Endy:Double stranding oligo libraries

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Order oligos and double-stranding primers

  • Dilute stocks to 100uM
  • Dilute working stocks of libraries and double-stranding primers to 10uM
  • Dilute working stocks of sequencing primers to 3.2uM (6.4uL of stock solution in 193.6uL water)
  • Some considerations:
    • Oligos should be the maximum length because this will help with PCR cleanup and ligation efficiency
    • Make sure you have some spacer sequence around the restriction site. NEB has a list of the length of the spacer sequence required for each restriction enzyme. (8bp is usually a safe bet)
    • Order the lowest concentration allowable for the size oligo you want – this will be 50nmole for the 100bp oligo. This will already be more than you’ll need.
    • If you don’t mind spending more money you can order special “doped” oligo pools where instead of even concentrations of A/T or A/T/C/G or A/T/C, you get 90%A/2%C/8%G, etc. This allows for you to generate a library which is much more likely to produce productive clones.

Double strand the library with modified PCR

  • Expected max library size is 108 molecules (limit set by transformation efficiency.) You want to load 10X the expected library size for a single library construction. Therefore, you would like to have 109 molecules for a single transformation.
    • 1pmol corresponds to ~1011 molecules
    • Use 25pmol of library to make enough for 2500 transformations
  • Total library DNA should be less than ~25pmol per 100uL reaction

Reaction Mix (100uL, 25pmol library)

Use the following reaction mix for each PCR reaction:

  • 10 μl 10x Thermo polymerase buffer
  • 10 μl 10x dNTPs (10x = 2.5 mM each dNTP)
  • 5 μl 10 μM FWD primer
  • 5 μl 10 μM REV primer
  • 1 μl Polymerase (taq or vent)
  • 66.5 μl H2O
  • 2.5 μl 10μM library stock

PCR protocol

  • 95oC for 2.5 minutes
  • Cycle 5 times:
    • 55oC (or whatever temperature is appropriate) for 30 seconds (annealing)
    • 72oC for 1.5 minutes (elongation)
  • 72oC for 10 minutes (final elongation)
  • 4oC forever

Perform PCR cleanup on the double-stranded library

  • This concentrates the samples and allows for the buffer to be switched to something more appropriate.
  • PCR purification columns can handle up to 10ug of DNA
    • 100pmol of a 100bp oligo is about 3ug, so multiple 100-ul reactions of 25pmol can be combined into one column
  • Expected recovery from a PCR purification reaction is 90% (from the Invitrogen package)
  • You can run a sample of the PCR product out on a gel against a sample of the original library to verify that the double stranding worked (double stranded DNA should run slightly faster than single stranded)
    Three libraries ~100bp; on the left is the single-stranded oligo; on the right are double-stranded oligos (different lanes are different primers)

Restriction digest the library

Perform PCR cleanup on the digest

  • This will remove the cut ends, since they are small.

Ligate the sample from the PCR cleanup with a vector

Transform into compotent cells