Theoretical and Experimental DNA Computation (Natural ...

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Create initial strand library Confirm correct construction Attempt removal of specific sequence Success? Redesign strands Create initial strand library 1-4 N Attempt removal of specific sequence 5-8 23-24 25-29 5.8 Experimental Investigations 123 9-12, 16-22 32 Adjust 13-15 conditions Fig. 5.11. Flowchart depicting experimental cycle
124 5 Physical Implementations Table 5.2. Sequences of primers Primer Sequence Tm v1 = red GCTCTGCTAAAAAATCTT 51.1 v1 = green GCTCTGCTGGGGGGTCT 66.8 v1 = blue GCTCTGCTCCCCCCTCTT 65.8 v2 = red AGCATGGTAAAAAAAGCA 55.8 v2 = green AGCATGGTGGGGGGAGC 71.5 v2 = blue AGCATGGTCCCCCCAGCA 71.5 v3 = red CTATGACGAAAAAATGCT 52.6 v3 = green CTATGACGGGGGGGTGCT 67.2 v3 = blue CTATGACGCCCCCCTGCT 67.4 v4 = red GAAGAGTTAAAAAAAACC 47.7 v4 = green GAAGAGTTGGGGGGAACC 63.3 v4 = blue GAAGAGTTCCCCCCAACC 63.3 v5 = red ACACCTACAAAAAAGGTC 51.1 v5 = green ACACCTACGGGGGGGGTC 68.2 v5 = blue ACACCTACCCCCCCGGTC 49.3 v6 = red CAATCTACAAAAAAAACC 49.3 v6 = green CAATCTACGGGGGGAACC 64.0 v6 = blue CAATCTACCCCCCCAACC 63.9 v7 = red ACACCTACAAAAAACACT 48.7 v7 = green ACACCTACGGGGGGCACT 66.7 v7 = blue ACACCTACCCCCCCCACT 65.4 v8 = red CTTTGCTTAAAAAAGATC 48.9 v8 = green CTTTGCTTGGGGGGGAT 66.6 v8 = blue CTTTGCTTCCCCCCGAT 66.7 Experiment 2. Library construction Two hybridization reactions were set up, one containing a full set of coloring oligos and the other a control containing only red coloring oligos. The products were labelled ALL and RED. Experiment 3. Amplification of template ALL Hybridization product ALL was amplified by PCR between v8 and a mixture of the three v1 primers. The primary aim was to generate a working stock containing a mixed population of colorings. The amplification was also used to confirm that the oligos had annealed correctly and that the polymerase/ligase step had repaired the gaps between oligos to produce double-stranded tile chains of the correct length. PCR template concentration and MgCl2 concentrations were titrated in order to optimize PCR conditions.
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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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Page 87 and 88: 72 4 Complexity Issues is that, alt
Page 89 and 90: 74 4 Complexity Issues The weak par
Page 91 and 92: 76 4 Complexity Issues 4.3 A Strong
Page 93 and 94: 78 4 Complexity Issues Ω = {∧,
Page 95 and 96: 80 4 Complexity Issues 0 1 0 1 x1 x
Page 97 and 98: 82 4 Complexity Issues connecting a
Page 99 and 100: 84 4 Complexity Issues Level simula
Page 101 and 102: 86 4 Complexity Issues At level D(S
Page 103 and 104: 88 4 Complexity Issues xANDy)) and
Page 105 and 106: 90 4 Complexity Issues Input matrix
Page 107 and 108: 92 4 Complexity Issues memory acces
Page 109 and 110: 94 4 Complexity Issues denoted by P
Page 111 and 112: 96 4 Complexity Issues The final st
Page 113 and 114: 98 4 Complexity Issues 1)), ADDR[])
Page 115 and 116: 100 4 Complexity Issues Size(STI)=O
Page 117 and 118: 102 4 Complexity Issues best attain
Page 119 and 120: 104 4 Complexity Issues 10. LDC 0 1
Page 121 and 122: 106 4 Complexity Issues ACC[] := bi
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
Page 144 and 145: Experiment 25. New full-length chai
Page 150 and 151: 5.9 Other Laboratory Implementation
Page 160: 5.11 Bibliographical Notes 145 whic
Page 163 and 164: 148 6 Cellular Computing of truly i
Page 165 and 166: 150 6 Cellular Computing 6.2 Succes
Page 167 and 168: 152 6 Cellular Computing are “glu
Page 169 and 170: 154 6 Cellular Computing x y z x (a
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,
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Natural Computing Series W.M. Spear
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