Assembly

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#  If one pancake can be flipped, reversed parts can be made.  This may actually be a good contribution, since it could be applied to reverse any part between two hix sites.
#  If one pancake can be flipped, reversed parts can be made.  This may actually be a good contribution, since it could be applied to reverse any part between two hix sites.
#  Can cut out a part with NotI, then religate in both orientations.
#  Can cut out a part with NotI, then religate in both orientations.
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'''Tips for Experiments'''
 
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Bacteria - JM109 will be used, has lacIq for overproduction of lac repressor, turning off Plac unless inducer such as IPTG or lactose is present.
 
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XbaI and SpeI can be inactivated by 65C for 20 minutes.  Both have good activity in NEB2 + BSA (100ug/ml final).
 
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Examples
Examples
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gaattcgcggccgcttctagag '''tttctcctcttt''' tactagtagcggccgctgcag
gaattcgcggccgcttctagag '''tttctcctcttt''' tactagtagcggccgctgcag
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'''Steps'''
 
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1. Design/Order DNA – Hix L, R, & C
 
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        - Want to do a Left to Right BioB addition:  Promoter + RBS w/AmpR -->Hix site-->
 
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          Term-->Hix(C)site-->TetR + Term
 
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2. On receiving – restrict/ligate BioBricks into plasmid w/resistance gene on one side
 
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    a. Promoter, RBS BioB
 
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    b. TetR BioB (Backwards)
 
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    c. Term BioB
 
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3.  Transform E. coli
 
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E = G/AATC
 
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X = T/CTAGA
 
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P = CGAT/CG
 
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S = A/CTAGT
 
== '''hix BioBricks''' ==
== '''hix BioBricks''' ==
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Do we want to be able to turn on a Start Promoter(i.e. LacP using IPTG) on/off so recombination occurs 1st; and then use a different inducible promoter to turn on transcription?
Do we want to be able to turn on a Start Promoter(i.e. LacP using IPTG) on/off so recombination occurs 1st; and then use a different inducible promoter to turn on transcription?
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==  '''Steps:''' ==
 
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Step 1:  Transform E. coli w/:
 
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        mRFP1 (BBa_E1010, Plate DNA-2, Spot 15M)
 
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        Double Forward (Term) (BBa_B0015 Plate DNA-1, Spot 1I)
 
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        pBad (BBa_I0500, Plate DNA-2, Spot 9I)
 
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        pLac (BBa_R0011, Plate DNA-1, Spot 7M)
 
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        pSB1A3 (Plate DNA-1, Spot 23E)
 
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Step 2:  Plasmid Preps.
 
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Step 3:  Use NotI to reverse TetR Gene
 
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Step 4:  Clone Hix DNA
 
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Step 5:  Assemble BioBricks
 

Revision as of 13:03, 16 June 2006

Contents

Parts to Make:

HixL: TTCTGGAAAA CCAAGGTTTT TGATAA

HixR: TTATCAAAAA CCTTCCAAAA GGAAAA

HixC: TTATCAAAAA CCATGGTTTT TGATAA

Backwards Parts

Because we wish to start with elements that are reversed (upside down pancakes), we need to think about how to get backwards parts. That is, parts that have the Prefix, then reversed element (promoter, term, CDS, RBS), then Suffix. Several possible ways:

  1. Some parts are backwards in the registry - terminators, for eg.
  2. Parts that are not long could be synthesized backwards.
  3. If one pancake can be flipped, reversed parts can be made. This may actually be a good contribution, since it could be applied to reverse any part between two hix sites.
  4. Can cut out a part with NotI, then religate in both orientations.

Examples

BBa_B0022 Terminator (Reverse B0012) Length: 84 Base Pairs Including BioBrick Ends

BBa_P1004 is ampR resistance cassette in reverse orientation Length: 984 Base Pairs Including BioBrick Ends (In planning stages only)

Bba_B0034 is a RBS with the sequence:

gaattcgcggccgcttctagag aaagaggagaaa tactagtagcggccgctgcag

It could be redesigned with the RBS reversed:

gaattcgcggccgcttctagag tttctcctcttt tactagtagcggccgctgcag


hix BioBricks

E - N - X - hix - S - N - P

Does there have to be a T between NotI and XbaI and an A between SpeI and NotI? All the parts we have looked at so far have this.

HixL

GAATTC GCGGCCGC T TCTAGA TTCTTGAAAACCAAGGTTTTTGATAA ACTAGT A GCGGCCGC CTGCAG

HixR

GAATTC GCGGCCGC T TCTAGA TTATCAAAAACCTTCCAAAAGGAAAA ACTAGT A GCGGCCGC CTGCAG

HixC

GAATTC GCGGCCGC T TCTAGA TTATCAAAAACCATGGTTTTTGATAA ACTAGT A GCGGCCGC CTGCAG

Oligos to order

HixL_top

AATTCGCGGCCGCTTCTAGATTCTTGAAAACCAAGGTTTTTGATAAACTAGTAGCGGCCGCCTGCA

HixL_bottom

GGCGGCCGCTACTAGTTTATCAAAAACCTTGGTTTTCAAGAATCTAGAAGCGGCCGCG

HixR_top

AATTCGCGGCCGCTTCTAGATTATCAAAAACCTTCCAAAAGGAAAAACTAGTAGCGGCCGCCTGCA

HixR_bottom

GGCGGCCGCTACTAGTTTTTCCTTTTGGAAGGTTTTTGATAATCTAGAAGCGGCCGCG

HixC_top

AATTCGCGGCCGCTTCTAGATTATCAAAAACCATGGTTTTTGATAAACTAGTAGCGGCCGCCTGCA

HixC_bottom

GGCGGCCGCTACTAGTTTATCAAAAACCATGGTTTTTGATAATCTAGAAGCGGCCGCG

Building

Biobricking in one hix site:

Hix ligation11.JPG

Example of a construct for one flip (terminator, although CDS would be better):

HIX Final.JPG

Biobricking hix sites onto parts:

Pan1.JPG

Assembly of One Pancake Test Construct:


Pan2.JPG

Assembly of Two Pancake Test Construct would be next. Probably want two genes.

Assembly of Multiple Pancake Test Constructs:

Pan3.JPG

First Transformations:

>1. Terminator T1 Bba_B0010 DNA-2 3P<

2. Promoter Pbad BBa_I13453

>3. Promoter w/RBS (TetR Repressed) BBa_J13002 DNA-2 3F <

4. Reverse Amp^r BBa_P1004 (Oops, planning)

5. Reverse CmR BBa_P1009 789 bp (Oops, planning)

>6. Double Forward Terminator BBa_B0015 DNA-1 1I <

>7. Tet^r Bba_P1001 DNA-2 23F <

Questions:

Will the TetR repressed promoter in BBa_J13002 be always on in JM109 cells?

Do we want to be able to turn on a Start Promoter(i.e. LacP using IPTG) on/off so recombination occurs 1st; and then use a different inducible promoter to turn on transcription?

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