Leonid T. Cherney

Universal Drag Tag for Direct Quantitative Analysis of Multiple MicroRNAs

Using microRNA (miRNA) as molecular markers of diseases requires a method for accurate measurement of multiple miRNAs in biological samples. Direct quantitative analysis of multiple miRNAs (DQAMmiR) has been recently developed based on a classical hybridization approach. In DQAMmiR, miRNAs are hybridized with excess fluorescently labeled complementary DNA probes. Capillary electrophoresis (CE) is used to separate the unreacted probes from the hybrids and the hybrids from each other. The challenging separation is achieved by using two types of mobility modifiers. Single-strand DNA binding protein (SSB) is added to the running buffer to bind and shift the single-stranded unreacted probes from the double-stranded hybrids. Different drag tags are built into the probes to introduce significant differential mobility between their respective hybrids. For the method to be practical it requires a universal extendable drag tag. Polymers are a logical choice for making extendable drag tags. Our recent theoretical work suggested that short peptides could provide a sufficient mobility shift to facilitate DQAMmiR. Here, we experimentally confirm this prediction in the analysis of five miRNAs: mir10b, mir21, mir125b, mir145, and mir155. We conjugated four fluorescently labeled DNA molecules with peptides of 5, 10, 15, or 20 neutral amino acids in length; the fifth probe was peptide-free. The peptide tags showed no interference with SSB binding to the probes and facilitated separation of the five hybrids. The mobilities of the five hybrids were used to refine the previously suggested theory. The analysis was performed in both a pure buffer and in cell lysate. Our analysis of the experimental data suggests that using DNA-peptide probes can readily facilitate simultaneous analysis of more than 10 miRNAs.

Extracting kinetics from affinity capillary electrophoresis (ACE) data: a new blade for the old tool.

We describe a mathematical approach that enables extraction of kinetic rate constants from thousands of studies conducted over the past two decades with affinity capillary electrophoresis (ACE). Previously, ACE has been used almost exclusively for obtaining equilibrium constants of intermolecular interactions. In this article, we prove that there exists an analytical solution of partial differential equations describing mass transfer in ACE. By using an in silico study, we demonstrate that the solution is applicable to experimental conditions that are typically used in ACE and found in most historical ACE experiments. The solution was validated by extracting rate constants from previously published ACE data and closely matching independently obtained results. Lastly, it was used to obtain previously unknown rate constants from historical ACE data. The new mathematical approach expands the applicability of ACE to a wider range of biomolecular interactions and enables both prospective and retrospective data analysis. The obtained kinetic information will be of significant practical value to the fields of pharmacology and molecular biology.

Separation-based approach to study dissociation kinetics of noncovalent DNA-multiple protein complexes.

Noncovalent binding of DNA with multiple proteins is pivotal to many regulatory cellular processes. Due to the lack of experimental approaches, the kinetics of assembly and disassembly of DNA-multiple proteins complexes have never been studied. Here, we report on a first method capable of measuring disassembly kinetics of such complexes. The method is based on continuous spatial separation of different complexes. The kinetics of multiple complex dissociation processes are also spatially separated, which in turn facilitates finding their rate constants. Our separation-based approach was compared with a conventional no-separation approach by using computer simulation of dissociation kinetics. It proved to be much more accurate than the no-separation approach and to be a powerful tool for testing hypothetical mechanisms of the disassembly of DNA-multiple proteins complexes. An experimental implementation of the separation-based approach was finally demonstrated by using capillary electrophoresis as a separation method. The interaction between an 80 nucleotide long single-stranded DNA and single-stranded DNA binding protein was studied. DNA-protein complexes with one and two proteins were observed, and rate constants of their dissociation were determined. We foresee that a separation approach will be also developed to study the kinetics of the formation of DNA-multiple protein complexes.

Prediction of protein-DNA complex mobility in gel-free capillary electrophoresis.

Selection of protein binders from highly diverse combinatorial libraries of DNA-encoded small molecules is a highly promising approach for discovery of small-molecule drug leads. Methods of kinetic capillary electrophoresis provide the high efficiency of partitioning required for such selection but require the knowledge of electrophoretic mobility of the protein-ligand complex. Here we present a theoretical approach for an accurate estimate of the electrophoretic mobility of such complexes. The model is based on a theory of the thin double layer and corresponding expressions used for the mobilities of a rod-like short oligonucleotide and a sphere-like globular protein. The model uses empirical values of mobilities of free protein, free ligand, and electroosmotic flow. The model was tested with a streptavidin-dsDNA complex linked through biotin (small molecule). The deviation of the prediction from the experimental mobility did not exceed 4%, thus confirming that not only is the model adequate but it is also accurate. This model will facilitate reliable use of KCE methods for selection of drug leads from libraries of DNA-encoded small molecules.

Steady‐State Continuous‐Flow Purification by Electrophoresis

Continuous-flow microsynthesis has a number of important advantages over batch synthesis, namely: increased product yield through atom economy, reduced costs associated with starting materials, safer operating conditions, 6] highthroughput production by numbering up, and automated optimization and control of reaction conditions. To fully exploit these advantages, continuous-flow microsynthesis should be supplemented with continuous-flow purification on a compatible scale. Such a combination has not yet been practically realized owing to the lack of a suitable purification technique. Continuous-flow purification can be achieved if a continuous-flow microreactor exits into a wide purification channel in which products are separated in the direction orthogonal to the flow and continuously collected at the exit of the channel. Our recent research efforts have been motivated by understanding that an existing continuousflow purification technique, free flow electrophoresis (FFE), is naturally suited for combination with continuous-flow microsynthesis in aqueous solution (Figure 1a). FFE facilitates continuous separation of molecules in a wide separation channel with a uniform hydrodynamic flow of an electrolyte solution and an electrical field non-parallel (typically orthogonal) to this flow. The sample is introduced into the separation channel through a narrow opening as schematically shown in Figure 1a. Advantageously, FFE devices can be made on a small scale to suit small flow rates used in continuous-flow microsynthesis. Unfortunately, small-scale FFE cannot be used for steady-state purification. Electrolysis of water leads to the formation of O2 and H2 bubbles on the surface of the electrodes. Bubble accumulation on the electrodes and subsequently in other parts of the device leads to progressing electric-field distortion and diminishing quality of purification within the first several minutes of operation. The regeneration of an FFE device requires complete bubble flush-out: a cumbersome and timeconsuming process. The goal of this work was to find a solution for the problem of FFE instability caused by bubble accumulation, thereby permitting reliable steady-state operation without the distortion of electric field or separation quality. Solving the bubble-accumulation problem is pivotal to FFE integration with other micro-systems. The previous approaches to the problem of bubble accumulation in FFE devices could be split into three major categories: 1) a mechanical barrier preventing the entry of bubbles into the separation channel, 2) separate electrode channels with fast flow for bubble removal, and 3) chemical agents that inhibit gas generation and bubble growth. While being useful, these measures only delay the accumulation of the deteriorating amount of bubbles. Bubbles still accumulate and prevent steady-state continuous separation. Because of bubble accumulation, electrical-current and sample-flow stability in FFE typically lasts for less than 0.5 h. The longest operational time demonstrated for smallscale FFE is 2 h. This work was inspired by an insight that a solution to the bubble-accumulation problem could be achieved by breaking the principle of a closed FFE device. Our logic was simple. Bubble removal into the atmosphere could be easy and natural if the electrolyte above the electrodes was open to the atmosphere. Further, engineering the “open-concept” FFE device requires vertical chimneys to hold a column of electrolyte that hydrostatically balances the pressure inside the device. Since the Archimedes force pushes the gas upwards, bubble entry into the separation channel can be Figure 1. a) Schematic top view of an integrated system for continuous-flow microsynthesis and subsequent continuous-flow purification. The reactants, R1 and R2, generate products, P1 and P2, which are separated by FFE. A conceptual comparison of cross-sections (section A–A in panel (a)) in devices for conventional FFE (b) and our OEFFE (c). In OEFFE, bubbles (*) generated at the electrodes (red dot) are vented out of the device into the atmosphere through the chimneys. d) General overview of an OEFFE device.

Using nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) for simultaneous determination of concentration and equilibrium constant.

Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) is a versatile tool for studying affinity binding. Here we describe a NECEEM-based approach for simultaneous determination of both the equilibrium constant, K(d), and the unknown concentration of a binder that we call a target, T. In essence, NECEEM is used to measure the unbound equilibrium fraction, R, for the binder with a known concentration that we call a ligand, L. The first set of experiments is performed at varying concentrations of T, prepared by serial dilution of the stock solution, but at a constant concentration of L, which is as low as its reliable quantitation allows. The value of R is plotted as a function of the dilution coefficient, and dilution corresponding to R = 0.5 is determined. This dilution of T is used in the second set of experiments in which the concentration of T is fixed but the concentration of L is varied. The experimental dependence of R on the concentration of L is fitted with a function describing their theoretical dependence. Both K(d) and the concentration of T are used as fitting parameters, and their sought values are determined as the ones that generate the best fit. We have fully validated this approach in silico by using computer-simulated NECEEM electropherograms and then applied it to experimental determination of the unknown concentration of MutS protein and K(d) of its interactions with a DNA aptamer. The general approach described here is applicable not only to NECEEM but also to any other method that can determine a fraction of unbound molecules at equilibrium.

Simplified universal method for determining electrolyte temperatures in a capillary electrophoresis instrument with forced-air cooling

Temperature increase due to resistive electrical heating is an inherent limitation of capillary electrophoresis (CE). Active cooling systems are used to decrease the temperature of the capillary, but their capacity is limited; and in addition, they leave “hot spots” at the detection interface and at the capillary ends. Until recently, the matter was complicated by the lack of a fast and generic method for temperature determination in efficiently and inefficiently cooled regions of the capillary. Our group recently introduced such a method, termed “Universal Method for determining Electrolyte Temperatures” (UMET). UMET is a probe‐less approach that requires only measuring current versus voltage for different voltages and processing the data using an iterative algorithm. Here, we apply UMET to develop a Simplified Universal Method of Temperature Determination (SUMET) for a CE instrument with a forced‐air cooling system using an Agilent 7100 CE instrument (Agilent Technologies, Saint Laurent, Quebec, Canada) as an example. We collected a wide set of empirical voltage–current data for a variety of buffers and capillary diameters. We further constructed empirical equations for temperature calculation in efficiently and inefficiently cooled parts of the capillary that require only the data from a single 1‐min voltage–current measurement. The equations are specific for the Agilent 7100 CE instrument (Agilent Technologies) but can be applied to all kinds of capillaries and buffers. Similar SUMET approaches can be developed for other CE instruments with forced‐air cooling using our approach.

Kinetic Size-Exclusion Chromatography with Mass Spectrometry Detection: An Approach for Solution-Based Label-Free Kinetic Analysis of Protein−Small Molecule Interactions

Studying the kinetics of reversible protein-small molecule binding is a major challenge. The available approaches require that either the small molecule or the protein be modified by labeling or immobilization on a surface. Not only can such modifications be difficult to do but also they can drastically affect the kinetic parameters of the interaction. To solve this problem, we present kinetic size-exclusion chromatography with mass spectrometry detection (KSEC-MS), a solution-based label-free approach. KSEC-MS utilizes the ability of size-exclusion chromatography (SEC) to separate any small molecule from any protein-small molecule complex without immobilization and the ability of mass spectrometry (MS) to detect a small molecule without a label. The rate constants of complex formation and dissociation are deconvoluted from the temporal pattern of small molecule elution measured with MS at the exit from the SEC column. This work describes the concept of KSEC-MS and proves it in principle by measuring the rate constants of interaction between carbonic anhydrase and acetazolamide.

Predicting Electrophoretic Mobility of Protein–Ligand Complexes for Ligands from DNA-Encoded Libraries of Small Molecules

Selection of target-binding ligands from DNA-encoded libraries of small molecules (DELSMs) is a rapidly developing approach in drug-lead discovery. Methods of kinetic capillary electrophoresis (KCE) may facilitate highly efficient homogeneous selection of ligands from DELSMs. However, KCE methods require accurate prediction of electrophoretic mobilities of protein-ligand complexes. Such prediction, in turn, requires a theory that would be applicable to DNA tags of different structures used in different DELSMs. Here we present such a theory. It utilizes a model of a globular protein connected, through a single point (small molecule), to a linear DNA tag containing a combination of alternating double-stranded and single-stranded DNA (dsDNA and ssDNA) regions of varying lengths. The theory links the unknown electrophoretic mobility of protein-DNA complex with experimentally determined electrophoretic mobilities of the protein and DNA. Mobility prediction was initially tested by using a protein interacting with 18 ligands of various combinations of dsDNA and ssDNA regions, which mimicked different DELSMs. For all studied ligands, deviation of the predicted mobility from the experimentally determined value was within 11%. Finally, the prediction was tested for two proteins and two ligands with a DNA tag identical to those of DELSM manufactured by GlaxoSmithKline. Deviation between the predicted and experimentally determined mobilities did not exceed 5%. These results confirm the accuracy and robustness of our model, which makes KCE methods one step closer to their practical use in selection of drug leads, and diagnostic probes from DELSMs.

Theoretical Modeling of Masking DNA Application in Aptamer- Facilitated Biomarker Discovery

In aptamer-facilitated biomarker discovery (AptaBiD), aptamers are selected from a library of random DNA (or RNA) sequences for their ability to specifically bind cell-surface biomarkers. The library is incubated with intact cells, and cell-bound DNA molecules are separated from those unbound and amplified by the polymerase chain reaction (PCR). The partitioning/amplification cycle is repeated multiple times while alternating target cells and control cells. Efficient aptamer selection in AptaBiD relies on the inclusion of masking DNA within the cell and library mixture. Masking DNA lacks primer regions for PCR amplification and is typically taken in excess to the library. The role of masking DNA within the selection mixture is to outcompete any nonspecific binding sequences within the initial library, thus allowing specific DNA sequences (i.e., aptamers) to be selected more efficiently. Efficient AptaBiD requires an optimum ratio of masking DNA to library DNA, at which aptamers still bind specific binding sites but nonaptamers within the library do not bind nonspecific binding sites. Here, we have developed a mathematical model that describes the binding processes taking place within the equilibrium mixture of masking DNA, library DNA, and target cells. An obtained mathematical solution allows one to estimate the concentration of masking DNA that is required to outcompete the library DNA at a desirable ratio of bound masking DNA to bound library DNA. The required concentration depends on concentrations of the library and cells as well as on unknown cell characteristics. These characteristics include the concentration of total binding sites on the cell surface, N, and equilibrium dissociation constants, K(nsL) and K(nsM), for nonspecific binding of the library DNA and masking DNA, respectively. We developed a theory that allows the determination of N, K(nsL), and K(nsM) based on measurements of EC50 values for cells mixed separately with the library and masking DNA (EC50 is the concentration of fluorescently labeled DNA at which half of the maximum fluorescence signal from DNA-bound cells is reached). We also obtained expressions for signals from bound DNA (measured by flow cytometry) in terms of N, K(nsL), and K(nsM). These expressions can be used for the verification of N, K(nsL), and K(nsM) values found from EC50 measurements. The developed procedure was applied to MCF-7 breast cancer cells, and corresponding values of N, K(nsL), and K(nsM) were established for the first time. The concentration of masking DNA required for AptaBiD with MCF-7 breast cancer cells was also estimated.