Novel acrylamido monomers with higher hydrophilicity and improved hydrolytic stability: III. DNA separations by capillary electrophoresis in poly(N-acryloylaminopropanol).

Separation of DNA fragments in a novel polymer network, consisting of N-acryloylaminopropanol (AAP) is reported. The performance of this novel monomer, as a sieving liquid polymer in capillary zone electrophoresis, was evaluated. In 50 μm ID capillaries, an 8% solution of poly(AAP) can afford apex-resolution of the 123/124 bp adjacent pair of DNA fragments in marker V, typically unresolved in any poly(acrylamide) formulation. It is proposed that the distal –OH group in the AAP molecule can form transient H-bonds with the DNA double helix. Molecular modeling shows a meandering structure for poly(AAP), lacing the walls of half a cylinder, with kinks protruding at regular intervals, potentially able to fit into the major groove of DNA. Contrary to previously held beliefs, there seems to be a minimum length of the polymer for proper sieving of DNAs. For poly(acrylamides), a weight average molecular mass Mw 30 000 polymer offers no resolution, whereas a polymer of 250 000 to 400 000 Da exhibits optimum resolving power. For poly(AAP), the optimal length is in excess of 450 000 Da in Mw. Thus, it is shown that both the chemical composition of the monomer and the length of the polymer play a subtle, cooperative role in DNA separation