384812 Transient Interactions in Networks of Worm-like Micelles and Their Application in Rapid DNA Electrophoresis
Electrophoretic DNA separations are a mainstay of bioanalytical chemistry and significant academic and industrial research has been focused on the development of new methods to electrophoretically sort DNA at greater speed, with higher resolution, and with a higher dynamic range. Because the electrophoretic mobility of DNA in free solution is roughly invariant with DNA length, a sieving matrix or gel is typically required to add a length-dependent friction to all DNA oligomers. This added friction greatly slows the process and limits the electric fields that can be applied without suffering Joule heating and attendant band broadening. Gels are difficult to install in microfluidic devices and are prone to clogging with repeated use.
We have developed a gel-free alternative (“micelle-ELFSE”) that provides for a very fast, free-solution separation with a minimal added friction. Here the DNA of interest is end-alkylated before electrophoresis in a buffer containing dilute (1-3 wt%) solutions of nonionic surfactant, above their CMC. Micelles in the buffer transiently interact with the DNA’s alkyl group, slightly retarding the DNA’s electrophoretic mobility in a length-dependent way. We demonstrate that capillary implementations of micelle-ELFSE give runtimes that are 10-100x faster than conventional capillary gel electrophoresis, with read lengths in excess of 600 bases. This success is based in part on the ability of surfactant micelles to rapidly sample different sizes during the run, ensuring a highly uniform drag for all oligomers in the sample.
To apply the micelle-ELFSE method to kilobase-long DNA, we need to increase the size of the micelles attached to the DNA. While attempts at using liposomes and microemulsion droplets gave poor size sampling, and hence broad peaks, solutions of worm-like micelles perform well. One apparent limit on the micelle size is the formation of an entangled network of micelles that would lead to a sieving mechanism. Work in other groups has shown that buffers of worm-like micelles indeed sieve DNA and this would greatly slow down runtime and introduce other adverse effects in micelle-ELFSE.
We have recently observed that end-alkylation of DNA defeats the sieving mechanism in favor of micelle-ELFSE, greatly extending the dynamic range of the method. We will present a model comparing the time scales of entanglement formation/breakage with micelle attachment to DNA and DNA stretching to explain this curious phenomenon. We will also present recent Brownian dynamics simulations suggesting that micelle-ELFSE can intensify microfluidic DNA separations in nanofilter arrays and results of microfluidics design optimization to extend the read length while reducing runtime. Finally, we will offer ideas on how end-tagged DNA oligomers can be used to better characterize networks of worm-like micelles.