Effect of the matrix on DNA electrophoretic mobility

An electroadhesive hydrogel interface prolongs porcine gastrointestinal mucosal theranostics

Establishing a robust and intimate mucosal interface that allows medical devices to remain within lumen-confined organs for extended periods has valuable applications, particularly for gastrointestinal theranostics. Here, we report the development of an electroadhesive hydrogel interface for robust and prolonged mucosal retention after electrical activation (e-GLUE). The e-GLUE device is composed of cationic polymers interpenetrated within a tough hydrogel matrix. An e-GLUE electrode design eliminated the need for invasive submucosal placement of ground electrodes for electrical stimulation during endoscopic delivery. With an electrical stimulation treatment of about 1 minute, the cationic polymers diffuse and interact with polyanionic proteins that have a relatively slow cellular turnover rate in the deep mucosal tissue. This mucosal adhesion mechanism increased the adhesion energy of hydrogels on the mucosa by up to 30-fold and enabled in vivo gastric retention of e-GLUE devices in a pig stomach for up to 30 days. The adhesion strength was modulated by polycationic chain length, electrical stimulation time, gel thickness, cross-linking density, voltage amplitude, polycation concentration, and perimeter-to-area ratio of the electrode assembly. In porcine studies, e-GLUE demonstrated rapid mucosal adhesion in the presence of luminal fluid and mucus exposure. In proof-of-concept studies, we demonstrated e-GLUE applications for mucosal hemostasis, sustained local delivery of therapeutics, and intimate biosensing in the gastrointestinal tract, which is an ongoing clinical challenge for commercially available alternatives, such as endoclips and mucoadhesive. The e-GLUE platform could enable theranostic applications across a range of digestive diseases, including recurrent gastrointestinal bleeding and inflammatory bowel disease.

Barcoded screening identifies nanocarriers for protein delivery to kidney

Targeted protein delivery with nanocarriers holds significant potential to enhance therapeutic outcomes by precisely directing proteins to specific organs or tissues. However, the complex interactions between nanocarriers and the biological environment pose considerable challenges in designing effective targeted delivery vehicles. In this study, we address this challenge by leveraging DNA-barcoded high-throughput screening. We construct a nanocapsule library via in-situ polymerization, incorporating various monomers to create nanocapsules with unique surface properties. In vitro and in vivo screening, using female mice, identify nanocapsules with high cell association and different biodistribution. Our investigation into kidney-enriched nanocapsules highlights the crucial role of polymer composition in biodistribution, demonstrating the potential of surface engineering for precise control over nanoparticle distribution. The kidney-enriched nanocapsule successfully delivers catalase, showcasing its therapeutic potential in mitigating cisplatin-induced acute kidney injury. Overall, our study presents an approach for identifying protein delivery vehicles, with the capacity to broaden the application of proteins as therapeutic agents or research tools.

DNA Aptamers That Bind to Alginate Hydrogels

Hydrogels have become common in wound treatment because they form very stable and biocompatible environments that promote healing. However, due to the highly porous hydrogel structure, any therapeutic added to these gels tends to diffuse quickly and impact delivery to the target site. Aptamers are short, single-stranded DNA or RNA sequences that bind specifically to a target, so aptamers that bind to hydrogels could serve as tags for therapeutics to prevent rapid diffusion and allow for extended delivery. An in vitro selection approach was developed to identify DNA aptamers for alginate hydrogels. Two DNA aptamers were shown to bind hydrogels ranging from 0.5 to 2% alginate and could be either encapsulated during gelation or introduced to preformed gels. Both aptamers also showed specificity for binding to alginate compared to agarose. To demonstrate the functional aspect of the aptamers as tethers for other biomolecules, both aptamers were conjugated to BSA. Aptamer-conjugated BSA was retained longer in the hydrogel during week-long diffusion studies both when encapsulated or introduced to preformed gels, which adds flexibility to how these aptamers can be deployed in a clinical setting.

Differential electrophoretic mobility of synthetic DNA motifs and duplex DNA in various counter ions

In this work, we analyzed the electrophoretic behavior of a double crossover (DX) DNA motif in various counter ions. The influence of the type and concentration of counter ions on electrophoretic behavior is different for the DX motif compared to a duplex of the same molecular weight. Higher concentrations of divalent ions Mg2+ and Ca2+ in the gel and running buffer reduce the electrophoretic migration of the DX motif. This effect is less pronounced in the monovalent ion Na+ while K+ ion did not have any significant effect on the electrophoretic behavior.

Screening of Cross-Reactive Aptamers for the Detection of 24 Quinolones by Using a Liebig's Law-Guided Parallel-Series Strategy

Quinolones, a widely used class of antibiotics, present significant environmental and health concerns if they excessively remain in the environment and in food. Aptamers specific to quinolones can be applied as bioreceptors for the detection of quinolone residues in the environment and food. The quinolone family contains dozens of different individuals that share the same core structure coupled with various substituents at six different positions. The diversity and complexity of the substitution sites make it a challenge to choose a set of representative molecules that encompass all the desired sites and preserve the core molecular framework for the screening of quinolone-specific aptamers via systematic evolution of ligands by exponential enrichment (SELEX). To address this challenge, we introduce a novel parallel-series strategy guided by Liebig's law for isolating quinolone-specific cross-reactive aptamers by using the library-immobilized SELEX method. Through this approach, we successfully identified 5 aptamers (Apt.AQ01-Apt.AQ05) with high binding affinity and excellent specificity to 24 different quinolone individuals. Among them, Apt.AQ03 showcased optimal performance with affinities ranging from 0.14 to 1.07 μM across the comprehensive set of 24 quinolones, exhibiting excellent specificity against nontarget interferents. The binding performance of Apt.AQ03 was further characterized with microscale thermophoresis, circular dichroism spectra, and an exonuclease digestion assay. By using Apt.AQ03 as a bioreceptor, a fluorescence resonance energy transfer (FRET) aptasensor was developed for the detection of 24 quinolones in milk, achieving a remarkable detection limit of 14.5-21.8 ng/mL. This work not only establishes a robust and effective strategy for selecting cross-reactive aptamers applicable to other small-molecule families but also provides high-quality aptamers for developing various high-throughput and reliable methods for the detection of multiple quinolone residues in food.

Real-time kinetic analysis and detection of glycated hemoglobin A1c using a quartz crystal microbalance-based aptasensor

Glycated hemoglobin (HbA1c) has been an important biomarker for long-term diagnosis and monitoring of diabetes mellitus. The development of a rapid, reliable, and less sophisticated device to measure HbA1c is imperative to facilitate efficient early-care diabetes management. To date, no existing aptamer-based biosensor (aptasensor) for detecting HbA1c has been developed using a quartz crystal microbalance (QCM). In this study, the aptamer specific to HbA1c as a novel biosensing receptor was covalently functionalized onto a QCM substrate via mixed self-assembled monolayers (SAMs). A portable QCM equipped with a liquid-flow module was used to investigate the biospecificity, sensitivity, and interaction dynamics of the aptamer functionalized surfaces. The real-time kinetic analysis of HbA1c binding to the surface-functionalized aptamers revealed "on" and "off" binding rates of 4.19 × 104 M-1 s-1 and 2.43 × 10-3 s-1, respectively. These kinetic parameters imply that the QCM-based aptasensor specifically recognizes HbA1c with an equilibrium dissociation constant as low as 57.99 nM. The linear detection of HbA1c spanned from 13 to 108 nM, with a limit of detection (LOD) of 26.29 nM. Moreover, the spiked plasma sample analysis offered compelling evidence that this aptasensor is a promising technique for developing a point-of-care device for diabetes mellitus.

A review of electrophoretic separations in temperature-responsive Pluronic thermal gels

Gel electrophoresis is a ubiquitous bioanalytical technique used in research laboratories to validate protein and nucleic acid samples. Polyacrylamide and agarose have been the gold standard gel materials for decades, but an alternative class of polymer has emerged with potentially superior performance. Pluronic thermal gels are water-soluble polymers that possess the unique ability to undergo a change in viscosity in response to changing temperature. Thermal gels can reversibly convert between low-viscosity liquids and high-viscosity solid gels using temperature as an adjustable parameter. The properties of thermal gels provide unmatched flexibility as a dynamic separations matrix to measure analytes ranging from small molecules to cells. This review article describes the physical and chemical properties of Pluronic thermal gels to provide a fundamental overview of polymer behavior. The performance of thermal gels is then reviewed to highlight their applications as a gel matrix for electrokinetic separations in capillary, microfluidic, and slab gel formats. The use of dynamic temperature-responsive gels in bioanalytical separations is an underexplored area of research but one that holds exciting potential to achieve performance unattainable with conventional static polymers.

A high-throughput 384-well CometChip platform reveals a role for 3-methyladenine in the cellular response to etoposide-induced DNA damage

The Comet or single-cell gel electrophoresis assay is a highly sensitive method to measure cellular, nuclear genome damage. However, low throughput can limit its application for large-scale studies. To overcome these limitations, a 96-well CometChip platform was recently developed that increases throughput and reduces variation due to simultaneous processing and automated analysis of 96 samples. To advance throughput further, we developed a 384-well CometChip platform that allows analysis of ∼100 cells per well. The 384-well CometChip extends the capacity by 4-fold as compared to the 96-well system, enhancing application for larger DNA damage analysis studies. The overall sensitivity of the 384-well CometChip is consistent with that of the 96-well system, sensitive to genotoxin exposure and to loss of DNA repair capacity. We then applied the 384-well platform to screen a library of protein kinase inhibitors to probe each as enhancers of etoposide induced DNA damage. Here, we found that 3-methyladenine significantly increased levels of etoposide-induced DNA damage. Our results suggest that a 384-well CometChip is useful for large-scale DNA damage analyses, which may have increased potential in the evaluation of chemotherapy efficacy, compound library screens, population-based analyses of genome damage and evaluating the impact of environmental genotoxins on genome integrity.

Analysis of therapeutic nucleic acids by capillary electrophoresis

Nucleic acids are getting increased attention to fulfill unmet medical needs. The past five years have seen more than ten FDA approvals of nucleic acid based therapeutics. New analytical challenges have been posed in discovery, characterization, quality control and bioanalysis of therapeutic nucleic acids. Capillary electrophoresis (CE) has proven to be an efficient separation technique and has been widely used for analyzing oligonucleotides and nucleic acids. This review discusses the recent technical advances of CE in nucleic acid analysis such as polymeric matrices, separation conditions and detection methods, and the applications of CE to various therapeutic nucleic acids including antisense oligonucleotide (ASO), small interfering ribonucleic acid (siRNA), messenger RNA (mRNA), gene editing tools such as clustered regularly interspaced short palindromic repeats (CRISPR)-based gene and cell therapy, and other nucleic acid related therapeutics.

Using biochar to strengthen the removal of antibiotic resistance genes: Performance and mechanism

In this study, the excess activated sludge was used for pyrolysis to produce biochar with Ce modification. The removal process and mechanism of ampicillin resistance gene (ARG_Amp) by biochar was investigated. The results showed that when pyrolyzing the excess sludge at 400 °C, the organic components in the sludge could be partially pyrolyzed and complexed with Ce. By accepting electrons from phenol or quinone, persistent free radicals (PFRs) were formed on the surface of biochar. On the optimized conditions with the initial ARG_Amp concentration of 41.43 mg/L, the removal ratios of ARG_Amp by adsorption, PFRs, hydroxyl free radicals (·OH) by adding H₂O₂ were 28.37%, 8.26%, and 27.56%. No melted DNA was detected in the treated samples. The oxidation process by PFRs and ·OH can directly destroy the ARG_Amp structure. The phosphodiester bond in the base stacking structure and the phosphate bond in the nucleotide are the possible action sites of PFRs. Treated ARG_Amp products were in the form of base pair residues or short-chain double helix structures. ·OH can be added to the bases of nucleotide molecules to form highly active free radical adducts. They can initiate molecular dehydrogenation and intermolecular proton transfer, resulting in oxidation of the base to the scission of the phosphate sugar backbone.

Regulation of cell attachment, spreading, and migration by hydrogel substrates with independently tunable mesh size

Hydrogels are widely used as substrates to investigate interactions between cells and their microenvironment as they mimic many attributes of the extracellular matrix. The stiffness of hydrogels is an important property that is known to regulate cell behavior. Beside stiffness, cells also respond to structural cues such as mesh size. However, since the mesh size of hydrogel is intrinsically coupled to its stiffness, its role in regulating cell behavior has never been independently investigated. Here, we report a hydrogel system whose mesh size and stiffness can be independently controlled. Cell behavior, including spreading, migration, and formation of focal adhesions is significantly altered on hydrogels with different mesh sizes but with the same stiffness. At the transcriptional level, hydrogel mesh size affects cellular mechanotransduction by regulating nuclear translocation of yes-associated protein. These findings demonstrate that the mesh size of a hydrogel plays an important role in cell-substrate interactions. STATEMENT OF SIGNIFICANCE: Hydrogels are ideal platforms with which to investigate interactions between cells and their microenvironment as they mimic many physical properties of the extracellular matrix. However, the mesh size of hydrogels is intrinsically coupled to their stiffness, making it challenging to investigate the contribution of mesh size to cell behavior. In this work, we use hydrogel-on-glass substrates with defined thicknesses whose stiffness and mesh size can be independently tuned. We use these substrates to isolate the effects of mesh size on cell behavior, including attachment, spreading, migration, focal adhesion formation and YAP localization in the nucleus. Our results show that mesh size has significant, yet often overlooked, effects, on cell behavior, and contribute to a further understanding of cell-substrate interactions.

Phosphorylation of the aggregate-forming protein alpha-synuclein on serine-129 inhibits its DNA-bending properties

Alpha-synuclein (aSyn) is a vertebrate protein, normally found within the presynaptic nerve terminal and nucleus, which is known to form somatic and neuritic aggregates in certain neurodegenerative diseases. Disease-associated aggregates of aSyn are heavily phosphorylated at serine-129 (pSyn), while normal aSyn protein is not. Within the nucleus, aSyn can directly bind DNA, but the mechanism of binding and the potential modulatory roles of phosphorylation are poorly understood. Here we demonstrate using a combination of electrophoretic mobility shift assay and atomic force microscopy approaches that both aSyn and pSyn can bind DNA within the major groove, in a DNA length-dependent manner and with little specificity for DNA sequence. Our data are consistent with a model in which multiple aSyn molecules bind a single 300 base pair (bp) DNA molecule in such a way that stabilizes the DNA in a bent conformation. We propose that serine-129 phosphorylation decreases the ability of aSyn to both bind and bend DNA, as aSyn binds 304 bp circular DNA forced into a bent shape, but pSyn does not. Two aSyn paralogs, beta- and gamma-synuclein, also interact with DNA differently than aSyn, and do not stabilize similar DNA conformations. Our work suggests that reductions in aSyn's ability to bind and bend DNA induced by serine-129 phosphorylation may be important for modulating aSyn's known roles in DNA metabolism, including the regulation of transcription and DNA repair.

Electrochemical Sensor for Directional Recognition and Measurement of Antibiotic Resistance Genes in Water

The establishment of rapid targeted identification and analysis of antibiotic resistance genes (ARGs) is very important. In this study, an electrochemical sensor, which can detect ARGs was obtained by modifying the sulfhydryl single-stranded DNA probe onto the thin-film gold electrode through self-assembly. The sensor can perform a hybridization reaction with a target sequence to obtain an electrochemical impedance spectroscopy signal. The results showed that when the concentration of the probe used to modify thin-film gold electrodes during preparation was 1 μM, the hybridization time was 1 h, and the hybridization temperature was 35 °C, the self-assembled sensor showed good detection performance for the ARGs encoding β-lactam hydrolase. The measurement ARG concentration linear range is 6.3-900.0 ng/mL, and the R² is 0.9992. The sensor shows good specific recognition ability for single-base, double-base, and three-base mismatch DNA. In addition, after 30 days of storage at 4 °C, the accurate identification and analysis of ARGs can still be maintained.

Simple, rapid, and reproducible capillary gel electrophoresis separation and laser-induced fluorescence detection of DNA topoisomers with unmodified fused silica separation capillaries

The topology of DNA is a critical quality attribute for plasmid-based pharmaceuticals, making quantification of trace levels of plasmid topoisomers an important analytical priority. An automated and cost-effective method based on capillary gel electrophoresis laser-induced fluorescence detection is described. The method outlined in this report is significant because it is easily implemented by any laboratory for which routine analyses of plasmid topology are critical for the development of new plasmid-based therapies as well as for quality control of gene therapies utilizing supercoiled DNA. Detection of topoisomers was achieved by incorporating ethidium bromide in the separation medium. The detector response was improved by 3 orders of magnitude by utilizing a 605-nm optical filter with a 15-nm bandwidth. Separations of linear, open circle, supercoiled, and multimer DNA plasmids ranging from 4.2 to 10.5 kbp were accomplished in under 6 min using an unmodified fused silica capillary (50-μm internal diameter). The background electrolyte was comprised of 0.5% gel, which was hydroxypropylmethyl cellulose, 1 mM ethylenediaminetetraacetic acid, and 50 mM N-(2-acetamido)-2-aminoethanesulfonic acid (pH of 6.25). The separations, which balanced the bulk electroosmotic flow, the electrophoretic mobility of the DNA, and gel sieving were dependent upon the pH of the electrolyte and the gel concentration. Reproducibility was dependent upon the procedure used to prepare the gel as well as other factors including the ethidium bromide concentration and capillary conditioning. A single unmodified capillary operated for more than 150 runs had an across-day migration time precision of 1% relative standard deviation and percent area precision of 10% relative standard deviation.

Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cations

This review describes the results obtained by using free-solution capillary electrophoresis to probe the electrostatic and hydrodynamic properties of DNA in solutions containing various monovalent cations. In brief, we found that the mobilities of double-stranded DNAs (dsDNAs) increase with increasing molecular weight before leveling off and becoming constant at molecular weights ≥400 bp. The mobilities of single-stranded DNAs (ssDNAs) go through a maximum at ∼10-20 nucleotides before decreasing and becoming constant for oligomers larger than ∼30-50 bases. The mobilities of both ss- and dsDNAs increase linearly with the logarithm of increasing charge per unit length and decrease linearly with the logarithm of increasing ionic strength. Surprisingly, ss- and dsDNA mobilities level off and become nearly constant at ionic strengths ≥0.6 M. The thermal stabilities of dsDNAs decrease linearly with increasing solution viscosity. The diffusion coefficients of dsDNA are modulated by the diffusion coefficients of their counterions because of electrostatic DNA-cation coupling interactions. Finally, the anomalously slow mobilities observed for A-tract-containing DNAs can be attributed both to differences in shape and to the preferential localization of small cations in the A-tract minor groove. Since many of these results are mirrored in other polyion-counterion systems, free-solution electrophoresis can be viewed as a reporter of the electrostatics and hydrodynamics of highly charged polyions. New results describing the mobilities of dsDNA analogues of a microRNA-messenger RNA complex are also presented.

Fundamentals of Capillary Electrophoretic Migration and Separation of SDS Proteins in Borate Cross-Linked Dextran Gels

Recent progress in the development and production of new, innovative protein therapeutics require rapid and adjustable high-resolution bioseparation techniques. Sodium dodecyl sulfate capillary gel electrophoresis (SDS-CGE) using a borate (B) cross-linked dextran (D) separation matrix is widely employed today for rapid consistency analysis of therapeutic proteins in manufacturing and release testing. Transient borate cross-linking of the semirigid dextran polymer chains leads to a high-resolution separation gel for SDS-protein complexes. To understand the migration and separation basis of the D/B gel, the present work explores various gel formulations of dextran monomer (2, 5, 7.5, and 10%) and borate cross-linker (2 and 4%) concentrations. Ferguson plots were analyzed for a mixture of protein standards with molecular weights ranging from 20 to 225 kDa, and the resulting nonlinear concave curves pointed to nonclassical sieving behavior. While the 2% D/4% B gel resulted in the fastest analysis time, the 10% D/2% B gel was found to produce the greatest separation window, even higher than with the 10% D/4% B gel, due to a significant increase in the electroosmotic flow of the former composition in the direction opposite to SDS-protein complex migration. The study then focused on SDS-CGE separation of a therapeutic monoclonal antibody and its subunits. A combination of molecular weight and shape selectivity as well as, to a lesser extent, surface charge density differences (due to glycosylation on the heavy chain) influenced migration. Greater molecular weight selectivity occurred for the higher monomer concentration gels, while improved glycoselectivity was obtained using a more dilute gel, even as low as 2% D/2% B. This latter gel took advantage of the dextran-borate-glycoprotein complexation. The study revealed that by modulating the dextran (monomer) and borate (cross-linker) concentration ratios of the sieving matrix, one can optimize the separation for specific biopharmaceutical modalities with excellent column-to-column, run-to-run, and gel-to-gel migration time reproducibilities (<0.96% relative standard deviation (RSD)). The widely used 10% dextran/4% borate gel represents a good screening option, which can then be followed by a modified composition, optimized for a specific separation as necessary.

A simplified model for gel electrophoresis of a hydrophobic rigid colloid

Electrophoresis of a charged dielectric hydrophobic colloid embedded in a charged hydrogel medium is addressed. A slip velocity condition at the particle surface is considered. The characteristic of the gel electrophoresis is different compared with the free-solution electrophoresis due to the presence of immobile charges of the gel medium, which induces a strong background electroosmotic flow and modifies the Debye layer of the colloid. The gel electrophoresis of the dielectric hydrophobic charged colloid is made based on first-order perturbation analysis. A closed form solution involving simple exponential integrals for the mobility is derived, which reduces to several existing mobility expressions under limiting conditions such as for the gel electrophoresis of hydrophilic particles and a hydrophobic colloid in free-solution electrophoresis. We find that the mobility reversal is achieved by varying the Debye length or gel permeability. For the present first-order perturbation analysis, unlike free-solution electrophoresis, the particle dielectric permittivity is found to influence the mobility. One of the intriguing features of the present study is the derivation of the simplified mobility expression, which can be easily computed for a given set of parameter values.

HIV detection from human serum with paper-based isotachophoretic RNA extraction and reverse transcription recombinase polymerase amplification

The number of people living with HIV continues to increase with the current total near 38 million, of which about 26 million are receiving antiretroviral therapy (ART). These treatment regimens are highly effective when properly managed, requiring routine viral load monitoring to assess successful viral suppression. Efforts to expand access by decentralizing HIV nucleic acid testing in low- and middle-income countries (LMICs) has been hampered by the cost and complexity of current tests. Sample preparation of blood samples has traditionally relied on cumbersome RNA extraction methods, and it continues to be a key bottleneck for developing low-cost POC nucleic acid tests. We present a microfluidic paper-based analytical device (μPAD) for extracting RNA and detecting HIV in serum, leveraging low-cost materials, simple buffers, and an electric field. We detect HIV virions and MS2 bacteriophage internal control in human serum using a novel lysis and RNase inactivation method, paper-based isotachophoresis (ITP) for RNA extraction, and duplexed reverse transcription recombinase polymerase amplification (RT-RPA) for nucleic acid amplification. We design a specialized ITP system to extract and concentrate RNA, while excluding harsh reagents used for lysis and RNase inactivation. We found the ITP μPAD can extract and purify 5000 HIV RNA copies per mL of serum. We then demonstrate detection of HIV virions and MS2 bacteriophage in human serum within 45-minutes.

Electrokinetic actuation of an uncharged polarizable dielectric droplet in charged hydrogel medium

Electrokinetic transport of an uncharged nonconducting microsized liquid droplet in a charged hydrogel medium is studied. Dielectric polarization of the liquid drop under the action of an externally imposed electric field induces a non-homogeneous charge density at the droplet surface. The interactions of the induced surface charge of the droplet with the immobile charges of the hydrogel medium generates an electric force to the droplet, which actuates the drop through the charged hydrogel medium. A numerical study based on the first principle of electrokinetics is adopted. Dependence of the droplet velocity on its dielectric permittivity, bulk ionic concentration, and immobile charge density of the gel is analyzed. The surface conduction is significant in presence of charged gel, which creates a concentration polarization. The impact of the counterion saturation in the Debye layer due to the dielectric decrement of the medium is addressed. The modified Nernst-Planck equation for ion transport and the Poisson equation for the electric field is considered to take into account the dielectric polarization. A quadrupolar vortex around the uncharged droplet is observed when the gel medium is considered to be uncharged, which is similar to the induced charge electroosmosis around an uncharged dielectric colloid in free-solution. We find that the induced charge electrokinetic mechanism creates a strong recirculation of liquid within the droplet and the translational velocity of the droplet strongly depends on its size for the dielectric droplet embedded in a charged gel medium.

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.

Simultaneous RNA purification and size selection using on-chip isotachophoresis with an ionic spacer

We present an on-chip method for the extraction of RNA within a specific size range from low-abundance samples. We use isotachophoresis (ITP) with an ionic spacer and a sieving matrix to enable size-selection with a high yield of RNA in the target size range. The spacer zone separates two concentrated ITP peaks, the first containing unwanted single nucleotides and the second focusing RNA of the target size range (2-35 nt). Our ITP method excludes >90% of single nucleotides and >65% of longer RNAs (>35 nt). Compared to size selection using gel electrophoresis, ITP-based size-selection yields a 2.2-fold increase in the amount of extracted RNAs within the target size range. We also demonstrate compatibility of the ITP-based size-selection with downstream next generation sequencing. On-chip ITP-prepared samples reveal higher reproducibility of transcript-specific measurements compared to samples size-selected by gel electrophoresis. Our method offers an attractive alternative to conventional sample preparation for sequencing with shorter assay time, higher extraction efficiency and reproducibility. Potential applications of ITP-based size-selection include sequencing-based analyses of small RNAs from low-abundance samples such as rare cell types, samples from fluorescence activated cell sorting (FACS), or limited clinical samples.

Analysis of DNA by Agarose Gel Electrophoresis

Electrophoresis through agarose or polyacrylamide gels is used to separate, analyze, identify, and purify DNA fragments. The technique is simple, rapid to perform, and capable of resolving fragments of DNA that cannot be separated adequately by other procedures, such as density gradient centrifugation. The location of bands of DNA within the gel can be determined directly by staining with low concentrations of fluorescent intercalating dyes, such as ethidium bromide or SYBR Gold; bands containing as little as 20 pg of double-stranded DNA can then be detected by direct examination of the gel in ultraviolet (UV) light. If necessary, these bands of DNA can be recovered from the gel.

Deciphering ion concentration polarization-based electrokinetic molecular concentration at the micro-nanofluidic interface: theoretical limits and scaling laws

The electrokinetic molecular concentration (EMC) effect at the micro-nanofluidic interface, which enables million-fold preconcentration of biomolecules, is one of the most compelling yet least understood nanofluidic phenomena. Despite the tremendous interests in EMC and the substantial efforts devoted, the detailed mechanism of EMC remains an enigma so far owing to its high complexity, which gives rise to the significant scientific controversies outstanding for over a decade and leaves the precise engineering of EMC devices infeasible. We report a series of experimental and theoretical new findings that decipher the mechanism of EMC. We demonstrate the first elucidation of two separate operating regimes of EMC, and establish the first theoretical model that analytically yet concisely describes the system. We further unveil the dramatically different scaling behaviors of EMC in the two regimes, thereby clarifying the long-lasting controversies. We believe this work represents important progress towards the scientific understanding of EMC and related nano-electrokinetic systems, and would enable the rational design and optimization of EMC devices for a variety of applications.

Force fields of charged particles in micro-nanofluidic preconcentration systems

Electrokinetic concentration devices based on the ion concentration polarization (ICP) phenomenon have drawn much attention due to their simple setup, high enrichment factor, and easy integration with many subsequent processes, such as separation, reaction, and extraction etc. Despite significant progress in the experimental research, fundamental understanding and detailed modeling of the preconcentration systems is still lacking. The mechanism of the electrokinetic trapping of charged particles is currently limited to the force balance analysis between the electric force and fluid drag force in an over-simplified one-dimensional (1D) model, which misses many signatures of the actual system. This letter studies the particle trapping phenomena that are not explainable in the 1D model through the calculation of the two-dimensional (2D) force fields. The trapping of charged particles is shown to significantly distort the electric field and fluid flow pattern, which in turn leads to the different trapping behaviors of particles of different sizes. The mechanisms behind the protrusions and instability of the focused band, which are important factors determining overall preconcentration efficiency, are revealed through analyzing the rotating fluxes of particles in the vicinity of the ion-selective membrane. The differences in the enrichment factors of differently sized particles are understood through the interplay between the electric force and convective fluid flow. These results provide insights into the electrokinetic concentration effect, which could facilitate the design and optimization of ICP-based preconcentration systems.

Determination of electroosmotic and electrophoretic mobility of DNA and dyes in low ionic strength solutions

Nanocoding, a genome analysis platform, relies on very low ionic strength conditions to elongate DNA molecules up to 1.06 (fully stretched DNA = 1). Understanding how electroosmotic and electrophoretic forces vary, as ionic strength decreases, will enable better Nanocoding devices, or other genome analysis platforms, to be developed. Using gel electrophoresis to determine overall mobility (includes contributions from electrophoretic and electroosmotic forces) in different ionic strength conditions, linear DNA molecules (pUC19 (2.7 kb), pBR322 (4.4 kb), ΦX174 (5.4 kb), and PSNAPf-H2B (6.2 kb)) were analyzed in varying gel concentrations (1.50, 1.25, 1.00, 0.75, and 0.50%). Additionally, buffer concentration (Tris-EDTA, TE) was varied to determine free solution mobility at different ionic strength solutions. As ionic strength decreased from 13.8 to 7.3 mM, overall mobility increased. As TE buffer decreased (< 7.3 mM), overall mobility drastically decreased as ionic strength decreased. Rhodamine B dye was utilized to determine the electroosmotic mobility. As the ionic strength decreased, electroosmotic mobility increased. The experimental electrophoretic mobility was compared to theoretical considerations for electrophoretic mobility (Pitts and Debye-Hückel-Onsager). Electroosmotic forces decreased the overall mobility of DNA molecules and bromophenol blue migration in a gel matrix as ionic strength decreased.

A novel 4-arm DNA/RNA Nanoconstruct triggering Rapid Apoptosis of Triple Negative Breast Cancer Cells within 24 hours

Measuring at ~30 nm, a fully customizable holliday junction DNA nanoconstruct, was designed to simultaneously carry three unmodified SiRNA strands for apoptosis gene knockout in cancer cells without any assistance from commercial transfection kits. In brief, a holliday junction structure was intelligently designed to present one arm with a cell targeting aptamer (AS1411) while the remaining three arms to carry different SiRNA strands by means of DNA/RNA duplex for inducing apoptosis in cancer cells. By carrying the three SiRNA strands (AKT, MDM2 and Survivin) into triple negative breast MDA-MB-231 cancer cells, cell number had reduced by up to ~82% within 24 hours solely from one single administration of 32 picomoles. In the immunoblotting studies, up-elevation of phosphorylated p53 was observed for more than 8 hours while the three genes of interest were suppressed by nearly half by the 4-hour mark upon administration. Furthermore, we were able to demonstrate high cell selectivity of the nanoconstruct and did not exhibit usual morphological stress induced from liposomal-based transfection agents. To the best of the authors' knowledge, this system represents the first of its kind in current literature utilizing a short and highly customizable holliday DNA junction to carry SiRNA for apoptosis studies.

New design of hydrogels with tuned electro-osmosis: a potential model system to understand electro-kinetic transport in biological tissues

A series of charged polymer gels with precisely controlled magnitude and direction of electro-osmotic flow was prepared and opens up the possibility for understanding the contribution of electro-osmosis to transport phenomenon in native biological tissues.

A rapidly-prototyped microfluidic device for size-based nucleic acid fractionation using isotachophoresis

We present a novel microfluidic device for size-based nucleic acid (NA) fractionation using isotachophoresis (ITP) and an ionic spacer.

The role of helper lipids in the intracellular disposition and transfection efficiency of niosome formulations for gene delivery to retinal pigment epithelial cells

In this work, we carried out a comparative study of four different niosome formulations based on the same cationic lipid and non-ionic tensoactive. The niosomes prepared by oil-in-water emulsion technique (o/w) only differed in the helper lipid composition: squalene, cholesterol, squalane or no helper lipid. Niosomes and nioplexes elaborated upon the addition of pCMS-EGFP reporter plasmid were characterized in terms of size, zeta potential and polydispersity index. The capacity of the niosomes to condense, release and protect the DNA against enzymatic degradation was evaluated by agarose gel electrophoresis. In vitro experiments were carried out to evaluate transfection efficiency and cell viability in retinal pigment epithelial cells. Moreover, uptake and intracellular trafficking studies were performed to further understand the role of the helper lipids in the transfection process. Interestingly, among all tested formulations, niosomes elaborated with squalene as helper lipid were the most efficient transfecting cells. Such transfection efficiency could be attributed to their higher cellular uptake and the particular entry pathways used, where macropinocytosis pathway and lysosomal release played an important role. Therefore, these results suggest that helper lipid composition is a crucial step to be considered in the design of niosome formulation for retinal gene delivery applications since clearly modulates the cellular uptake, internalization mechanism and consequently, the final transfection efficiency.

The influence of the polar head-group of synthetic cationic lipids on the transfection efficiency mediated by niosomes in rat retina and brain

The development of novel non-viral delivery vehicles is essential in the search of more efficient strategies for retina and brain diseases. Herein, optimized niosome formulations prepared by oil-in water (o/w) and film-hydration techniques were characterized in terms of size, PDI, zeta potential, morphology and stability. Three ionizable glycerol-based cationic lipids containing a primary amine group (lipid 1), a triglycine group (lipid 2) and a dimethylamino ethyl pendent group (lipid 3) as polar head-groups were part of such niosomes. Upon the addition of pCMS-EGFP plasmid, nioplexes were obtained at different cationic lipid/DNA ratios (w/w). The resultant nioplexes were further physicochemically characterized and evaluated to condense, release and protect the DNA against enzymatic digestion. In vitro experiments were performed to evaluate transfection efficiency and cell viability in HEK-293, ARPE-19 and PECC cells. Interestingly, niosome formulations based on lipid 3 showed better transfection efficiencies in ARPE-19 and PECC cells than the rest of cationic lipids showed in this study. In vivo experiments in rat retina after intravitreal and subretinal injections together with in rat brain after cerebral cortex administration showed promising transfection efficiencies when niosome formulations based on lipid 3 were used. These results provide new insights for the development of non-viral vectors based on cationic lipids and their applications for efficient delivery of genetic material to the retina and brain.

Topological patterns in two-dimensional gel electrophoresis of DNA knots

Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. Although there is a large body of experimental work that allows us to accurately separate different topoisomers of a molecule, a full theoretical understanding of these experiments has not yet been achieved. Here we show that the mobility of DNA knots depends crucially and subtly on the physical properties of the gel and, in particular, on the presence of dangling ends. The topological interactions between these and DNA molecules can be described in terms of an "entanglement number" and yield a nonmonotonic mobility at moderate fields. Consequently, in 2D electrophoresis, gel bands display a characteristic arc pattern; this turns into a straight line when the density of dangling ends vanishes. We also provide a novel framework to accurately predict the shape of such arcs as a function of molecule length and topological complexity, which may be used to inform future experiments.

Electrophoretic Interpretation of PEGylated NP Structure with and without Peripheral Charge

Anchoring poly(ethylene glycol) (PEG) to inorganic nanoparticles (NPs) permits control over NP properties for a variety of technological applications. However, the core-shell structure tremendously complicates the interpretation of the ubiquitous ζ-potential, as furnished by electrophoretic light-scattering, capillary electrophoresis or gel electrophoresis. To advance the ζ-potential-and the more fundamental electrophoretic mobility-as a quantitative diagnostic for PEGylated NPs, we synthesized and characterized Au NPs bearing terminally anchored 5 kDa PEG ligands with univalent carboxymethyl end groups. Using the electrophoretic mobilities, acquired over a wide range of ionic strengths, we developed a theoretical model for the distributions of polymer segments, charge, electrostatic potential, and osmotic pressure that envelop the core: knowledge that will help to improve the performance of soft NPs in fundamental research and technological applications.

Electrophoretic mobility of semi-flexible double-stranded DNA in defect-controlled polymer networks: Mechanism investigation and role of structural parameters

Our previous studies have reported an empirical model, which explains the electrophoretic mobility (μ) of double-stranded DNA (dsDNA) as a combination of a basic migration term (Rouse-like or reptation) and entropy loss term in polymer gels with ideal network structure. However, this case is of exception, considering a large amount of heterogeneity in the conventional polymer gels. In this study, we systematically tune the heterogeneity in the polymer gels and study the migration of dsDNA in these gels. Our experimental data well agree with the model found for ideal networks. The basic migration mechanism (Rouse-like or reptation) persists perfectly in the conventional heterogeneous polymer gel system, while the entropy loss term continuously changes with increase in the heterogeneity. Furthermore, we found that in the limit where dsDNA is shorter than dsDNA persistence length, the entropy loss term may be related to the collisional motions between DNA fragments and the cross-links.

Analysis of small interfering RNA by capillary electrophoresis in hydroxyethylcellulose solutions

The analysis of small interfering RNA (siRNA) is important for gene function studies and drug developments. We employed CE to study the separation of siRNA ladder marker, which were ten double-stranded RNA (dsRNA) fragments ranged from 20 to 1000 bp, in solutions of hydroxyethylcellulose (HEC) polymer with different concentrations and molecular weights (Mws). Migration mechanism of dsRNA during CE was studied by the mobility and resolution length (RL) plots. We found that the RL depended on not only the concentration of HEC, but also the Mw of HEC. For instance, RL of small dsRNA fragment was more influenced by concentration of high Mw HEC than large dsRNA fragment and RL of large dsRNA fragment was more influenced by concentration of low Mw HEC than small dsRNA fragment. In addition, we found electrophoretic evidence that the structure of dsRNA was more compact than dsDNA with the same length. In practice, we succeeded to separate the glyceraldehyde 3-phosphate dehydrogenase siRNA in the mixture of the siRNA ladder marker within 4 min.

Rings in random environments: sensing disorder through topology

In this paper we study the role of topology in DNA gel electrophoresis experiments via molecular dynamics simulations. The gel is modelled as a 3D array of obstacles from which half edges are removed at random with probability p, thereby generating a disordered environment. Changes in the microscopic structure of the gel are captured by measuring the electrophoretic mobility of ring polymers moving through the medium, while their linear counterparts provide a control system as we show they are insensitive to these changes. We show that ring polymers provide a novel, non-invasive way of exploiting topology to sense microscopic disorder. Finally, we compare the results from the simulations with an analytical model for the non-equilibrium differential mobility, and find a striking agreement between simulation and theory.

Palindromic genes in the linear mitochondrial genome of the nonphotosynthetic green alga Polytomella magna

Organelle DNA is no stranger to palindromic repeats. But never has a mitochondrial or plastid genome been described in which every coding region is part of a distinct palindromic unit. While sequencing the mitochondrial DNA of the nonphotosynthetic green alga Polytomella magna, we uncovered precisely this type of genic arrangement. The P. magna mitochondrial genome is linear and made up entirely of palindromes, each containing 1–7 unique coding regions. Consequently, every gene in the genome is duplicated and in an inverted orientation relative to its partner. And when these palindromic genes are folded into putative stem-loops, their predicted translational start sites are often positioned in the apex of the loop. Gel electrophoresis results support the linear, 28-kb monomeric conformation of the P. magna mitochondrial genome. Analyses of other Polytomella taxa suggest that palindromic mitochondrial genes were present in the ancestor of the Polytomella lineage and lost or retained to various degrees in extant species. The possible origins and consequences of this bizarre genomic architecture are discussed.