Single-molecule analysis enables free solution hydrodynamic separation using yoctomole levels of DNA

Single-Particle Spectroscopic Chromatography Reveals Heterogeneous RNA Loading and Size Correlations in Lipid Nanoparticles

Lipid nanoparticles (LNP) have emerged as pivotal delivery vehicles for RNA therapeutics. Previous research and development usually assumed that LNPs are homogeneous in population, loading density, and composition. Such perspectives are difficult to examine due to the lack of suitable tools to characterize these physicochemical properties at the single-nanoparticle level. Here, we report an integrated spectroscopy-chromatography approach as a generalizable strategy to dissect the complexities of multicomponent LNP assembly. Our platform couples cylindrical illumination confocal spectroscopy (CICS) with single-nanoparticle free solution hydrodynamic separation (SN-FSHS) to simultaneously profile population identity, hydrodynamic size, RNA loading levels, and distributions of helper lipid and PEGylated lipid of LNPs at the single-particle level and in a high-throughput manner. Using a benchmark siRNA LNP formulation, we demonstrate the capability of this platform by distinguishing seven distinct LNP populations, quantitatively characterizing size distribution and RNA loading level in wide ranges, and more importantly, resolving composition-size correlations. This SN-FSHS-CICS analysis provides critical insights into a substantial degree of heterogeneity in the packing density of RNA in LNPs and size-dependent loading-size correlations, explained by kinetics-driven assembly mechanisms of RNA LNPs.

Payload distribution and capacity of mRNA lipid nanoparticles

Lipid nanoparticles (LNPs) are effective vehicles to deliver mRNA vaccines and therapeutics. It has been challenging to assess mRNA packaging characteristics in LNPs, including payload distribution and capacity, which are critical to understanding structure-property-function relationships for further carrier development. Here, we report a method based on the multi-laser cylindrical illumination confocal spectroscopy (CICS) technique to examine mRNA and lipid contents in LNP formulations at the single-nanoparticle level. By differentiating unencapsulated mRNAs, empty LNPs and mRNA-loaded LNPs via coincidence analysis of fluorescent tags on different LNP components, and quantitatively resolving single-mRNA fluorescence, we reveal that a commonly referenced benchmark formulation using DLin-MC3 as the ionizable lipid contains mostly 2 mRNAs per loaded LNP with a presence of 40%–80% empty LNPs depending on the assembly conditions. Systematic analysis of different formulations with control variables reveals a kinetically controlled assembly mechanism that governs the payload distribution and capacity in LNPs. These results form the foundation for a holistic understanding of the molecular assembly of mRNA LNPs.

Lipid nanoparticles (LNPs) are effective vehicles to deliver mRNA vaccines and therapeutics but assessing the mRNA packaging characteristics in LNPs is challenging. Here, the authors report that mRNA and lipid contents in LNP formulations can be quantitatively examined by multi-laser cylindrical illumination confocal spectroscopy at the single-nanoparticle level.

Extension of hydrodynamic chromatography to DNA fragment sizing and quantitation

Hydrodynamic chromatography (HDC) is a technique originally developed for separating particles. We have recently extended it to DNA fragment sizing and quantitation. In this review, we focus on this extension. After we briefly introduce the history of HDC, we present the evolution of open tubular HDC for DNA fragment sizing. We cover both the theoretical aspect and the experimental implementation of this technique. We describe various approaches to execute the separation, discuss its representative applications and provide a future perspective of this technique in the conclusion section of this review.

Multi-detector hydrodynamic chromatography of colloids: following in Hamish Small's footsteps

Hamish Small, scientist extraordinaire, is best known as the inventor of both ion chromatography and hydrodynamic chromatography (HDC). The latter has experienced a renaissance during the last decade-plus, thanks principally to its coupling to a multiplicity of physicochemical detection methods and to the structural and compositional information this provides. Detection methods such as light scattering (both multi-angle static and dynamic), viscometry, and refractometry can combine to yield insight into macromolecular or colloidal size, structure, shape, and molar mass, all as a function of one another and continuously across a sample's chromatogram. It was the author's great fortune to have known Hamish during the last decade of his life, before his passing in 2019. Here, a brief personal recollection is followed by an introduction to HDC and its application, in quadruple-detector packed-column mode, to the analysis of a commercial colloidal silica with an elongated shape.

Characterization and minimization of band broadening in DNA electrohydrodynamic migration for enhanced size separation

The combination of hydrodynamic actuation with an opposing electrophoretic force in viscoelastic liquids enables the separation, concentration, and purification of DNA. Obtaining good analytical performances despite the use of hydrodynamic flow fields, which dramatically enhance band broadening due to Taylor dispersion, constitutes a paradox that remains to be clarified. Here, we study the mechanism of band broadening in electrohydrodynamic migration with an automated microfluidic platform that allows us to track the migration of a 600 bp band in the pressure-electric field parameter space. We demonstrate that diffusion in the electrohydrodynamic regime is controlled predominantly by the electric field and marginally by the hydrodynamic flow velocity. We explain this response with an analytical model of diffusion based on Taylor dispersion arguments. Furthermore, we demonstrate that the electric field can be modulated over time to monitor and minimize the breadth of a DNA band, and suggest guidelines to enhance the resolution of DNA separation experiments. Altogether, our report is a leap towards to the development of high-performance analytical technologies based on electrohydrodynamic actuation.

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.

Visual and real-time imaging focusing for highly sensitive laser-induced fluorescence detection at yoctomole levels in nanocapillaries

We developed a highly sensitive laser-induced fluorescence detection system, involving visual and real-time imaging focusing instead of the use of fluorescent reagents, for the detection of analytes in nanocapillaries.

Versatile Analysis of DNA-Biomolecule Interactions in Solution by Hydrodynamic Separation and Single Molecule Detection

DNA can interact with a wide array of molecules with a range of binding affinities, stoichiometry, and size-scales. We present a sensitive, quantitative, and versatile platform for sensing and evaluating these diverse DNA-biomolecule interactions and DNA conformational changes in free solution. Single molecule free solution hydrodynamic separation utilizes differences in hydrodynamic mobility to separate bound DNA-biomolecule complexes from unbound DNA and determine the associated size change that results from binding. Single molecule detection enables highly quantitative analysis of the fraction of DNA in the bound and unbound state to characterize binding behavior including affinity, stoichiometry, and cooperativity. A stacked injection scheme increases throughput to enable practical analysis of DNA-biomolecule interactions using only picoliters of sample per measurement. To demonstrate analysis of DNA-protein interactions on a local scale, we investigate binding of the E. coli single stranded binding protein to two DNA oligos both individually and in direct competition. We show that stoichiometry and cooperativity is a function of DNA length and verify these differences in binding characteristics through direct competition. To demonstrate analysis of DNA-small molecule interactions and global conformational changes, we also assess DNA condensation with the polyamine spermidine. We use hydrodynamic mobility to evaluate the size of spermidine-condensed DNA and single molecule burst analysis to evaluate DNA packing within the condensed globules relative to free-coiled DNA. This platform thus presents a versatile tool capable of quantitative and sensitive evaluation of diverse biomolecular interactions, complex properties, and binding characteristics.

Single Molecule Free Solution Hydrodynamic Separation for Size Profiling of Serum Cell-Free DNA

Circulating cell-free DNA (cfDNA) has accumulated significant interest as a noninvasive biomarker. One important accessible parameter, the cfDNA size distribution, appears to be of significant value. Here, we introduce our single molecule free solution hydrodynamic separation platform (SML-FSHS) for robust characterization of the cfDNA size profile from human serum. The platform utilizes hydrodynamic separation for DNA sizing and cylindrical illumination confocal spectroscopy (CICS) for highly sensitive single molecule detection and quantification of DNA molecules. We first used a custom wide dynamic range DNA ladder (50 bp-23 kbp) stained with an intercalating dye to create a calibration curve relating DNA retention time to DNA size in base pairs. From this, we demonstrate that the system can profile the cfDNA size distributions in a clinical sample with wide sizing dynamic range and high resolution ~5% of fragment length) all in a single run. The method consumes negligible (3pL) volume of precious sample and minimizes sample processing bias that affects other methods such as PCR and sequencing. We also compare the cfDNA size distributions from stage 1V cancer patients with normal patient samples and demonstrate that specific cfDNA size ranges may correlate with disease state. In addition, we can absolutely quantify cfDNA and gate out the contributions of cellular contamination by size. With these properties, we believe that this platform can help to accelerate future circulating DNA research.

A Multiplex Ligation Assay for miRNA Copy Number Profiling

Ligo-miR is an assay technology that can perform multiplexed detection of miRNAs from a wide range of biological sources. At its core are two sequential ligation steps. First in the capture ligation, template molecules are created by ligating a DNA adapter to the 3' end of all miRNA molecules. Then in the coding ligation these templates are used to generate, linearly amplified, DNA products encoded by length. The resultant number of each DNA product is proportional to the original number of miRNA molecules. The products and their corresponding miRNA can be identified and quantified using common DNA sizing methods such as electrophoresis.

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.

Determination of absolute expression profiles using multiplexed miRNA analysis

Accurate measurement of miRNA expression is critical to understanding their role in gene expression as well as their application as disease biomarkers. Correct identification of changes in miRNA expression rests on reliable normalization to account for biological and technological variance between samples. Ligo-miR is a multiplex assay designed to rapidly measure absolute miRNA copy numbers, thus reducing dependence on biological controls. It uses a simple 2-step ligation process to generate length coded products that can be quantified using a variety of DNA sizing methods. We demonstrate Ligo-miR's ability to quantify miRNA expression down to 20 copies per cell sensitivity, accurately discriminate between closely related miRNA, and reliably measure differential changes as small as 1.2-fold. Then, benchmarking studies were performed to show the high correlation between Ligo-miR, microarray, and TaqMan qRT-PCR. Finally, Ligo-miR was used to determine copy number profiles in a number of breast, esophageal, and pancreatic cell lines and to demonstrate the utility of copy number analysis for providing layered insight into expression profile changes.

On-chip hydrodynamic chromatography of DNA through centimeters-long glass nanocapillaries

This study demonstrates hydrodynamic chromatography of DNA fragments in a microchip. The microchip contains a highly regular array of nanofluidic channels (nanocapillaries) that are essential for resolving DNA in this chromatography mode. The nanocapillaries are self-enclosed robust structures built inside a doped glass layer on silicon using low-resolution photolithography and standard semiconductor processing techniques. Additionally, the unique nanocapillaries feature a cylindrical inner radius of 600 nm maintained over a length scale of 5 cm. The microchip with bare open nanocapillaries is shown to rapidly separate a digest of lambda DNA in free solution (<5 min under the elution pressure of 60 to 120 psi), relying entirely on pressure-driven flows and, in doing so, avoiding the field-induced DNA aggregations encountered in gel-free electrophoresis. The nanocapillaries, despite their relatively short length, are observed to fractionate DNA fragments reasonably well with a minimum resolvable size difference below 5 kbp. In the chromatograms obtained, the number of theoretical plates exceeds 10⁵ plates per m for 3.5 and 21 kbp long DNA fragments. The relative mobility of fragments in relation to their size is found to be in excellent agreement with the simple quadratic model of hydrodynamic chromatography. The model is shown to estimate greater effective hydrodynamic radii than those of respective fragments being unconfined in bulk solution, implying increased drag forces and reduced diffusion coefficients, which is also a noticeable trend among diffusion coefficient estimates derived from the experimentally obtained plate heights. This robust mass-producible microchip can be further developed into a fully integrated bioanalytic microsystem.

Confocal laser-induced fluorescence detector for narrow capillary system with yoctomole limit of detection

Laser-induced fluorescence (LIF) detectors for low-micrometer and sub-micrometer capillary on-column detection are not commercially available. In this paper, we describe in details how to construct a confocal LIF detector to address this issue. We characterize the detector by determining its limit of detection (LOD), linear dynamic range (LDR) and background signal drift; a very low LOD (~70 fluorescein molecules or 12 yoctomole fluorescein), a wide LDR (greater than 3 orders of magnitude) and a small background signal drift (~1.2-fold of the root mean square noise) are obtained. For detecting analytes inside a low-micrometer and sub-micrometer capillary, proper alignment is essential. We present a simple protocol to align the capillary with the optical system and use the position-lock capability of a translation stage to fix the capillary in position during the experiment. To demonstrate the feasibility of using this detector for narrow capillary systems, we build a 2-μm-i.d. capillary flow injection analysis (FIA) system using the newly developed LIF prototype as a detector and obtain an FIA LOD of 14 zeptomole fluorescein. We also separate a DNA ladder sample by bare narrow capillary - hydrodynamic chromatography and use the LIF prototype to monitor the resolved DNA fragments. We obtain not only well-resolved peaks but also the quantitative information of all DNA fragments.

A Simple Thermoplastic Substrate Containing Hierarchical Silica Lamellae for High-Molecular-Weight DNA Extraction

An inexpensive, magnetic thermoplastic nanomaterial is developed utilizing a hierarchical layering of micro- and nanoscale silica lamellae to create a high-surface-area and low-shear substrate capable of capturing vast amounts of ultrahigh-molecular-weight DNA. Extraction is performed via a simple 45 min process and is capable of achieving binding capacities up to 1 000 000 times greater than silica microparticles.

DNA separation and enrichment using electro-hydrodynamic bidirectional flows in viscoelastic liquids

DNA size separation followed by purification and enrichment constitute essential operations for genetic engineering. These processes are mostly carried out using DNA electrophoresis in gels or in polymer solutions, a well-established yet lengthy technique which has been notably improved using Lab-on-Chip technologies. So far, innovations for DNA separation or enrichment have been mostly undertaken separately, and we present an approach that allows us to perform these two processes simultaneously for DNA fragments spanning 0.2-50 kilo base pairs (kbp) in length. Our technology involves an electric field and a counter hydrodynamic flow in viscoelastic liquids, in which we show the occurrence of transverse forces oriented toward the walls. These forces increase with DNA molecular weight (MW) and hence induce a progressive reduction in DNA migration speed that triggers size separation in microfluidic channels as well as in capillaries. The separation of MW markers in the range 1-50 kbp is achieved in 15 minutes, thus outperforming gel electrophoresis that takes ∼3 hours for this sample. Furthermore, the use of a funnel, where electric and flow fields are modulated spatially, enables us to adjust the transverse forces so as to stall the motion of DNA molecules at a position where they accumulate at factors of up to 1000 per minute. In this configuration, we establish that the operations of DNA enrichment and separation can be carried out simultaneously for the bands of a DNA MW marker between 0.2-1.5 kbp diluted at 0.02 ng μL(-1) in 30 s. Altogether, our technology, which can readily be integrated as an in-line module in Lab-on-Chips, offers unique opportunities for sample preparation and analysis of minute genomic samples.

Analysis of single nucleic acid molecules in micro- and nano-fluidics

Nucleic acid analysis has enhanced our understanding of biological processes and disease progression, elucidated the association of genetic variants and disease, and led to the design and implementation of new treatment strategies. These diverse applications require analysis of a variety of characteristics of nucleic acid molecules: size or length, detection or quantification of specific sequences, mapping of the general sequence structure, full sequence identification, analysis of epigenetic modifications, and observation of interactions between nucleic acids and other biomolecules. Strategies that can detect rare or transient species, characterize population distributions, and analyze small sample volumes enable the collection of richer data from biosamples. Platforms that integrate micro- and nano-fluidic operations with high sensitivity single molecule detection facilitate manipulation and detection of individual nucleic acid molecules. In this review, we will highlight important milestones and recent advances in single molecule nucleic acid analysis in micro- and nano-fluidic platforms. We focus on assessment modalities for single nucleic acid molecules and highlight the role of micro- and nano-structures and fluidic manipulation. We will also briefly discuss future directions and the current limitations and obstacles impeding even faster progress toward these goals.

Single Molecule Hydrodynamic Separation Allows Sensitive and Quantitative Analysis of DNA Conformation and Binding Interactions in Free Solution

Limited tools exist that are capable of monitoring nucleic acid conformations, fluctuations, and distributions in free solution environments. Single molecule free solution hydrodynamic separation enables the unique ability to quantitatively analyze nucleic acid biophysics in free solution. Single molecule fluorescent burst data and separation chromatograms can give layered insight into global DNA conformation, binding interactions, and molecular distributions. First, we show that global conformation of individual DNA molecules can be directly visualized by examining single molecule fluorescent burst shapes and that DNA exists in a dynamic equilibrium of fluctuating conformations as it is driven by Poiseuille flow through micron-sized channels. We then show that this dynamic equilibrium of DNA conformations is reflected as shifts in hydrodynamic mobility that can be perturbed using salt and ionic strength to affect packing density. Next, we demonstrate that these shifts in hydrodynamic mobility can be used to investigate hybridization thermodynamics and binding interactions. We distinguish and classify multiple interactions within a single sample, and demonstrate quantification amidst large concentration differences for the detection of rare species. Finally, we demonstrate that these differences can resolve perfect complement, 2 bp mismatched, and 3 bp mismatched sequences. Such a system can be used to garner diverse information about DNA conformation and structure, and potentially be extended to other molecules and mixed-species interactions, such as between nucleic acids and proteins or synthetic polymers.

Determination of enantiomers by FESI-sweeping with an acid-labile sweeper in nonaqueous capillary electrophoresis

An acid-labile sweeper based on-line NACE concentration method was developed for analyzing trace enantiomers.

Simultaneously sizing and quantitating zeptomole-level DNA at high throughput in free solution

Determining the sizes and measuring the quantities of DNA molecules are fundamental tasks in molecular biology. DNA sizes are usually evaluated by gel electrophoresis, but this method cannot simultaneously size and quantitate a DNA at low zeptomole (zmol) levels of concentration. We have recently developed a new technique, called bare-narrow-capillary/hydrodynamic-chromatography or BaNC-HDC, for resolving DNA based on their sizes without using any sieving matrices. In this report, we utilize BaNC-HDC for measuring the sizes and quantities of DNA fragments at zmol to several-molecule levels of concentration. DNA ranging from a few base pairs to dozens of kilo base pairs are accurately sized and quantitated at a throughput of 15 samples per hour, and each sample contains dozens of DNA strands of different lengths. BaNC-HDC can be a cost-effective means and an excellent tool for high-throughput DNA sizing and quantitation at extremely low quantity level.

An integrated, multiparametric flow cytometry chip using "microfluidic drifting" based three-dimensional hydrodynamic focusing

In this work, we demonstrate an integrated, single-layer, miniature flow cytometry device that is capable of multi-parametric particle analysis. The device integrates both particle focusing and detection components on-chip, including a "microfluidic drifting" based three-dimensional (3D) hydrodynamic focusing component and a series of optical fibers integrated into the microfluidic architecture to facilitate on-chip detection. With this design, multiple optical signals (i.e., forward scatter, side scatter, and fluorescence) from individual particles can be simultaneously detected. Experimental results indicate that the performance of our flow cytometry chip is comparable to its bulky, expensive desktop counterpart. The integration of on-chip 3D particle focusing with on-chip multi-parametric optical detection in a single-layer, mass-producible microfluidic device presents a major step towards low-cost flow cytometry chips for point-of-care clinical diagnostics.

Hydrodynamic chromatography

Hydrodynamic chromatography (HDC) has experienced a resurgence in recent years for particle and polymer characterization, principally because of its coupling to a multiplicity of physical detection methods. When coupled to light scattering (both multiangle static and quasi-elastic), viscometric, and refractometric detectors, HDC can determine the molar mass, size, shape, and structure of colloidal analytes continuously and as a function of one another, all in a single analysis. In so doing, it exposes the analytes to less shear force (and, hence, less potential for flow-induced degradation) than in, for instance, size-exclusion chromatography. In this review, we discuss the fundamental chromatographic underpinnings of this technique in terms of retention, band broadening, and resolution, and we describe the power of multidetector HDC with examples from the recent literature.