Theoretical and Experimental DNA Computation (Natural ...

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Vector Strand to be inserted (target DNA) Restriction New molecules containing target sequence 1.4 Operations on DNA 19 Ligation Fig. 1.16. Insertion of target strand into vector DNA take up the vector. In order to improve this situation, we may use a technique known as electroporation. A high voltage pulse is passed through the solution containing the vectors and bacteria, causing the cell membranes to become permeable. This increases the probability of vector uptake. The vector then multiplies within the cell, producing numerous copies of itself (including the inserted sequence). The infection cycle of M13 proceeds as follows. The phage attaches to a pilus (an appendage on the surface of the cell) and injects its DNA into the bacterium (Fig. 1.17a). The M13 DNA is not integrated into the DNA of the bacterium, but is still replicated within the cell. In addition, new phages are continually assembled within and released from the cell (Fig. 1.17b), which go on to infect other bacteria (Fig. 1.17c). When sufficient copies of the specific sequence have been made, the single-stranded M13 DNA may be retrieved from the medium. The process by which this is achieved is depicted in Fig. 1.18
20 1 DNA: The Molecule of Life (c) ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ (a) (b) Pilus M13 phage M13 DNA Bacterium M13 DNA molecules Fig. 1.17. M13 phage infection cycle ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ ¢ £ £ £ £ £ £ £ £ £ £ £ £ £ £ £ ¢ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¤ ¥ ¥ ¥ ¥ ¥ ¥ ¥ ¥ ¥ ¥ ¥ ¥ ¤ ¨ ¨ ¨ © © © © © © ¨ ¨ ¨ M13 molecules (a) Culture of infected cells (b) Centrifuge to (c) Add PEG to phage suspension remove cells then centrifuge (g) Resuspend M13 DNA in small volume M13 phage suspension Pelleted cells M13 DNA Protein Phenol ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦ ¦ § § § § § § § § § § § § ¦ M13 phage suspension M13 DNA (f) Remove acqueous (e) Add phenol to (d) Resuspend phage layer, add ethanol, then centrifuge remove protein sheath in buffer Fig. 1.18. Preparation of M13 DNA from infected culture of bacteria (see also [104]). Once a sufficient volume of infected culture has been obtained we centrifuge it to pellet the bacteria (i.e., separate the bacteria from the phage particles). We then precipitate the phage particles with polyethylene glycol (PEG), add phenol to strip off the protein coats and then precipitate the resulting DNA using ethanol.
Page 2 and 3: Natural Computing Series Series Edi
Page 4: Martyn Amos Department of Computer
Page 8 and 9: Preface DNA computation has emerged
Page 10: Preface IX acknowledged. Finally, I
Page 13 and 14: XII Contents 4 Complexity Issues ..
Page 16 and 17: Introduction “Where a calculator
Page 18 and 19: Introduction 3 Even though their un
Page 20 and 21: 1 DNA: The Molecule of Life “All
Page 22 and 23: 1.3 DNA as the Carrier of Genetic I
Page 24 and 25: 1.3 DNA as the Carrier of Genetic I
Page 26 and 27: Synthesis 1.4 Operations on DNA 11
Page 28 and 29: Gel electrophoresis 1.4 Operations
Page 30 and 31: 5’ 3’ A T A G A G T T 3’ TCA
Page 32 and 33: 1.4 Operations on DNA 17 Others may
Page 36: 1.5 Summary 1.6 Bibliographical Not
Page 39 and 40: 24 2 Theoretical Computer Science:
Page 61 and 62: 46 3 Models of Molecular Computatio
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70 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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98 4 Complexity Issues 1)), ADDR[])
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100 4 Complexity Issues Size(STI)=O
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102 4 Complexity Issues best attain
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104 4 Complexity Issues 10. LDC 0 1
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106 4 Complexity Issues ACC[] := bi
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5 Physical Implementations “No am
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5.3 Initial Set Construction Within
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Vertex 1 Vertex 2 Vertex 3 ¡ ¡ ¡
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5.5 Evaluation of Adleman’s Imple
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5.6 Implementation of the Parallel
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5.8 Experimental Investigations 119
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Create initial strand library Confi
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Experiment 25. New full-length chai
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5.9 Other Laboratory Implementation
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5.11 Bibliographical Notes 145 whic
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148 6 Cellular Computing of truly i
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150 6 Cellular Computing 6.2 Succes
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152 6 Cellular Computing are “glu
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154 6 Cellular Computing x y z x (a
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156 6 Cellular Computing 6.7 Biblio
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158 References 14. Martyn Amos, Ste
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160 References 53. Dónall A. Mac D
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162 References 92. D. Knuth. The Ar
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164 References 135. Kensaku Sakamot
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Index ALGOL, 102 AND, 23-24, 42, 87
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iological, 74, 114, 150 Feynman, R.
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Petrinet,63 phage, 18-20 phosphate,
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Natural Computing Series W.M. Spear
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