Theoretical and Experimental DNA Computation (Natural ...

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PROMOTER STRUCTURAL GENE(S) TERMINATOR Fig. 6.1. Major regions found within a bacterial operon lacI Operator lacZ lacY lacA Repressor Promoter 6.1 Introduction 149 Fig. 6.2. Repressed state of the lac operon by the lacI gene product Promoter lacI lacZ lacY lacA Repressor ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ RNA polymerase CAP-cAMP complex ¦ ¦ ¦ ¦ ¦ § § § § § § ¦ ¨ © © ¨ � � � � � � � � Inducer Cap binding site ¤ ¤ ¤ ¤ ¤ ¥ ¥ ¥ ¥ ¥ ¥ ¤ ¢ ¢ £ £ £ ¢ Fig. 6.3. Induced state of the lac operon complex, whose level increases as the amount of available glucose decreases. Therefore, if lactose were present as the sole carbon source, the lacI repression would be relaxed and the high CAP-cAMP levels would activate transcription, leading to the synthesis of the lacZYA gene products (Fig. 6.3). Thus, the promoter is under the control of two sugars, and the lacZYA operon is only transcribed when lactose is present and glucose is absent. It is clear that we may view the lac operon in terms of the Boolean AND function, in that it has output value 1 if transcribed, and 0 otherwise. The presence/absence of glucose corresponds to the gate’s first input being equal to 0/1, and the presence/absence of lactose corresponds to the gate’s second input being 1/0 (note the difference in representation between the two sugars).
150 6 Cellular Computing 6.2 Successful Implementations We now briefly introduce several successful examples of how bacteria have been successfully re-engineered for the purposes of computation. In 1999, Weiss et al. [158] described a technique for mapping digital logic circuits onto genetic regulatory networks such that the resulting chemical activity within the cell corresponds to the computations specified by the digital circuit. There was a burst of activity in 2000, when two papers appeared in the same issue of Nature, both being seminal contributions to the field. In [57], Elowitz and Leibler described the construction of an oscillator network that periodically caused a culture of E.coli to glow by expressing a fluorescent protein. Crucially, the period of oscillation was slower than the cell division cycle, indicating that the state of the oscillator is transmitted from generation to generation. In [62], Gardner et al. implemented a genetic toggle switch in E.coli. The switch is flipped from one stable state to another by either chemical or heat induction. These “single cell” experiments demonstrated the feasibility of implementing artificial logical operations using genetic modification. In [137], Savageau addresses the issue of finding general design principles among microbial genetic circuits, citing several examples. Several more examples of successful work on cellular computing may be found in [7]. 6.3 Gene Unscrambling in Ciliates Ciliate is a term applied to any member of a group of around 10,000 different types of single-celled organism that are characterized by two features: the possession of hair-like cilia for movement, and the presence of two kinds of nuclei instead of the usual one. One nucleus (the micronucleus) isusedfor sexual exchange of DNA, and the other (the macronucleus) is responsible for cell growth and proliferation. Crucially, the DNA in the micronucleus contains an “encoded” description of the DNA in the working macronucleus, which is decoded during development. This encoding “scrambles” fragments of the functional genes in the macronucleus by both the permutation (and possible inversion) of partial coding sequences and the inclusion of non-coding sequences. A picture of the ciliate Oxytricha nova is shown in Fig. 6.4. It is the macronucleus (that is, the “housekeeping” nucleus) that provides the RNA “blueprints” for the production of proteins. The micronucleus, on the other hand, is a dormant nucleus which is activated only during sexual reproduction, when at some point a micronucleus is converted into a macronucleus in a process known as gene assembly. During this process the micronuclear genome is converted into the macronuclear genome. This conversion reorganizes the genetic material in the micronucleus by removing noncoding sequences and placing coding sequences in their correct order. This “unscrambling” may be interpreted as a computational process.
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Natural Computing Series Series Edi
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Martyn Amos Department of Computer
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Preface DNA computation has emerged
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Preface IX acknowledged. Finally, I
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XII Contents 4 Complexity Issues ..
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Introduction “Where a calculator
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Introduction 3 Even though their un
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1 DNA: The Molecule of Life “All
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1.3 DNA as the Carrier of Genetic I
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1.3 DNA as the Carrier of Genetic I
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Synthesis 1.4 Operations on DNA 11
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Gel electrophoresis 1.4 Operations
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5’ 3’ A T A G A G T T 3’ TCA
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1.4 Operations on DNA 17 Others may
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Vector Strand to be inserted (targe
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1.5 Summary 1.6 Bibliographical Not
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24 2 Theoretical Computer Science:
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46 3 Models of Molecular Computatio
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72 4 Complexity Issues is that, alt
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74 4 Complexity Issues The weak par
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76 4 Complexity Issues 4.3 A Strong
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78 4 Complexity Issues Ω = {∧,
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80 4 Complexity Issues 0 1 0 1 x1 x
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82 4 Complexity Issues connecting a
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84 4 Complexity Issues Level simula
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86 4 Complexity Issues At level D(S
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88 4 Complexity Issues xANDy)) and
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90 4 Complexity Issues Input matrix
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92 4 Complexity Issues memory acces
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94 4 Complexity Issues denoted by P
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96 4 Complexity Issues The final st
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Page 124 and 125: 5 Physical Implementations “No am
Page 126 and 127: 5.3 Initial Set Construction Within
Page 128 and 129: Vertex 1 Vertex 2 Vertex 3 ¡ ¡ ¡
Page 130 and 131: 5.5 Evaluation of Adleman’s Imple
Page 132 and 133: 5.6 Implementation of the Parallel
Page 134 and 135: 5.8 Experimental Investigations 119
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Page 171 and 172: 156 6 Cellular Computing 6.7 Biblio
Page 173 and 174: 158 References 14. Martyn Amos, Ste
Page 175 and 176: 160 References 53. Dónall A. Mac D
Page 177 and 178: 162 References 92. D. Knuth. The Ar
Page 179 and 180: 164 References 135. Kensaku Sakamot
Page 182 and 183: Index ALGOL, 102 AND, 23-24, 42, 87
Page 184 and 185: iological, 74, 114, 150 Feynman, R.
Page 186 and 187: Petrinet,63 phage, 18-20 phosphate,
Page 188: Natural Computing Series W.M. Spear
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