Chris:LabNotes/sci-Methyl Seq/Calendar/2017/2017-5-17

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sci-Methyl Seq Barcode 1 Design v2[edit]

Background[edit]

  • Previously, I've designed Adapter 1 with a CG sticky end that would anneal directly onto MspI digested DNA. However, as previous tests have shown, this approach doesn't work because of the high amounts of adapter-adapter and template-template annealing that goes on.
  • Dr. Zhang then suggested that we look into using end-repair/dA-tailing prior to adapter ligation. This will ensure that the majority of ligated product are template+adapter. Consequently, we want to make a slight edit to the Adapter 1 test design to include a T-overhang instead of current CG overhang

Barcode 1 Adapter Design (v2)[edit]

  • Based on what we know from dA-tailing, an A will be added to the 3' end of blunt-ended DNA. Consequently, the DNA fragment after end-repair/dA-tailing would be:
5'  -------------------A 3'
3' A-------------------  5'
  • Consequently, our Adapter 1 v2 design should be as follows: (remember we want to create a dsDNA adapter for ligation)
5' /5Phos/------------------- 3'
3'       T------------------- 5'
  • Below are the sequences we want to order from IDT:
Adpt1_v2          5' /5Phos/TTAGAGGTGGTCCCTCCTACCCGGCGTTT 3'
Adpt1_v2_comp     3'       TAATCTCCACCAGGGAGGATGGGCCGCAAA 5'