Towards <i>De Novo</i> Design of Deoxyribozyme Biosensors for GMO Detection

May, Elebeoba; Dolan, Patricia; Crozier, Paul; Brozik, Susan M.; Manginell, Monica

doi:10.1109/jsen.2008.923945

Cited by 37 publications

(40 citation statements)

References 18 publications

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“…However, the main expected shorter term practical benefit of biomolecular computing systems is their ability to process biochemical information received in the form of chemical inputs directly from biological systems, offering the possibility to operate in biological environments [40], for biomedical/diagnostic [35] and homeland security applications [41]. Biomolecular logic gates and their networks can recognize various biomarkers associated with diseases [42] or injuries [43] and generate a biomedical conclusion in the binary form ''YES''/''NO'' upon logic processing of the biomarker concentration patterns. The produced binary output can be extended to a chemical actuation resulting in drug release or bioelectronic system activation controlled by logic conclusions derived from the information processed by biomolecular systems [44].…”

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confidence: 99%

Biomolecular Computing: From Unconventional Computing to “Smart” Biosensors and Actuators – Editorial Introduction

Katz

2012

Biomolecular Information Processing

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Chemical computing [1] as a subarea of unconventional computing [2] has achieved tremendous development in the past two decades, driven mostly by the idea of making revolutionary changes in computing technology. While the conventional silicon-based electronic technology comes to the physical limit of miniaturization [3], chemical systems might operate at the level of single molecules, bringing information processing systems from the present microsize to novel nanosize [4]. Even more importantly, chemical systems can perform massively parallel computational operations with involvement of as many as 10 23 molecules, resulting in a speed of information processing presently impossible in silicon-based computers [5]. Motivated by these ideas from computer science, chemists designed sophisticated switchable molecules and supramolecular complexes to perform logic operations and mimic computing systems [6]. Complex chemical reactions with unusual kinetics (e.g., oscillating diffusional systems -Belousov-Zhabotinsky reactions) [7] were suggested as media performing computing operations [8]. Extensive research in the area of reaction-diffusion computing systems [9] resulted in the formulation of conceptually novel circuits performing information processing with the use of subexcitable chemical media [10]. Novel conceptual approaches required for the usage of new chemical ''hardware'' were designed, resulting in algorithms potentially capable of solving ''hard-to-solve'' computational problems, thus demonstrating potential advantages of the novel unconventional chemical computing systems over classic silicon-based systems. The present state of the art of the unconventional chemical computing was summarized in the recent Wiley-VCH book: ''Molecular and Supramolecular Information Processing: From Molecular Switches to Logic Systems,'' E. Katz -Editor.It should be noted, however, that chemical systems designed for information processing usually suffer from two major problems: (i) They are very difficult to prepare -in other words -the synthetic processes required for their preparation are so complex that only a few laboratories are able to prepare and study the switchable molecules operating as the chemical computing ''hardware.'' This problem is technical rather than conceptual, and it could be solved at the present level of technology if the molecular computing elements find real applications. (ii) The main challenge in further development of chemical information processing systems is Biomolecular Information Processing: From Logic Systems to Smart Sensors and Actuators, First Edition. Edited by Evgeny Katz.

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confidence: 99%

Biomolecular Computing: From Unconventional Computing to “Smart” Biosensors and Actuators – Editorial Introduction

Katz

2012

Biomolecular Information Processing

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“…18,19 Biomolecular computing systems in biochemical and biotechnological environments 20 promise design of novel biosensors capable of multiplexing and processing several biochemical signals in the binary format, 0 and 1, with the information processing carried out by (bio)chemical processes rather than electronics. 21,22 Specifically, biomolecular logic has been explored [23][24][25][26][27][28][29][30][31] for prospective biomedical/diagnostic applications aiming at analysis of biomarkers characteristic of various pathophysiological conditions of interest in diagnostics of diseases or injuries. respectively.…”

Section: Molecularmentioning

confidence: 99%

Enzyme-Based Logic Analysis of Biomarkers at Physiological Concentrations: AND Gate with Double-Sigmoid “Filter” Response

et al. 2012

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We report the first realization of a biomolecular AND gate function with double-sigmoid response (sigmoid in both inputs). Two enzyme biomarker inputs activate the gate output signal which can then be used as indicating liver injury, but only when both of these inputs have elevated pathophysiological concentrations, effectively corresponding to logic-1 of the binary gate functioning. At lower, normal physiological concentrations, defined as logic-0 inputs, the liver-injury output levels are not obtained. High-quality gate functioning in handling of various sources of noise, on time scales of relevance to potential applications is enabled by utilizing "filtering" effected by a simple added biocatalytic process. The resulting gate response is sigmoid in both inputs when proper system parameters are chosen, and the gate properties are theoretically analyzed within a model devised to evaluate its noise-handling properties.

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“…It has been observed that a single nucleotide polymorphism (SNP) in one position of the input DNA probe differs phenotypically from a SNP in another, causing the activated deoxyribozyme to produce distinct fluorescence signatures, Figure 2 [25], [1]. When there is a single base mishybridization between the input probe sequence and the recognition loop of the deoxyribozyme, there is a change in the the thermodynamic stability of the system.…”

Section: A Hybridization and Error Controlmentioning

confidence: 99%

The Emergence of biological coding theory as a mathematical framework for modeling, monitoring, and modulating biomolecular systems

May

2009

2009 43rd Annual Conference on Information Sciences and Systems

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In this work we will discuss the implications of understanding hybridization using the mathematical framework of error control coding theory and how this requires not only the use of information theoretic analysis tools, but compels us to view and model biomolecular systems as information transmission and processing systems. Using the genetic communication theory paradigm, we investigate coding theory algorithms for in silico categorization of single nucleotide polymorphisms based on the calculation of syndromes [1]. We explore the use of coding theory frameworks in the design of in vitro computational biosensors [2] and design of error correcting biosensors [3] for monitoring biomolecular systems. We conclude by briefly investigating the necessity of biological coding theory in the emerging field of synthetic biology [4] where incorporation of error control codes into synthetic DNA, an established area of research in the field of DNA computing [5], is becoming an area of growing interest in order to increase the robustness of engineered biomolecular systems.

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Towards De Novo Design of Deoxyribozyme Biosensors for GMO Detection

Cited by 37 publications

References 18 publications

Biomolecular Computing: From Unconventional Computing to “Smart” Biosensors and Actuators – Editorial Introduction

Biomolecular Computing: From Unconventional Computing to “Smart” Biosensors and Actuators – Editorial Introduction

Enzyme-Based Logic Analysis of Biomarkers at Physiological Concentrations: AND Gate with Double-Sigmoid “Filter” Response

The Emergence of biological coding theory as a mathematical framework for modeling, monitoring, and modulating biomolecular systems

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