Biomod/2013/Titech/SMM2

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<a href="http://openwetware.org/wiki/Biomod">Biomod<a/>|<a href="http://openwetware.org/wiki/Biomod/2013">2013</a>

Design of the sequence

We designed Input (A, B, C) and Output complex(X, Y, Z). To realize “Permutation color-directing system”, Input (A, B, C) should be designed so as to react with Output complex (X, Y, Z) (strand-exchange reaction), and so as to interrupt Input (C, A, B). Therefore, we designed that 5’ end of Input (A, B, C) is the complementary sequence with 3’ end of Input (C, A, B).

<img src="https://upload.wikimedia.org/wikipedia/commons/e/e5/2-3_inputA.png" width="250">Input-A <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/a/ad/2-3_inputA_seq.png/800px-2-3_inputA_seq.png" width="400">
<img src="https://upload.wikimedia.org/wikipedia/commons/1/12/2-3_inputB.png" width="250">Input-B <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/7/74/2-3_inputB_seq.png/800px-2-3_inputB_seq.png" width="400">
<img src="https://upload.wikimedia.org/wikipedia/commons/6/6c/2-3_inputC.png" width="250">Input-C <img src="https://upload.wikimedia.org/wikipedia/commons/thumb/9/91/2-3_inputC_seq.png/800px-2-3_inputC_seq.png" width="400">

Fig. 1. Sequence of Input (A, B, C)

In addition, we designed the sequence of Output complex (X, Y, Z) as Fig. 2. If each Output complex has single-stranded portion of DNA, it is possible for us to design the sequence of that portion. But this time, we didn’t designed like that in order to make the calculation of the rate of strand-exchange reaction and simulation.

<img src="https://upload.wikimedia.org/wikipedia/commons/b/bb/New_2-3_Output-X_complex.png" width="250">Output-X complex <img src="https://upload.wikimedia.org/wikipedia/commons/5/57/2-3_Output-X_complex_seq.png" width="400">
<img src="https://upload.wikimedia.org/wikipedia/commons/9/91/2-3_Output-Y_complex.png" width="250">Output-Y complex <img src="https://upload.wikimedia.org/wikipedia/commons/3/3a/2-3_Output-Y_complex_seq.png" width="400">
<img src="https://upload.wikimedia.org/wikipedia/commons/1/10/2-3_Output-Z_complex.png" width="250">Output-Z complex <img src="https://upload.wikimedia.org/wikipedia/commons/2/27/2-3_Output-Z_complex_seq.png" width="400">


Fig. 2. Sequence of Output complex (X, Y, Z)