Koch Lab:Protocols/Sequences/Unzipping oligos
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Oligos for ligating onto the BstXI sticky end from PCR on pRL574 plasmid
Top adapter 1a - TCGA, ATCG
Oligo #1: Top adapter 1a - TCGA, ATCG Sequence 5' to 3': TCGAGTCTGAATTCTAATGTAGTATAGTAATCCGCTCATCG Modification: 5' phosphate
Bottom adapter 1a - Biotin
Oligo #2: Bottom adapter 1a - Biotin Sequence 5' to 3': GAGCGGATXACTATACTACATTAGAATTCAGAC Modification: X = biotin-dT
Bottom adapter 1b - Biotin, CATG
Oligo #3: Bottom adapter 1b - Biotin, CATG Sequence 5' to 3': GAGCGGATXACTATACTACATTAGAATTCAGACTCGACATG Modification: X = biotin-dT
Hairpin Adapter 1
Oligo #4: Hairpin Adapter 1 Sequence 5' to 3': GAGCGGATXACTATACTACATTAGAATTCAAACTCGAGAGAGTAATCTCTCGAGTTTGAATTCTAATGTAGTATAGTAATCCGCTCATCG Modifications: X = biotin-dT
Kochlab note: we also have slightly modified biotinylated versions of the above that are missing the T (due to an error in the way we ordered them).
Hairpin Adapter 2
Name: Hairpin Adapter 2 -- NotI Scale: 1 micromol Sequence 5' to 3': GAGCGGATXACTATACTACATTAGAATTCAAAGCGGCCGCAGAGTAATCTGCGGCCGCTTTGAATTCTAATGTAGTATAGTAATCCGCTCATCG Modification: X = biotinylated dT Purification: PAGE Note: This oligo is a self-complementary hairpin.
Top Adapter -- BstXI / SapI
Name: Top Adapter -- BstXI / SapI Scale: 200 nmol Sequence 5' to 3': 5’-Phosphate- GCTGTCTGAATTCTAATGTAGTATAGTAATCCGCTCATCG Modification: 5'-phosphate Purification: OPC (Unless you think PAGE would significantly improve purity)
Mfold verification of hybridization with Bottom Adatper 1a: Image:New Top Strand Adapter.png
Caps
Sap Cap AGC
Name: Sap Cap AGC Scale: 200 nmol Sequence 5' to 3': 5'-Phosphate- AGCGGCGACCTAGCGTAAGCTAGGTCGCC Modification: 5'-P Purification: OPC