GlowyEyes.gil

#target Human

import "Elements"

//Set up the glowing stuff
Elements: .Opticin
{
    Elements: Neonothopanus_CPH
}

Elements: .Opticin
{
    Elements: Neonothopanus_HISPS
}

Elements: .Opticin
{
    /*
    All the TRAPs are on the same strand as the nnLuz because that makes sure they're closer to the target. Cells are big compared to 
    RNA molecules, but this guarantees that the ribozymes will be fairly close to their substrate. I added the PolyA sequences to 
    make sure there's enough unpaired bases for the RNA to rotate freely
    */
    Elements: TRAPzyme1

    Elements: PolyA40    //Seperator sequence
    Elements: TRAPzyme2_AA    //TRAP 2 attenuator sequence
    Elements: PolyA40

    Elements: TRAPzyme2
    Elements: PolyA40    //Seperator sequence
    
    Elements: TRAPzyme3    //Detects RAX if DetectRAX sequence exits
    Elements: PolyA40


    Elements: Neonothopanus_Luc
}

Elements: .Opticin
{
    Elements: Neonothopanus_NNH3H
}

Elements: DetectRAX    //Produces TRAPzyme 3's AA sequence if RAX promoter is active
Elements: DetectPer1



/*
I'm planning to add features to CadBerry to automate parts of this, but for now I had to do this by hand. Here are the notes I used as
I was designing the ribozymes

Per1 target:
GTACCAGCCA

Possible sequences:
ACACACAGAAGGAAGAGCAA
TGTGTGTCTTCCTTCTCGTT

CCAGAGCGCCGGGGCAAGGG
GGTCTCGCGGCCCCGTTCCC

Attenuator +8:
AACAAAAA

Attenuator:
CCAGAGCGCCGGGGCAAGGGAACAAAAA

CTGA.GA(A|G)....

(Interfering strand - inverted) AGGAGAAG
(Target - inverted) AGGAGAAGTCCGTCTTCTGC
(AA - inverted) AGGAGAAGTCCGTCTTCTGCTTGTTTTT
(Attenuator) TCCTCTCAGGCAGAAGACGAACAAAAA

TRAP2 AA: CCCTCCCTCCCC|

Target strand:
Search: ......(A|C|T)T....
CCCTCC|C|TCCCC

TRAPzyme 1:
TCCTCTCAGGCAGAAGACGAACAAAAA|GGGGA|AAG|CTCA|AAAG|TGAG|AGGAGTC|GGAGGG

TRAPzyme 2:
AA: GGGGAGGGAGGG|CCGGAGTA
Attenuator: TACTCCGGCCCTCCCTCCCC
Tar: TTGCCT|C|TGCAA

Code:
TACTCCGGCCCTCCCTCCCC|TTGCA|AAG|CCGG|AAAG|CCGG|AGTAGTC|AGGCAA

Per1=>TRAP1=>TRAP2=>nnLuz

TRAPzyme 3: (Detects attenuator produced with RAX promoter)
AA: GGGGAGGGAGGG|AAAAAGTA
Attenuator: TACTTTTTCCCTCCCTCCCC
Tar: TTGCCT|C|TGCAA

Code:
TACTTTTTCCCTCCCTCCCC|TTGCA|AAG|TTTT|CCCT|AAAA|AGTAGTC|AGGCAA

Steps:
1. Create TRAP1 which acts on TRAP2's attenuator
    1. Create TRAP2's attenuator
2. Create TRAP2 which acts on nnLuz
*/