Theoretical and Experimental DNA Computation (Natural ...

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.