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Next is our noncomplementary version of the machine, which is the same except that the rewriting oligos are:
5'- 1 2 -3'
5'- 2 1 -3'
Below is a simulation of this version, under identical conditions. We
see that in this machine, progress is only made on alternate steps,
since we only include oligos that bind to positive templates. Also,
notice that on step 5, the perfectly-matched oligo happened to bind
before the imperfect one, illustrating how these competitive-binding
situtations can further slow the rate of progress. However, this
particular line of descendants does eventually reach the final state,
after 7 cycles.
----------------------------------------------------------------------
sim restrict3.olig -T 30 -t 600 -n
Parameters: file = restrict3.olig, T = 303.15, c = 1e-07, t = 600,
p = 0, s = 796558321
Command: ?
[!prim1 ][!1 ][!0 ][!0 ][!0 ][prim2 ]
3'-GGCGCCCGCCGCACTGAGCTCTTGACTCAGCTGTTGACTCAGCTGTTGACTCAGCTGTTGGGCGGCCCGCGG-5'
:::::::::::: DG0 = -22.8233
5'-CCGCGGGCGGCG-3' k = 2.90848e+16
[prim1 ] p = 1.000000
::::::::::::::::X::X:::: DG0 = -14.1205
5'-TGACTCGAGAACTGAGCCGGCAAC-3' k = 1.53405e+10
[1 ][2 ] p = 0.999349
Below .01 probability of binding:
:::X::::X:::::::X::X:::: DG0 = -0.280819
5'-TGACTCGAGAACTGAGCCGGCAAC-3' k = 1.5943
[1 ][2 ] p = 0.000000
Command:
Cycle = 1, time = 10:00, temp = 30.00.
[prim1 ][1 ][2 ]
CCGCGGGCGGCGTGACTCGAGAACTGAGCCGGCAAC
::::::::::::::::::::::::::::X::X::::
GGCGCCCGCCGCACTGAGCTCTTGACTCAGCTGTTGACTCAGCTGTTGACTCAGCTGTTGGGCGGCCCGCGG
[!prim1 ][!1 ][!0 ][!0 ][!0 ][prim2 ]
Command: ?
[!prim2 ][0 ][0 ][2 ][1 ][prim1 ]
3'-CCGCGGGCCGCCCAACAGCTGAGTCAACAGCTGAGTCAACGGCCGAGTCAAGAGCTCAGTGCGGCGGGCGCC-5'
:::::::::::: DG0 = -22.0749
5'-GGCGCCCGGCGG-3' k = 8.3905e+15
[prim2 ] p = 1.000000
Below .01 probability of binding:
DG0 = 10.241 X::XX::X::::
k = 4.09856e-08 5'-GGCGCCCGGCGG-3'
p = 0.000000 [prim2 ]
Command:
Cycle = 2, time = 10:00, temp = 30.00.
[prim2 ]
GGCGCCCGGCGG
::::::::::::
CCGCGGGCCGCCCAACAGCTGAGTCAACAGCTGAGTCAACGGCCGAGTCAAGAGCTCAGTGCGGCGGGCGCC
[!prim2 ][0 ][0 ][2 ][1 ][prim1 ]
Command: ?
[!prim1 ][!1 ][!2 ][!0 ][!0 ][prim2 ]
3'-GGCGCCCGCCGCACTGAGCTCTTGACTCGGCCGTTGACTCAGCTGTTGACTCAGCTGTTGGGCGGCCCGCGG-5'
:::::::::::::::::::::::: DG0 = -30.916
5'-TGACTCGAGAACTGAGCCGGCAAC-3' k = 2.00134e+22
[1 ][2 ] p = 1.000000
:::::::::::: DG0 = -22.8233
5'-CCGCGGGCGGCG-3' k = 2.90848e+16
[prim1 ] p = 1.000000
:::::::::::::::X::::X::: DG0 = -17.0763
5'-TGAGCCGGCAACTGACTCGAGAAC-3' k = 2.07994e+12
[2 ][1 ] p = 0.999995
Below .01 probability of binding:
:::X::::X:::::::X::X:::: DG0 = -0.280
5'-TGACTCGAGAACTGAGCCGGCAAC-3' k = 1.5943
[1 ][2 ] p = 0.000000
Command:
Cycle = 3, time = 10:00, temp = 30.00.
[prim1 ] [2 ][1 ]
CCGCGGGCGGCG TGAGCCGGCAACTGACTCGAGAAC
:::::::::::: :::::::::::::::X::::X:::
GGCGCCCGCCGCACTGAGCTCTTGACTCGGCCGTTGACTCAGCTGTTGACTCAGCTGTTGGGCGGCCCGCGG
[!prim1 ][!1 ][!2 ][!0 ][!0 ][prim2 ]
Command:
Cycle = 4, time = 10:00, temp = 30.00.
[prim2 ]
GGCGCCCGGCGG
::::::::::::
CCGCGGGCCGCCCAACAGCTGAGTCAAGAGCTCAGTCAACGGCCGAGTCAAGAGCTCAGTGCGGCGGGCGCC
[!prim2 ][0 ][1 ][2 ][1 ][prim1 ]
Command:
Cycle = 5, time = 10:00, temp = 30.00.
[prim1 ] [2 ][1 ]
CCGCGGGCGGCG TGAGCCGGCAACTGACTCGAGAAC
:::::::::::: ::::::::::::::::::::::::
GGCGCCCGCCGCACTGAGCTCTTGACTCGGCCGTTGACTGAGCTCTTGACTCAGCTGTTGGGCGGCCCGCGG
[!prim1 ][!1 ][!2 ][!1 ][!0 ][prim2 ]
Command:
Cycle = 6, time = 10:00, temp = 30.00.
[prim2 ]
GGCGCCCGGCGG
::::::::::::
CCGCGGGCCGCCCAACAGCTGAGTCAAGAGCTCAGTCAACGGCCGAGTCAAGAGCTCAGTGCGGCGGGCGCC
[!prim2 ][0 ][1 ][2 ][1 ][prim1 ]
Command:
Cycle = 7, time = 10:00, temp = 30.00.
[prim1 ][1 ][2 ][1 ][2 ]
CCGCGGGCGGCGTGACTCGAGAACTGAGCCGGCAACTGACTCGAGAACTGAGCCGGCAAC
::::::::::::::::::::::::::::::::::::::::::::::::::::X::X::::
GGCGCCCGCCGCACTGAGCTCTTGACTCGGCCGTTGACTGAGCTCTTGACTCAGCTGTTGGGCGGCCCGCGG
[!prim1 ][!1 ][!2 ][!1 ][!0 ][prim2 ]
----------------------------------------------------------------------