Gel-Purify, columns or silica matrix?

[scuellar]

Hi,
I’m building some solexa libraries from PCR products and got poor DNA recovering, after gel size selection of linked products, using GFX pharmacia columns. I’m switching to Qiagen columns (QIAquick gel recovery extraction kit) or silica matrix (NucleoTrap gel extraction kit). Any suggestion?

Thanks

[GW_OK]

None of the above. Use Agencourt Ampure beads. They're way, way better than even Qiagen columns.

[scuellar]

Thanks for your fast answer. I'm wondering if which buffer do you use for dissolve the agarose?

[GW_OK]

With the Ampure beads I don't even do gel size selection any more.

[scuellar]

that's nice... thanks

[KimUTA]

I have large and small, unwanted fragments. And an unopened QiaQuick Gel extraction kit. Is the resulting product clean enough for direct use in a library?

I am intrigued by using the AMPure beads to size select. Do you do a 2 step approach, similar to the following NEB protocol? The first bead ratio is used to bind and discard the larger fragments, the second step retains and cleans the desired smaller band. https://www.neb.com/protocols/1/01/0...election-e6270

[GW_OK]

Yep. Works fine.