polymorphic bases; the identity of each base (A or T) is used to encode the value of a binary bit (TRUE or FALSE). Computation and readout occur by hybridization to complementary capture DNA oligonucleotides bound to magnetic beads in the microfluidic device. Beads are loaded into sixteen capture chambers in the processor and suspended in place by an external magnetic field. Integrated microfluidic valves and pumps circulate the input DNA population through the bead suspensions. In this example, a program consisting of a series of capture/rinse/release steps is executed and the DNA molecules remaining at the end of the computation provide the solution to a three-variable, four-clause Boolean satisfiability problem. The improved capture kinetics, transfer efficiency, and single-base specificity enabled by microfluidics make our processor well-suited for performing larger-scale DNA computations.
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Affiliation(s)
- William H Grover
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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A tissue P system and a DNA microfluidic device for solving the shortest common superstring problem. Soft comput 2004. [DOI: 10.1007/s00500-004-0398-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
A novel approach to designing a DNA library for molecular computation is presented. The method is employed for encoding binary information in DNA molecules. It aims to achieve a practical discrimination between perfectly matched DNA oligomers and those with mismatches in a large pool of different molecules. The approach takes into account the ability of DNA strands to hybridize in complex structures like hairpins, internal loops, or bulge loops and computes the stability of the hybrids formed based on thermodynamic data. A dynamic programming algorithm is applied to calculate the partition function for the ensemble of structures, which play a role in the hybridization reaction. The applicability of the method is demonstrated by the design of a twelve-bit DNA library. The library is constructed and experimentally tested using molecular biology tools. The results show a high level of specific hybridization achieved for all library words under identical conditions. The method is also applicable for the design of primers for PCR, DNA sequences for isothermal amplification reactions, and capture probes in DNA-chip arrays. The library could be applied for integrated DNA computing of twelve-bit instances of NP-complete combinatorial problems by multi-step DNA selection in microflow reactors.
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Affiliation(s)
- Robert Penchovsky
- Biomolecular Information Processing (BioMIP), Fraunhofer Gesellschaft, Schloss Birlinghoven, D-53754 Sankt Augustin, Germany.
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Hug H, Schuler R. Measurement of the number of molecules of a single mRNA species in a complex mRNA preparation. J Theor Biol 2003; 221:615-24. [PMID: 12713944 DOI: 10.1006/jtbi.2003.3211] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The normalization of data obtained from hybridization experiments with DNA chips to determine mRNA expression and concentration (gene expression profiling) is an unsolved problem. Furthermore, slight changes in mRNA expression or small numbers of mRNA molecules which may be relevant to disease cannot be detected so far. We have designed a method to calculate the number of molecules of a single mRNA species in a complex mRNA preparation. The basic concept is the transformation of a quantitative problem into a qualitative problem. Individual molecules pertaining to the same molecular species (IMPSMS) are transformed to a mixture of new different molecular species (DMS) and amplified. We propose two implementations of the method. The first procedure is based on a method for cloning tagged nucleic acid molecules onto the surface of micro-beads. It should be possible to transform and determine up to 10(6) IMPSMS into new DMS. The second strategy uses multimeric linkers, a method frequently used in DNA computing to assemble random DNA. The second strategy should be easier to implement but is limited to a few hundred IMPSMS.
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Affiliation(s)
- Hubert Hug
- University Children's Hospital, Prittwitzstrasse 43, D-89075 Ulm, Germany.
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Cascadable Hybridisation Transfer of Specific DNA between Microreactor Selection Modules. DNA COMPUTING 2002. [DOI: 10.1007/3-540-48017-x_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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