On-chip purification of genomic material from crude biological samples such as whole blood is crucial for developing point-of-care field devices for use at home and abroad. Our group has synthesized and previously reported on a series of water-soluble block copolymers containing acrylamide and hydrophobic N,N,-dialkylacrylamides, which can adsorb molecules containing hydrophobic moieties such as proteins during electrophoresis while allowing genomic material to pass through. We have theorized that protein removal is not only dependent on the polymer structure, but also on the environments in which they are used, most notably the running temperature of the system. As hydrophobic interactions generally become stronger with temperature, based on increased exposure of hydrophobic groups due to denaturing and thermodynamic effects, the effectiveness of the polymer networks is shown to be dramatically enhanced with increased temperature. Tests were performed in 10 °C increments from 25 °C to 65 °C on an 8-cm long glass microfluidic chip dynamically coated with poly(N-hydroxyethyl-acrylamide) (pHEA); the proteins studied were fluorescently labeled with Alexa Fluor 488 and detected using a homebuilt LIF system. Results have shown that by increasing the temperature to 65°C, and utilizing a 600-kDA (Mw) copolymer containing only ~ 0.20 mol% dihexylacrylamide, we can remove a larger percentage of bovine serum albumin proteins than previously possible. Remarkably, proteins that have few exposed hydrophobic amino acids at room temperature, such as trypsin inhibitor, which previously passed through the hydrophobic copolymer network unhindered, has also been successfully removed while allowing DNA to pass through freely. The effectiveness of this technique at elevated temperatures also allows for copolymers containing smaller concentrations of hydrophobe to be utilized while obtaining similar results to those containing a larger percentage. This is crucial, as the viscosity of the polymer solution is sensitive to the percentage of hydrophobic moiety present in the copolymer, and the ability to utilize less hydrophobe at elevated temperatures will decrease pressure and strength requirements for loading the polymer solution into the microchannels at ambient temperature. Based on these results, future testing of crude biological samples as well as the development of microchips and copolymers specifically tailored to this system will be pursued.