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

Microbe-sediment interactions in Great Lakes recreational waters: Implications for human health risk

Microbial assessments of recreational water have traditionally focused on culturing or DNA-based approaches of the planktonic water column, omitting influence from microbe-sediment relationships. Sediment (bed and suspended) has been shown to often harbour levels of bacteria higher than the planktonic phase. The fate of suspended sediment (SS) bacteria is extensively related to transport dynamics (e.g., deposition) of the associated sediment/floc. When hydraulic energy allows, SS will settle, introducing new (potentially pathogenic) organisms to the bed. With turbulence, including waves, currents and swimmers, the risk of human ingestion is elevated due to resuspension of bed sediment and associated microbes. This research used multiplex nanofluidic reverse transcriptase quantitative PCR on RNA of bacteria associated with bed and SS to explore the active bacteria in freshwater shorelines. Bacterial genes of human health concern regarding recreational water use were targeted, such as faecal indicator bacteria (FIB), microbial source tracking genes and virulence factors from waterborne pathogens. Results indicate avian sources (i.e., gulls, geese) to be the largest nonpoint source of FIB associated with sediment in Great Lakes shorelines. This research introduces a novel approach to microbial water quality assessments and enhances our understanding of microbe-sediment dynamics and the quality of freshwater beaches.

Effect of Mono- and Divalent Metal Ions on Current-Voltage Features of a λ-DNA Solution Electrically Driven in a Microfluidic Capillary

The interactions of DNA molecules and metal ions lead to changes in their configuration and conformation, which in turn influence the current characteristics of the solution as DNA molecules are translocated through a micro/nanofluidic channel and ultimately cause serious impacts on the practical applications of DNA/gene chips for precisely manipulating and studying the molecular properties of single DNA molecules. In this study, the current characteristics of λ-DNA solutions without or with metal ions (i.e., K⁺, Na⁺, Mg²⁺, and Ca²⁺) were experimentally investigated when they were transported through a 5 μm microcapillary under an external electric field with asymmetric electrodes. Experimental data indicated some meaningful results. First, the current-voltage relations of the metal ion solutions were all linear, while those of λ-DNA solutions without or with metal ions were all nonlinear and followed power functions, of which the indices were related to the type, valence, and mobility of ions. Furthermore, as the concentrations of metal ions increased, the power indices of the λ-DNA solutions with monovalent metal ions increased, while those of the λ-DNA solutions with divalent ions decreased. Finally, the main reasons for the current characteristics were theoretically attributed to two possible mechanisms: the polarizations on the asymmetric electrodes and the interactions between λ-DNA and metal ions. These findings are helpful for the design of new biomedical micro/nanofluidic sensors and labs on a chip for accurately manipulating single DNA molecules.

Light fueled mixing in open surface droplet microfluidics for rapid probe preparation

In this study, a contactless, flexible, and interference-free light fueled method has been developed to enhance the mixing between the ssDNA and dynabeads in a droplet, which enables rapid probe preparation for promoting the probe technology based on open surface droplet microfluidics. In this light fueled method, the use of the photothermal effect of a focused infrared laser can easily create non-uniform temperature distribution and accordingly the surface tension gradient over the interface as a result of the localized heating effect, which thereby initiates the Marangoni flow in a droplet. Experimental results confirm that the light-induced Marangoni flow greatly enhances the mixing, ensuring rapid and efficient binding between the ssDNA and dynabeads. Moreover, the mixing intensity and degree can be simply tuned by controlling the laser intensity and laser heating time. The light fueled rapid mixing method developed in the present study paves the way for rapid bio-chemical detection.

DNA fragmentation in complicated flow fields created by micro-funnel shapes

Micro-funnels have been widely applied to produce extensionally dominant flows for DNA manipulation, such as DNA extension for DNA mapping and DNA fragmentation for gene sequencing. However, it still lacks a systematic understanding of DNA fragmentation behaviors in complicated flow fields regulated by different funnel shapes with high flow rates. This limits the rational design and application scope of related microfluidic devices. In this study, fragmentation experiments of λ DNA were carried out in microfluidic chips with four different micro-funnel shapes, namely a sudden finish, a linear contraction, a constant acceleration, and an increasing extension rate funnel. The experimental results demonstrated a significant effect of the micro-funnel shape on the produced DNA fragment size. Then, the dynamical behaviors of DNA molecules in flow fields created by different micro-funnels were simulated using a numerical method of Brownian dynamics-computational fluid dynamics. The numerical simulation revealed that both the magnitude and distribution of the extension rate of flow fields were drastically altered by the funnel shape, and the extension rate at the micro-scale was the dominant factor of DNA fragmentation. The different DNA fragmentation behaviors in four micro-funnels were investigated from the perspectives including the fragment size distribution, fragmentation location, percentage of broken molecules, conformational type and stretched length of DNA before fragmentation. The results elucidated the significant impact of funnel shape on the dynamical behaviors of DNA fragmentation. This study offers insights into the rational design of microfluidic chips for DNA manipulation.

Nucleic Acid Tests for Clinical Translation

Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.

When Fluorescent Sensing Meets Electrochemical Amplifying: A Powerful Platform for Gene Detection with High Sensitivity and Specificity

Ultrasensitive and ultraselective detection of the gene requires emergency development to meet the medical demands and infectious disease control. Herein we report a versatile and scalable method based on electrochemical-chemical-cyclic amplification (EC-CA) and fluorescence detection for ultrasensitive gene sensing. The EC-CA is achieved by an electro-Fenton reaction (EFR). The hydroxyl radicals generated at EFR are trapped by terephthalic acid to form highly fluorescent 2-hydroxyterephthalic acid, which can be sensitively detected by a fluorescence spectrophotometer. The method is the first to be able to amplify the signal and reduce the noise simultaneously by using the conventional analytical methods directly. This described method can be used for reliable Fe³⁺ quantification in the range from 0.1 nM to 0.08 mM. The calculated limit of detection (LOD) is 0.02 nM. Then, hepatitis B virus (HBV) and p53 gene were detected by this proposed method through introducing the Fe₃O₄ nanoparticles into the gene hybridization system. The LODs for HBV and p53 gene even topped out at 2.6 pM and 1.7 fM, respectively. We demonstrated that the finally recorded signal was triply amplified through the EC cycle, Fe₃O₄ nanoparticles, and sensitive fluorescence detection. At the same time, the background signal arisen from matrix effects and readout noise was effectively suppressed. This method shows it is simple, convenient, and operational through the detection of Fe³⁺, HBV, and the p53 gene in blood samples, respectively. We believe our method will make a significant, near-term impact on the development of high-sensitivity methods that are versatile and scalable.

Technological Advances in Multiscale Analysis of Single Cells in Biomedicine

Single-cell analysis has recently received significant attention in biomedicine. With the advances in super-resolution microscopy, fluorescence labeling, and nanoscale biosensing, new information may be obtained for the design of cancer diagnosis and therapeutic interventions. The discovery of cellular heterogeneity further stresses the importance of single-cell analysis to improve our understanding of disease mechanism and to develop new strategies for disease treatment. To this end, many studies are exploited at the single-cell level for high throughput, highly parallel, and quantitative analysis. Technically, microfluidics are also designed to facilitate single-cell isolation and enrichment for downstream detection and manipulation in a robust, sensitive, and automated manner. Further achievements are made possible by consolidating optically label-free, electrical, and molecular sensing techniques. Moreover, these technologies are coupled with computing algorithms for high throughput and automated quantitative analysis with a short turnaround time. To reflect on how the technological developments have advanced single-cell analysis, this mini-review is aimed to offer readers an introduction to single-cell analysis with a brief historical development and the recent progresses that have enabled multiscale analysis of single-cells in the last decade. The challenges and future trends are also discussed with the view to inspire forthcoming technical developments.

Transfection Efficiency Evaluation and Endocytosis Exploration of Different Polymer Condensed Agents

DNA condensed agents can improve the transfection efficiency of the cationic liposome delivery system. However, various condensed agents have distinct transfection efficiency and cellular cytotoxicity. The object of this study was to screen the optimal agents with the high transfection efficiency and low cytotoxicity from four polymer compressive materials, polyethylenimine (PEI), chitosan, poly-l-lysine (PLL), and spermidine. DNA was precompressed with these four agents and then combined to cationic liposomes. Subsequently, the entrapment and transfection efficiency of the obtained complexes were investigated. Finally, the particle sizes, cytotoxicity, and endocytosis fashion of these copolymers (Lipo-PEI, Lipo-chitosan, Lipo-PLL, and Lipo-spermidine) were examined. It was found that these four copolymers had significantly lower cytotoxicity and higher transfection efficiency (45.5%, 42.4%, 36.8%, and 47.4%, respectively) than those in the control groups. The transfection efficiency of Lipo-PEI and Lipo-spermidine copolymers were better than the other two copolymers. In 293T cells, nystatin significantly inhibited the transfection efficiency of Lipo-PEI-DNA and Lipo-spermidine-DNA (51.88% and 46.05%, respectively), which suggest that the endocytosis pathway of Lipo-spermidine and Lipo-PEI copolymers was probably caveolin dependent. Our study indicated that these dual-degradable copolymers especially liposome-spermidine copolymer could be used as the potential biocompatible gene delivery carriers.

Transverse migration and microfluidic concentration of DNA using Newtonian buffers

We present experimental evidence that DNA can be concentrated due to an electrohydrodynamic coupling between a pressure-driven flow and a parallel electric field. The effects of buffer properties on the process were measured in a microfluidic channel. The concentration rates and the efficiency of trapping DNA were quantified as functions of the ion and polymer concentrations of the buffer solution. Buffers with large ion concentrations hindered the ability to trap DNA, reducing the short-time efficiency of the concentration process from nearly 100% to zero. Importantly, DNA was trapped in the microfluidic channel even when the buffer solution lacked any measurable viscoelastic response. These observations indicate that electrohydrodynamic migration drives the concentration of DNA. We found no evidence of viscoelastic migration in these experiments.

Microfluidic DNA combing for parallel single-molecule analysis

DNA combing is a widely used method for stretching and immobilising DNA molecules on a surface. Fluorescent labelling of genomic information enables high-resolution optical analysis of DNA at the single-molecule level. Despite its simplicity, the application of DNA combing in diagnostic workflows is still limited, mainly due to difficulties in analysing multiple small-volume DNA samples in parallel. Here, we report a simple and versatile microfluidic DNA combing technology (μDC), which allows manipulating, stretching and imaging of multiple, microliter scale DNA samples by employing a manifold of parallel microfluidic channels. Using DNA molecules with repetitive units as molecular rulers, we demonstrate that the μDC technology allows uniform stretching of DNA molecules. The stretching ratio remains consistent along individual molecules as well as between different molecules in the various channels, allowing simultaneous quantitative analysis of different samples loaded into parallel channels. Furthermore, we demonstrate the application of μDC to characterise UVB-induced DNA damage levels in human embryonic kidney cells and the spatial correlation between DNA damage sites. Our results point out the potential application of μDC for quantitative and comparative single-molecule studies of genomic features. The extremely simple design of μDC makes it suitable for integration into other microfluidic platforms to facilitate high-throughput DNA analysis in biological research and medical point-of-care applications.

Nanochannel-Confined TAMRA-Polypyrrole Stained DNA Stretching by Varying the Ionic Strength from Micromolar to Millimolar Concentrations

Large DNA molecules have been utilized as a model system to investigate polymer physics. However, DNA visualization via intercalating dyes has generated equivocal results due to dye-induced structural deformation, particularly unwanted unwinding of the double helix. Thus, the contour length increases and the persistence length changes so unpredictably that there has been a controversy. In this paper, we used TAMRA-polypyrrole to stain single DNA molecules. Since this staining did not change the contour length of B-form DNA, we utilized TAMRA-polypyrrole stained DNA as a tool to measure the persistence length by changing the ionic strength. Then, we investigated DNA stretching in nanochannels by varying the ionic strength from 0.06 mM to 47 mM to evaluate several polymer physics theories proposed by Odijk, de Gennes and recent papers to deal with these regimes.

Microgels and apparatus for PAGE of nucleic acids in one or two dimensions

We describe a system for horizontal 1D or 2D PAGE comprising an apparatus and microgels. There is no buffer outside the gel, making handling and sample loading easy. Specially designed electrodes on all four sides allow 2D electrophoresis without gel rotation. Electrophoresis is completed within 20 min and sensitivity is in the subnanogram range. The system is temperature controlled for speed, denaturation of nucleic acid molecules and maintaining molecules single-stranded. The system allows characterization of structure, conformation and damage in complex nucleic acid preparations. Besides quick 1D PAGE, 2D applications include characterization of efficiency of complex molecular procedures, checking quality of biosamples and detecting DNA damage in cells and body fluids. The system should also run protein gels.

High-Throughput Optofluidic Acquisition of Microdroplets in Microfluidic Systems

Droplet optofluidics technology aims at manipulating the tiny volume of fluids confined in micro-droplets with light, while exploiting their interaction to create "digital" micro-systems with highly significant scientific and technological interests. Manipulating droplets with light is particularly attractive since the latter provides wavelength and intensity tunability, as well as high temporal and spatial resolution. In this review study, we focus mainly on recent methods developed in order to monitor real-time analysis of droplet size and size distribution, active merging of microdroplets using light, or to use microdroplets as optical probes.

Target Confinement in Small Reaction Volumes Using Microfluidic Technologies: A Smart Approach for Single-Entity Detection and Analysis

Over the last decades, the study of cells, nucleic acid molecules, and proteins has evolved from ensemble measurements to so-called single-entity studies. The latter offers huge benefits, not only as biological research tools to examine heterogeneities among individual entities within a population, but also as biosensing tools for medical diagnostics, which can reach the ultimate sensitivity by detecting single targets. Whereas various techniques for single-entity detection have been reported, this review focuses on microfluidic systems that physically confine single targets in small reaction volumes. We categorize these techniques as droplet-, microchamber-, and nanostructure-based and provide an overview of their implementation for studying single cells, nucleic acids, and proteins. We furthermore reflect on the advantages and limitations of these techniques and highlight future opportunities in the field.

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.

Chip-scale alignment of long DNA nanofibers on a patterned self-assembled monolayer

Controlled alignment of long DNA nanofibers is challenging. This communication reports a method to align human genomic DNA with nearly unlimited length using lithographically produced micro-patterns of self-assembled monolayers (SAMs) with positively charged terminal groups. The micro-patterns act as local DNA reservoirs to supply DNAs for nanofiber formation, and can also stretch and align DNA nanofibers to form an ordered array by controlling the dewetting profile. By reducing the size and inter-patch distance of a micro-patch, a nearly uniform array of long DNA nanofibers can be patterned over a large area. A controlled motion of a DNA containing droplet allows for free patterning of DNA nanofibers and production of complex structures without a transfer process. Bending of DNA nanofibers due to local distortion of the contact line bridges more adjacent micro-patches and increases the chance of producing continuous nanofibers. The interplay between surface tension and electrostatic attraction of positively charged micro-patterns allows the production of long DNA nanofibers in a simple yet powerful way.

Stretching of surface-tethered polymers in pressure-driven flow under confinement

We study the effect of pressure-driven flow on a single surface-tethered DNA molecule confined between parallel surfaces. The influence of flow and channel parameters as well as the length of the molecules on their extension and orientation is explored. In the experiments the chain conformations are imaged by laser scanning confocal microscopy. We find that the fractional extension of the tethered DNA molecules mainly depends on the wall shear stress, with effects of confinement being very weak. Experiments performed with molecules of different contour length show that the fractional extension is a universal function of the product of the wall shear stress and the contour length, a result that can be obtained from a simple scaling relation. The experimental results are in good agreement with results from coarse-grained molecular dynamics/Lattice-Boltzmann simulations.

Ionic Current-Based Mapping of Short Sequence Motifs in Single DNA Molecules Using Solid-State Nanopores

Nanopore sensors show great potential for rapid, single-molecule determination of DNA sequence information. Here, we develop an ionic current-based method for determining the positions of short sequence motifs in double-stranded DNA molecules with solid-state nanopores. Using the DNA-methyltransferase M.TaqI and a biotinylated S-adenosyl-l-methionine cofactor analogue we create covalently attached biotin labels at 5'-TCGA-3' sequence motifs. Monovalent streptavidin is then added to bind to the biotinylated sites giving rise to additional current blockade signals when the DNA passes through a conical quartz nanopore. We determine the relationship between translocation time and position along the DNA contour and find a minimum resolvable distance between two labeled sites of ∼200 bp. We then characterize a variety of DNA molecules by determining the positions of bound streptavidin and show that two short genomes can be simultaneously detected in a mixture. Our method provides a simple, generic single-molecule detection platform enabling DNA characterization in an electrical format suited for portable devices for potential diagnostic applications.

Model studies of the effects of intracellular crowding on nucleic acid interactions

Molecular interactions and reactions in living cells occur with high concentrations of background molecules and ions. Many research studies have shown that intracellular molecules have characteristics different from those obtained using simple aqueous solutions. To better understand the behavior of biomolecules in intracellular environments, biophysical experiments were conducted under cell-mimicking conditions in a test tube. It has been shown that the molecular environments at the physiological level of macromolecular crowding, spatial confinement, water activity and dielectric constant, have significant effects on the interactions of DNA and RNA for hybridization, higher-order folding, and catalytic activity. The experimental approaches using in vitro model systems are useful to reveal the origin of the environmental effects and to bridge the gap between the behaviors of nucleic acids in vitro and in vivo. This paper highlights the model experiments used to evaluate the influences of intracellular environment on nucleic acid interactions.

Optical DNA mapping in nanofluidic devices: principles and applications

Optical DNA mapping has over the last decade emerged as a very powerful tool for obtaining long range sequence information from single DNA molecules. In optical DNA mapping, intact large single DNA molecules are labeled, stretched out, and imaged using a fluorescence microscope. This means that sequence information ranging over hundreds of kilobasepairs (kbp) can be obtained in one single image. Nanochannels offer homogeneous and efficient stretching of DNA that is crucial to maximize the information that can be obtained from optical DNA maps. In this review, we highlight progress in the field of optical DNA mapping in nanochannels. We discuss the different protocols for sequence specific labeling and divide them into two main categories, enzymatic labeling and affinity-based labeling. Examples are highlighted where optical DNA mapping is used to gain information on length scales that would be inaccessible with traditional techniques. Enzymatic labeling has been commercialized and is mainly used in human genetics and assembly of complex genomes, while the affinity-based methods have primarily been applied in bacteriology, for example for rapid analysis of plasmids encoding antibiotic resistance. Next, we highlight how the design of nanofluidic channels can been altered in order to obtain the desired information and discuss how recent advances in the field make it possible to retrieve information beyond DNA sequence. In the outlook section, we discuss future directions of optical DNA mapping, such as fully integrated devices and portable microscopes.