When it comes to purification of PCR fragments, nothing is more frustrating than losing your product due to unreliable gel extraction methods. Clontech helps alleviate that frustration with its Nucleotrap Nucleic Acid Purification Kit. At the heart of this kit is a special matrix that binds DNA and separates it from contaminants. Clontech claims their version of this matrix differs from other kits because the beads in the matrix are all uniform size – according to them, this allows purification of large DNA fragments without shearing, increasing the yield of your desired product. The bead suspension is also free from impurities that could inhibit downstream applications (e.g. ligations or restriction digests).
The Nucleotrap matrix binds the nucleic acid in the presence of chaotropic salts. The salts disrupt the water surrounding the nucleic acid, which permits the attachment of the nucleic acid to the beads. As a part of this (simple) procedure, the matrix is washed to remove the impurities present in the initial sample. The desired nucleic acid can then be eluted using either water or a low salt buffer like TE. The eluted product can be used directly for applications such as end-labeling or cloning.
I have found that this kit streamlines purification of PCR products. While similar results can be obtained by gel extraction, this kit is much quicker purification and I have found that it yields an excellent quality product. The Nucleotrap PCR mix only binds DNA fragments that are larger than 120 bps, thus ensuring that primers will stay in solution during the purification. Prior to using this kit, I would generally see a lower molecular-weight band below my product, even after gel extraction. The Nucleotrap kit has eliminated that second, unwanted band.
The only negative with this kit is that the amount of matrix that is provided will run out before the buffers do. You can purchase additional matrix, however, it is much more economical to simply purchase another kit. This kit definitely improved the quality of DNA that I used for end labeling experiments and I would highly recommend it!
Katie Kalivoda
PhD Candidate
University of Illinois Champaign-Urbana