Electrophoresis, Vol.27, No.16, 3181-3194, 2006
Electrophoretic mobility of linear and star-branched DNA in semidilute polymer solutions
Electrophoresis of large linear T2 (162 kbp) and 3-arm star-branched (N-Arm = 48.5 kbp) DNA in linear polyacrylamide (LPA) solutions above the overlap concentration c* has been investigated using a fluorescence visualization technique that allows both the conformation and mobility mu of the DNA to be determined. LPA solutions of moderate polydispersity index (PI similar to 1.7-2.1) and variable polymer molecular weight M-w (0.59-2.05 MDa) are used as the sieving media. In unentangled semidilute solutions (c*< c < c(e)), we find that the conformational dynamics of linear and star-branched DNA in electric fields are strikingly different; the former migrating in predominantly U- or I-shaped conformations, depending on electric field strength E, and the latter migrating in a squid-like profile with the star-arms outstretched in the direction opposite to E and dragging the branch point through the sieving medium. Despite these visual differences, It for linear and star-branched DNA of comparable size are found to be nearly identical in semidilute, unentangled LPA solutions. For LPA concentrations above the entanglement threshold (c > c(e)), the conformation of migrating linear and star-shaped DNA manifest only subtle changes from their unentangled solution features, but P for the stars decreases strongly with increasing LPA concentration and molecular weight, while mu for linear DNA becomes nearly independent of c and M-w. These findings are discussed in the context of current theories for electrophoresis of large polyelectrolytes.
Keywords:electrophoretic mobility;entanglements;linear polyacrylamide;semidilute polymer solutions;star-branched DNA