Daniel:Notebook/ComboLock/2016-8-5
Positive Control Amplicon Production
In order to test the latch-padlock binding better, I am going to use a positive control oligonucleotide. The oligo is designed to contain only the parts of the C probes (and antibody oligos) that bind to the latch and padlock, as well as barcodes. The oligos will also have biotin, which means I'll have a good method for pulldown.
Oligonucleotide Design
First thing is to design the oligos. The following table indicates the created oligonucleotide sequences. The LatchX1, C1 amplicon and C2 amplicon were ordered from IDT. The reason for the additional latch is to remove the UMI on the normal latch sequences. Since the UMI is a degenerate sequence I can't design an oligo to bind to it. Therefore I replaced the UMI on the normal latch sequences with a second barcode for the LatchX1 probe. There are two amplicons because IDT doesn't allow you to attach a biotin to ultramers (>60 bp).
Name | Sequence | Reverse Complement | Length (bp) | Components |
primer2 | ACGGCGGACCTCGCACGG | CCGTGCGAGGTCCGCCGT | 18 | |
primer4 | CCGTGGACGGTCGCGTTC | GAACGCGACCGTCCACGG | 18 | |
primer6 | CGGCGATGCGTGATCGGG | CCCGATCACGCATCGCCG | 18 | |
primer12 | CCCGCCCAGTAACCGGCG | CGCCGGTTACTGGGCGGG | 18 | |
LatchX1 Barcode | CATTTAGTATACGGGC | GCCCGTATACTAAATG | 16 | |
Latch 8 barcode | TATTTGTA | TACAAATA | 8 | |
Latch 9 barcode | GCGCCTAC | GTAGGCGC | 8 | |
Total Amplicon | ACGGCGGACCTCGCACGGTATTT GTACCGTGGACGGTCGCGTTCGCCCGTATAC TAAATGCGGCGATGCGTGATCGGGGCG CCTACCCCGCCCAGTAACCGGCG | CGCCGGTTACTGGGCGGGGTAGG CGCCCCGATCACGCATCGCCGCATTTAGTAT ACGGGCGAACGCGACCGTCCACGGTAC AAATACCGTGCGAGGTCCGCCGT | 104 | Primer2-Latch8BC-Primer4-LatchX1BCRevComp-Primer6-Latch9BC-Primer12 |
C1 Amplicon | ACGGCGGACCTCGCACGGTATTTGTACCGTGGACGGTCGCGTTCACTAAATG | CATTTAGTGAACGCGACCGTCCACGGTACAAATACCGTGCGAGGTCCGCCGT | 52 | |
C2 Amplicon | GCCCGTATCGGCGATGCGTGATCGGGGCGCCTACCCCGCCCAGTAACCGGCG | CGCCGGTTACTGGGCGGGGTAGGCGCCCCGATCACGCATCGCCGATACGGGC | 52 | |
Latch X1 | CAAGATCATAAGAGTTCGTTCGTCCACCACACAGCGACGAGACCG | CGGTCTCGTCGCTGTGTGGTGGACGAACGAACTCTTATGATCTTG | 45 | primer6RC-bclp0001-bclp0002-primer4RC |
Ligation Reaction
Since the amplicon is in pieces right now, I need to ligate the C1 and C2 amplicons together.
Theory
C1 Amplicon: 5ACGGCGGACCTCGCACGGTATTTGTACCGTGGACGGTCGCGTTCACTAAATG3
C2 Amplicon: 5GCCCGTATCGGCGATGCGTGATCGGGGCGCCTACCCCGCCCAGTAACCGGCG/Biotin/3
LatchX1: 5CAAGATCATAAGAGTTCGTTCGTCCACCACACAGCGACGAGACCG3
Update: LatchX1 was a misorder. I need to use Latch X2 instead
LatchX2: 5CCCGATCACGCATCGCCGATACGGGCCATTTAGTGAACGCGACCGTCCACGG3
Reaction Trimer:
LX2 C1|C2 3GGCACCTGCCAGCGCAAGTGATTTAC|CGGGCATAGCCGCTACGCACTAGCCC5 ACGGCGGACCTCGCACGGTATTTGTACCGTGGACGGTCGCGTTCACTAAATG|GCCCGTATCGGCGATGCGTGATCGGGGCGCCTACCCCGCCCAGTAACCGGCG/Biotin/