title: Hydrophobically modified polyacrylamide block copolymers for fast, high-resolution DNA sequencing in microfluidic chips.
abstract: By using a microfluidic electrophoresis platform to perform DNA sequencing, genomic information can be obtained more quickly and affordably than the currently employed capillary array electrophoresis instruments. Previous research in our group has shown that physically cross-linked, hydrophobically modified polyacrylamide matrices separate dsDNA more effectively than linear polyacrylamide (LPA) solutions. Expanding upon this work, we have synthesized a series of LPA-co-dihexylacrylamide block copolymers specifically designed to electrophoretically sequence ssDNA quickly and efficiently on a microfluidic device. By incorporating very small amounts of N,N-dihexylacrylamide, a hydrophobic monomer, these copolymer solutions achieved up to approximately 10% increases in average DNA sequencing read length over LPA homopolymer solutions of matched molar mass. Additionally, the inclusion of the small amount of hydrophobe does not significantly increase the polymer solution viscosities, relative to LPA solutions, so that channel loading times between the copolymers and the homopolymers are similar. The resulting polymer solutions are capable of providing enhanced sequencing separations in a short period of time without compromising the ability to rapidly load and unload the matrix from a microfluidic device.
authors.affiliation: Department of Materials Science and Engineering, Northwestern University, Evanston, IL, USA.
authors.forename: Ryan E
authors.initials: RE
authors.lastname: Forster
authors.forename: Thomas N
authors.initials: TN
authors.lastname: Chiesl
authors.forename: Christopher P
authors.initials: CP
authors.lastname: Fredlake
authors.forename: Corin V
authors.initials: CV
authors.lastname: White
authors.forename: Annelise E
authors.initials: AE
authors.lastname: Barron
mesh_terms: D000180:Acrylic Resins / Q000138:chemical synthesis / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000235:genetics; D046209:Electrophoresis, Microchip / Q000379:methods*; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D008856:Microscopy, Fluorescence; D012212:Rheology; D017422:Sequence Analysis, DNA / Q000379:methods*; D014783:Viscosity; D000099166:Polyacrylamides
chemical_list: D000180:Acrylic Resins; D004277:DNA, Single-Stranded; D000099166:Polyacrylamides