Design of C dog oligos in J-GGA Scaffold

C dogs Used

BD2 (lowest)

>BBa_J119025 Part-only sequence (88 bp)

gggcccaagttcacttaaaaaggagatcaacaatgaaagcaattttcgtactgaaacatcttaatcatgctaaggaggttttctaatg

BD18 (medium)

>BBa_J119024 Part-only sequence (88 bp)

gggcccaagttcacttaaaaaggagatcaacaatgaaagcaattttcgtactgaaacatcttaatcatgcgacggagcgtttctaatg

Aligned

BD2 gggcccaagttcacttaaaaaggagatcaacaatgaaagcaattttcgtactgaaacatcttaatcatgctaaggaggttttctaatg

BD18 Gggcccaagttcacttaaaaaggagatcaacaatgaaagcaattttcgtactgaaacatcttaatcatgcgacggagcgtttctaatg

Cons Gggcccaagttcacttaaaaaggagatcaacaatgaaagcaattttcgtactgaaacatcttaatcatgckacggagsktttctaatg

Number of Sequences = 2 power 3 = 8

New J-GGA Scaffold (after PCR mutagenesis with above primers)

Prefix: Gaattcgcggccgcttctagag

Junction A: Atagtctgttcatggtgc

Spacer: acgt

Junction B: ggctgatgtagttaaggc

Spacer: cgga

Junction C: gttctaatggggaccatc

Spacer: ttag

Junction D: cggagctatgtattcctg

Suffix: tactagtagcggccgctgcag

Sticky ends needed:

Junction B: AGGC

Junction C: GTTC

Oligos to be Ordered

BD2_top; AGGCgggcccaagttcacttaaaaaggagatcaacaatgaaagcaattttcgtactgaaacatcttaatcatgctaaggaggt

BD2_bot; GAACACCTCCTTAGCATGATTAAGATGTTTCAGTACGAAAATTGCTTTCATTGTTGATCTCCTTTTTAAGTGAACTTGGGCCC

BD2_18Cons_Top;

AGGCGggcccaagttcacttaaaaaggagatcaacaatgaaagcaattttcgtactgaaacatcttaatcatgckacggagsk

BD2_18Cons_Top;

GAACMSCTCCGTMGCATGATTAAGATGTTTCAGTACGAAAATTGCTTTCATTGTTGATCTCCTTTTTAAGTGAACTTGGGCCC

Annealed

BD2_ AGGCGGGCCCAAGTTCACTTAAAAAGGAGATCAACAATGAAAGCAATTTTCGTACTGAAACATCTTAATCATGCTAAGGAGGT

        CCCGGGTTCAAGTGAATTTTTCCTCTAGTTGTTACTTTCGTTAAAAGCATGACTTTGTAGAATTAGTACGATTCCTCCACAAG

BD2_18CONS

AGGCGGGCCCAAGTTCACTTAAAAAGGAGATCAACAATGAAAGCAATTTTCGTACTGAAACATCTTAATCATGCKACGGAGSK

   CCCGGGTTCAAGTGAATTTTTCCTCTAGTTGTTACTTTCGTTAAAAGCATGACTTTGTAGAATTAGTACGMTGCCTCSMCAAG

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