User:Pakpoom Subsoontorn/Notebook/Genetically Encoded Memory/2008/10/06

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mini-Project: Synthetic Jumping DNA from integrase/excisionase systems
really have full control over the state of the system.
 * Motivation:
 * Inspired by TS Ham et al's double inversion switch, we would like to design other genetically encoded memory unit that function more efficiently. There are two major problem with TS Ham et al' system. First, the efficiency of invertase is low so most of the cells that are triggered to inverted their DNA don't do so. Second, the reaction by invertase is reversible so one can't
 * Bacteriophage's integrase/excisionase system can a promising tools for directional change in genetic code. In Nature, the expression of integrase alone cause attP site on viral DNA to insert into attB site on bacterial genome with high efficiency and specificity. The reaction by integrase itself is irreversible. However, when integrase and excisionase are present together, the process can be reverted, yielding the complete and separated viral genome and bacteria genome

system design and mechanism
upon the expression of two different intergrase/excisionase systems. the free circular plasmid. The chromosomal DNA has two different bacterial integration sites for integrase, attB-1 and attB-2. The plasmid also has two different phage-integration sites for integrase, attP-1 and attP-2. the system from state-A to state-B. On the other hand, the expression of integrase-2 will insert attP-2 into attB-2, changing the system from state-A to state-C
 * The genetic systems has two states: A, B, C. The state can be changed
 * In state A, the cell has two pieces of DNA, the chromosomal DNA and
 * The expression of the integrase-1 will insert attP-1 into attB-1, changing
 * The inserted piece of DNA can removed by expressing excisionase, together with integrase. Thus, we could reverse state-B or state-C back to state-A again.

Challenges
is a possibility that we can loss the jumping piece of DNA
 * Control the expression time/level of each integrase and excisionase
 * Efficiency and timing of insertion must be fast enough. Otherwise, there

Questions

 * What're the rough time scales for integrase/excisionase system? esp comparing to cell cycle


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