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Services – Columns, DNA Size-Select

• Columns for DNA Size-Selection

• Alternative DNA Size-Selection methods

• Online Submission Request

• Physical Submission of Samples

DNA Purification & Size-Selection

The Core uses the Zymo columns described below for rapid DNA size-selection. For more information, visit either the distributor's website (Genesee Scientific) or the manufacturer's website (Zymo Research).

Select-A-Size DNA Clean & Concentrator Kit — (Cat #D4080):
  • Size-Select DNA with retention points of ≥50-bp, ≥100-bp, ≥150-bp, ≥200-bp, ≥300-bp (other cutoffs between 50-300 bp can be attempted by titration).
  • Clean and concentrate up to 3 µg DNA in as little as 10-µl elution with 0-µl wash residue carryover.
  • Eluted DNA is of high quality and well suited for NGS, ligations, restriction endonuclease digestions, and library preparation cleanup.
  • DNA Size Limits: 50 bp to 23 kb.
  • Note 1: Maximum depletion of a lower-size fragment requires that the selected cutoff value be at least 50-bp higher than the unwanted fragment size; using this criterion, we have been extremely successful at eliminating adapter-dimers from NGS libraries while retaining the bulk of the desired fragment sizes.
  • Note 2: Conversely, maximum enrichment of desired fragments requires that the lower cut-off be at least 100-bp lower than the desired fragments; thus, there can be a tension between depletion of adapter-dimers and retention of the desired fraction of library if the difference in sizes is <100-bp. In that case, adjustments to the protocol can be attempted to find a happy 'medium' between the two objectives.
  • Note 3: Although we highly recommend the 'lower-cutoff' size-selection protocol with this kit, we recommend caution with respect to using the double-size selection protocol (i.e., lower cutoff = 300 bp; upper cutoff = 700-bp). Nevertheless, it should be noted that we have performed the double-size selection protocol on only a few libraries; thus, it is possible that the problems we encountered with that protocol were library-specific rather than any reflection on the functionality of the Select-A-Size DNA Clean & Concentrator Kit.

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    Alternative DNA Size-Selection methods

    Depending on your research needs, DNA size-selection by the BluePippin or E-gel might be more appropriate. For product specifications and other information regarding these platforms, please see the following web pages:

  • BluePippin
  • E-gel
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    Online Submission Request

  • Log In to the website, and click on "Services Page":
    • Make the necessary 'selections'.
    • In the "Client Memo" field, specify the desired elution volume and any other information. [Note: Unless otherwise requested, DNA will be eluted with TVLE (10 mM Tris, 0.05 mM EDTA).
    • Click the 'check box', and submit your request.
  • If you make an error in your request, you may revise that request if you do so before we begin processing it.
  • You will receive an automated email when your samples are processed and ready for pick-up.
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    Physical Submission of Samples

  • Tubes:  Samples exceeding ~25 ul should be submitted in 0.5-1.5 ml tubes (standard or Eppendorf LoBind); otherwise, 0.2-ml tubes are acceptable.
  • Label Submission:  Upon successful submission of your online request, the 'Submission #" will appear on your screen. Then, label the tube rack itself with:
    • Submission #;
    • Date;
    • PI's Last Name; and,
    • Submitter name or initials.
  • Delivery site:  Transfer tubes to a Genomics Core rack (taking your own rack back to your lab), and put samples in the Mini-fridge (by sink) in the Genomics Core (A628 Life Science Annex).

    [Note: If the Core is locked, put your samples in the plastic "After-Hours" GC drop-box located in the adjacent Cold Room (beside sink, Rm. A650).]

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