Dynamic computer simulations of electrophoresis: 2010-2020

The transport of components in liquid media under the influence of an applied electric field can be described with the continuity equation. It represents a nonlinear conservation law that is based upon the balance laws of continuous transport processes and can be solved in time and space numerically. This procedure is referred to as dynamic computer simulation. Since its inception four decades ago, the state of dynamic computer simulation software and its use has progressed significantly. Dynamic models are the most versatile tools to explore the fundamentals of electrokinetic separations and provide insights into the behavior of buffer systems and sample components of all electrophoretic separation methods, including moving boundary electrophoresis, CZE, CGE, ITP, IEF, EKC, ACE, and CEC. This article is a continuation of previous reviews (Electrophoresis 2009, 30, S16–S26 and Electrophoresis 2010, 31, 726–754) and summarizes the progress and achievements made during the 2010 to 2020 time period in which some of the existing dynamic simulators were extended and new simulation packages were developed. This review presents the basics and extensions of the three most used one‐dimensional simulators, provides a survey of new one‐dimensional simulators, outlines an overview of multi‐dimensional models, and mentions models that were briefly reported in the literature. A comprehensive discussion of simulation applications and achievements of the 2010 to 2020 time period is also included.

Electrode-Free Concentration and Recovery of DNA at Physiologically Relevant Ionic Concentrations

Advances in microanalytical and microfluidic technologies have enabled rapid and amplification-free detection of DNA with a high signal-to-noise ratio. The low sample volume, however, poses a limit in the DNA detection sensitivity, which can be challenging for analyzing rare DNA in physiological samples. One way to improve the sensitivity is to concentrate the DNA in the sample prior to the analysis. The most common DNA concentration techniques are based on electrokinetics, which require an external electric field and generally become ineffective in high ionic concentration conditions. In this work, we present a facile method termed high-salt molecular rheotaxis (HiSMRT) to concentrate and recover DNA from samples with physiologically relevant ionic concentrations without any external electric field. HiSMRT requires only pressure-driven flow and ion concentration gradient to induce a stable local electric field and achieve DNA concentration, making it impervious to high ionic concentrations. We demonstrate that HiSMRT performs robustly at ionic concentrations equivalent to 2%-20% of the ionic concentration in blood serum. HiSMRT can concentrate DNA by up to 960-fold and recover an average of 96.4% of the DNA fragments from 2.0 to 23 kbp uniformly. The concentration process using HiSMRT takes as little as 7.5 min. Moreover, we show that this technique can be easily integrated to perform DNA concentration, size separation, and single-molecule detection all in one platform. We anticipate that this technique will be applicable to a wide range of biological samples and will help to improve the sensitivity of nucleic acid detection for low-abundance DNA biomarkers.

Molecular rheotaxis directs DNA migration and concentration against a pressure-driven flow

In-line preconcentration techniques are used to improve the sensitivity of microfluidic DNA analysis platforms. The most common methods are electrokinetic and require an externally applied electric field. Here we describe a microfluidic DNA preconcentration technique that does not require an external field. Instead, pressure-driven flow from a fluid-filled microcapillary into a lower ionic strength DNA sample reservoir induces spontaneous DNA migration against the direction of flow. This migratory phenomenon that we call Molecular Rheotaxis initiates in seconds and results in a concentrated DNA bolus at the capillary orifice. We demonstrate the ease with which this concentration method can be integrated into a microfluidic total analysis system composed of in-line DNA preconcentration, size separation, and single-molecule detection. Paired experimental and numerical simulation results are used to delineate the parameters required to induce Molecular Rheotaxis, elucidate the underlying mechanism, and optimize conditions to achieve DNA concentration factors exceeding 10,000 fold.

Implementing a nucleic acid preconcentration method can improve the sensitivity of microfluidic analysis systems. Here Friedrich et al. concentrate DNA by many orders of magnitude using pressure-driven flow, which could lead to a simple and practical microanalysis platform.

Gel electrophoresis in a polyvinylalcohol coated fused silica capillary for purity assessment of modified and secondary-structured oligo- and polyribonucleotides

Application of a polyvinylalcohol-coated (PVA-coated) capillary in capillary gel electrophoresis (CGE) enables the selective separation of oligoribonucleotides and their modifications at high resolution. Quality assessment of shorter oligomers of small interfering RNA (siRNA) is of key importance for ribonucleic acid (RNA) technology which is increasingly being applied in medical applications. CGE is a technique of choice for calculation of chemically synthesized RNAs and their modifications which are frequently obtained as a mixture including shorter oligoribonucleotides. The use of CGE with a PVA-coated capillary to analyze siRNA mixtures presents an alternative to conventionally employed techniques. Here, we present study on identification of the length and purity of RNA mixture ingredients by using PVA-coated capillaries. Also, we demonstrate the use of PVA-coated capillaries to identify and separate phosphorylated siRNAs and secondary structures (e.g. siRNA duplexes).