Microchannel DNA sequencing matrices with switchable viscosities

Abstract

We review the variety of thermo-responsive and shear-responsive polymer solutions with "switchable" viscosities that have been proposed for application as DNA sequencing matrices for capillary and microfluidic chip electrophoresis. Generally, highly entangled polymer solutions of high-molar mass polymers are necessary for the attainment of long DNA sequencing read lengths (> 500 bases) with short analysis times (< 3 h). However, these entangled polymer matrices create practical difficulties for microchannel electrophoresis with their extremely high viscosities, necessitating high-pressure loading into capillaries or chips. Shear-responsive (shear-thinning) polymer matrices exhibit a rapid drop in viscosity as the applied shear force is increased, but still require a high initial pressure to initiate flow of the solution into a microchannel. Polymer matrices designed to have thermo-responsive properties display either a lowered (thermo-thinning) or raised (thermo-thickening) viscosity as the temperature of the solution is elevated. These properties are generally designed into the polymers by the incorporation of moderately hydrophobic groups in some part of the polymer structure, which either phase-separate or hydrophobically aggregate at higher temperatures. In their low-viscosity states, these matrices that allow rapid loading of capillary or chip microchannels under low applied pressure. The primary goal of work in this area is to design polymer matrices that exhibit this responsive behavior and hence easy microchannel loading, without a reduction in DNA separation performance compared to conventional matrices. While good progress has been made, thermo-responsive matrices have yet to offer sequencing performance as good as nonthermo-responsive networks. The challenge remains to accomplish this goal through the innovative design of novel polymer structures.

Theory of DNA electrophoresis (∼ 1999 –2002 ½)

“…13) Recent advances in DNA sequencing by capillary and microdevice electrophoresis [197]. [199]. An excellent review of the various types of novel polymers being developed to carry out DNA sequencing in microchannel systems.…”

Aspergillus Collagen-Like Genes ( acl ): Identification, Sequence Polymorphism, and Assessment for PCR-Based Pathogen Detection

“…Linear gels are viscous additives that provide good separation performance and do not need to be polymerized in the capillary. Issues associated with the introduction of highly viscous materials into narrow-bore capillaries have spawned the use of thermally reversible sieving materials (76)(77)(78), including phospholipid nanogels (36). These materials are introduced into the capillary at a temperature that generates low viscosity and then converted into a highly viscous separation additive in the capillary by changing the separation temperature.…”

Analysis of Nucleic Acids and Proteins in Capillary Electrophoresis and Microchip Capillary Electrophoresis Using Polymers as Additives of the Background Electrolytes

“…Thermo-responsive polymers are generally copolymers consisting of hydrophobic and hydrophilic blocks such as polyisopropylacrylamide grafted with PEO chains [76][77][78][79]. The viscosity for a moderately hydrophobic copolymer is high because of formation of entangled networks at room temperature, while it decreases rapidly at temperature higher than a certain critical elevated temperature, where a phase transition occurs [48,[76][77][78][79][80][81][82][83]. It is thus suggested that filling of such a polymer solution is carried out at high temperature, while the separation is performed at low temperature for high resolving power.…”

“…It is thus suggested that filling of such a polymer solution is carried out at high temperature, while the separation is performed at low temperature for high resolving power. A series of linear copolymers of N,N'-dimethylacrylamide (DMA) and N,N'-diethylacrylamide (DEA) with different monomer compositions such as the copolymer consisting of 42% DEA and 58% DMA and that of 53% DEA and 47% DMA have been prepared and tested for DNA separations [80,81]. The authors have pointed out that the resolution decreases with increasing the hydrophobicity of the polymer solution [80][81][82][83].…”