Theoretical and Experimental DNA Computation (Natural ...

5.8 Experimental Investigations 121
Table 5.1. Sequences chosen to represent vertex/color combinations
Coloring Sequence Tm
v1 = red GCTCTGCTAAAAAATCTTGATTTCACAGCATGGT 74.1
v1 = green GCTCTGCTGGGGGGTCTTGATTTCACAGCATGGT 83.1
v1 = blue GCTCTGCTCCCCCCTCTTGATTTCACAGCATGGT 82.5
v2 = red CGTCATAGGATCACCATGCTTTTTTTACCATGCTGTGAAATCAAGA 81.5
v2 = green CGTCATAGGATCACCATGCTCCCCCCACCATGCTGTGAAATCAAGA 88.4
v2 = blue CGTCATAGGATCACCATGCTGGGGGGACCATGCTGTGAAATCAAGA 88.4
v3 = red AGCATGGTGATCCTATGACGAAAAAATGCTGCTAAGACGAAGAGTT 80.9
v3 = green AGCATGGTGATCCTATGACGGGGGGGTGCTGCTAAGACGAAGAGTT 86.6
v3 = blue AGCATGGTGATCCTATGACGCCCCCCTGCTGCTAAGACGAAGAGTT 86.7
v4 = red GTAGGTGTGATCCAGTGGTTTTTTTTAACTCTTCGTCTTAGCAGCA 79.2
v4 = green GTAGGTGTGATCCAGTGGTTCCCCCCAACTCTTCGTCTTAGCAGCA 86.0
v4 = blue GTAGGTGTGATCCAGTGGTTGGGGGGAACTCTTCGTCTTAGCAGCA 86.0
v5 = red AACCACTGGATCACACCTACAAAAAAGGTCTTCGGCGGCAATCTAC 83.7
v5 = green AACCACTGGATCACACCTACGGGGGGGGTCTTCGGCGGCAATCTAC 89.9
v5 = blue AACCACTGGATCACACCTACCCCCCCGGTCTTCGGCGGCAATCTAC 89.9
v6 = red GTAGGTGTGATCCAGTGGTTTTTTTTGTAGATTGCCGCCGAAGACC 83.8
v6 = green GTAGGTGTGATCCAGTGGTTCCCCCCGTAGATTGCCGCCGAAGACC 89.5
v6 = blue GTAGGTGTGATCCAGTGGTTGGGGGGGTAGATTGCCGCCGAAGACC 89.5
v7 = red AACCACTGGATCACACCTACAAAAAACACTGACAAGACCTTTGCTT 80.8
v7 = green AACCACTGGATCACACCTACGGGGGGCACTGACAAGACCTTTGCTT 87.4
v7 = blue AACCACTGGATCACACCTACCCCCCCCACTGACAAGACCTTTGCTT 86.8
v8 = red GCGGAATTCCTCTGCTGATCTTTTTTAAGCAAAGGTCTTGTCAGTG 81.9
v8 = green GCGGAATTCCTCTGCTGATCCCCCCCAAGCAAAGGTCTTGTCAGTG 89.1
v8 = blue GCGGAATTCCTCTGCTGATCGGGGGGAAGCAAAGGTCTTGTCAGTG 89.1
3’
5’
V 1 V 3
V 5
V 7
V 2 V 4 V 6 V8
Fig. 5.9. Library construction
Sequences representing odd-numberedverticesruninthe3’→ 5’ direction. Sequences
representing even-numbered vertices run in the 5’ → 3’ direction (see
Fig. 5.9). We now describe the structure of the binding sections of strands representing
even-numbered vertices. The “left-hand” binding section of strands
representing vn (where n is even) is the complement of the “right-hand” binding
section of strands representing vn−1. Similarly, the “right-hand” binding
section of strands representing vn is the “left-hand” binding section of strands
representing vn+1.
We also construct a single biotinylated oligo, corresponding to the complement
of the “right-hand” binding section of strands representing v8. This
allows us to purify strands encoding colorings away from the splint strands.
The use of hybridization extraction does not cause a problem at this stage,
5’
3’