Daniel:Notebook/PosSequencing/Oligos

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Oligonucleotides[edit]

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Components:

Component Sequence Reverse Complement Length Tm (C, 0.5 uM Primer concentration)
Adapter 0 CCTCATGCGTATCCGAT ATCGGATACGCATGAGG 17 53.54
Adapter 1 (Primer2) AACAGTGCTCTTCCAGTCTA TAGACTGGAAGAGCACTGTT 20 50.94
Add PolydT NBAAAAAAAAAAAAAAAAAAAATAGACTGGAAGAGCACTGTT AACAGTGCTCTTCCAGTCTATTTTTTTTTTTTTTTTTTTTVN 42 53.9
dcProbe6-488 (barcode 1) CACGCTTACGATCCCGCTAT ATAGCGGGATCGTAAGCGTG 20 60.93
dcProbe6-Cy3 (barcode 2) TCGTAACCCGTGCGAAGTGC GCACTTCGCACGGGTTACGA 20 65.15
dcProbe6-Cy5 (barcode 3) CTCTCGTAGCGTGCGATGAG CTCATCGCACGCTACGAGAG 20 60.68
  • Note: From this paper the working formula for adding formamide is -0.58 +/- 0.05 C/% FA. According to this a 25% formamide solution will affect Tm by 14.7C give or take 1C.

Biotin Uracil Primer 1

5-/5BiotinTEG/CAGTGTUCCTCATGCGTATCCGAT-3

Biotin EcoRI Primer 1

5-/5BiotinTEG/GGAATTCCCCTCATGCGTATCCGAT-3

BarcodeOligov1 (dcProbe6-488)

5TAGACTGGAAGAGCACTGTTCATCATCAT-GGGTAGTGTGTAGGAATTCC-CACGCTTACGATCCCGCTAT-ATCGGATACGCATGAGG3

BarcodeOligov2 (dcProbe6-Cy3)

5TAGACTGGAAGAGCACTGTTCGATGTACG-GGGTAGTGTGTAGGAATTCC-TCGTAACCCGTGCGAAGTGC-ATCGGATACGCATGAGG3

BarcodeOligov3 (dcProbe6-Cy5)

5TAGACTGGAAGAGCACTGTTGGACTTGAA-GGGTAGTGTGTAGGAATTCC-CTCTCGTAGCGTGCGATGAG-ATCGGATACGCATGAGG3