View source for Design of C dog oligos in J-GGA Scaffold

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