Effects of novel quasi-interpenetrating network/gold nanoparticles composite matrices on DNA sequencing performances by CE

Gold nanoparticles (GNPs) with particle sizes of about 20, 40, and 60 nm were prepared and added into a quasi-interpenetrating network (quasi-IPN) composed of linear polyacrylamide (LPA) with different viscosity-average molecular masses of 1.5, 3.3, and 6.5 MDa and poly-N,N-dimethylacrylamide (PDMA) to form polymer/metal composite matrices, respectively. These novel matrices could improve ssDNA sequencing performances due to interactions between GNPs and polymer chains and the formation of physical cross-linking points as demonstrated by intrinsic viscosities and glass transition temperatures. The effects of the parameters in relation to quasi-IPN/GNPs matrices, such as GNP contents, GNP particle sizes, LPA molecular masses, and solution concentrations, on ssDNA sequencing performances were studied. In the presence of GNPs, the separation had the advantages of high resolution, speediness, excellent reproducibility, long shelf life and easy automation. Therefore, less viscous matrix solutions (with moderate size GNPs) due to lower solution concentration and lower-molecular-mass LPA could be used to replace more viscous solutions (without GNPs) due to higher solution concentration or higher-molecular-mass LPA to separate DNA, while the sieving performances were approximate even higher, which helped to achieve full automation especial for capillary array electrophoresis (CAE) and microchip electrophoresis (MCE).     

Nanogels as Pharmaceutical Carriers: Finite Networks of Infinite Capabilities

Nanogels are swollen nanosized networks composed of hydrophilic or amphiphilic polymer chains. They are developed as carriers for the transport of drugs, and can be designed to spontaneously incorporate biologically active molecules through formation of salt bonds, hydrogen bonds, or hydrophobic interactions. Polyelectrolyte nanogels can readily incorporate oppositely charged low‐molecular‐mass drugs and biomacromolecules such as oligo‐ and polynucleotides (siRNA, DNA) as well as proteins. The guest molecules interact electrostatically with the ionic polymer chains of the gel and become bound within the finite nanogel. Multiple chemical functionalities can be employed in the nanogels to introduce imaging labels and to allow targeted drug delivery. The latter can be achieved, for example, with degradable or cleavable cross‐links. Recent studies suggest that nanogels have a very promising future in biomedical applications.     

Self-Assembled Cationic Polypeptide Supramolecular Nanogels for Intracellular DNA Delivery

Supramolecular nanogels are an emerging class of polymer nanocarriers for intracellular delivery, due to their straightforward preparation, biocompatibility, and capability to spontaneously encapsulate biologically active components such as DNA. A completely biodegradable three-component cationic supramolecular nanogel was designed exploiting the multivalent host-guest interaction of cyclodextrin and adamantane attached to a polypeptide backbone. While cyclodextrin was conjugated to linear poly-L-lysine, adamantane was grafted to linear as well as star shaped poly-L-lysine. Size control of nanogels was obtained with the increase in the length of the host and guest polymer. Moreover, smaller nanogels were obtained using the star shaped polymers because of the compact nature of star polymers compared to linear polymers. Nanogels were loaded with anionic model cargoes, pyranine and carboxyfluorescein, and their enzyme responsive release was studied using protease trypsin. Confocal microscopy revealed successful transfection of mammalian HeLa cells and intracellular release of pyranine and plasmid DNA, as quantified using a luciferase assay, showing that supramolecular polypeptide nanogels have significant potential in gene therapy applications.     

Hybrid nanogels with physical and chemical cross-linking structures as nanocarriers

Polymerizable nanogels were prepared by self-assembly of cholesteryl group-bearing pullulan (CHP) with methacryloyl groups (CHPMA). The CHPMA nanogel was polymerized with 2-methacryloyloxyethyl phosphorylcholine (MPC) by radical polymerization in dilute aqueous solution. The solution properties of the polymers in water were investigated by TEM, SEC-MALS, and fluorescence quenching technique. Monodispersed hybrid nanogels of CHPMA-MPC (CM nanogels) (25-30 nm in radius of gyration) were obtained by using CHPMA nanogel as a seed-nanogel. CM nanogels have a dual cross-linking structure that is physically cross-linked with the cholesteryl groups and chemically cross-linked with the MPC polymer chains. CM nanogels trap heat-denatured carbonic anhydrase B (CAB) and prevent their aggregations. The nanogels maintained the ability of trapping and releasing enzymes by host-guest interaction of cholesteryl group and cyclodextrin.     

Gradient polymer networks formed by photopolymerization with self‐floating polysiloxane‐containing nanogel

Polysiloxane‐containing nanogels can be used as a fast, convenient and environmentally friendly method to control gradient photopolymerization and to obtain gradient polymer network because of its self‐floating feature. The chain length of polysiloxane is a key factor that influences the self‐floating capability of the polysiloxane‐containing nanogel. This paper reports a series of nanogels compositions synthesized with methacrylate‐modified polysiloxanes with different chain lengths, urethane dimethacrylate (UDMA) and isobornyl methacrylate (IBMA) at a molar ratio of 10:20:70 in the presence of a thiol chain transfer agent. The effect of polysiloxane chain length on self‐floating capability of the nanogel and gradient polymer network was researched. The results show that polysiloxane chain length is the main driving force for the self‐floating capability of the nanogels. The nanogel with long polysiloxane chain length exhibits good self‐floating capability in the monomer–polymer matrix because of the lower surface tension of polysiloxane. Furthermore, the gradient polymer network containing the nanogel with long polysiloxane chain length presents lower dispersion surface energy and greater hardness and thermostability. Copyright © 2016 John Wiley & Sons, Ltd.     

Divergent dispersion behavior of ssDNA fragments during microchip electrophoresis in pDMA and LPA entangled polymer networks

Resolution of DNA fragments separated by electrophoresis in polymer solutions ("matrices") is determined by both the spacing between peaks and the width of the peaks. Prior research on the development of high-performance separation matrices has been focused primarily on optimizing DNA mobility and matrix selectivity, and gave less attention to peak broadening. Quantitative data are rare for peak broadening in systems in which high electric field strengths are used (>150 V/cm), which is surprising since capillary and microchip-based systems commonly run at these field strengths. Here, we report results for a study of band broadening behavior for ssDNA fragments on a glass microfluidic chip, for electric field strengths up to 320 V/cm. We compare dispersion coefficients obtained in a poly(N,N-dimethylacrylamide) (pDMA) separation matrix that was developed for chip-based DNA sequencing with a commercially available linear polyacrylamide (LPA) matrix commonly used in capillaries. Much larger DNA dispersion coefficients were measured in the LPA matrix as compared to the pDMA matrix, and the dependence of dispersion coefficient on DNA size and electric field strength were found to differ quite starkly in the two matrices. These observations lead us to propose that DNA migration mechanisms differ substantially in our custom pDMA matrix compared to the commercially available LPA matrix. We discuss the implications of these results in terms of developing optimal matrices for specific separation (microchip or capillary) platforms.     

Novel quasi-interpenetrating network/gold nanoparticles composite matrices for DNA sequencing by CE

In order to further improve ssDNA sequencing performances using quasi-interpenetrating network (quasi-IPN) as a matrix composed of linear polyacrylamide (LPA) with lower viscosity-average molecular mass (3.3 MDa) and poly(N,N-dimethylacrylamide) (PDMA), gold nanoparticles (GNPs) were prepared and added into this quasi-IPN to form polymer/metal composite sieving matrices. The studies of intrinsic viscosity and differential scanning calorimetry (DSC) on quasi-IPN and quasi-IPN/GNPs indicate that there were interactions between GNPs and polymer chains. The sequencing performances on ssDNA using quasi-IPN and quasi-IPN/GNPs (with different GNPs concentrations) as sieving matrices were studied and compared by CE at different temperatures. The results show that resolutions of quasi-IPN/GNPs were higher than those of quasi-IPN without GNPs and approximated those of quasi-IPN composed of LPA with higher MW (6.5 MDa) and PDMA without GNPs in the bare fused-silica capillaries. Furthermore, the sequencing time of quasi-IPN/GNPs was shorter than that of quasi-IPN under the same sequencing conditions. The influences of GNPs and sequencing temperature on the sequencing performances of ssDNA were also discussed. The separation reproducibility of quasi-IPN/GNPs solution was excellent and its shelf life was more than 8 months.     

Geometrical characteristics of polyelectrolyte nanogel particles and their polyelectrolyte complexes studied by dynamic and static light scattering

The geometric characteristics of nanogel particles in aqueous solutions were studied by determining their ratios of radius of gyration (mean-square radius; Rg) to hydrodynamic radius (Rh), Rg/Rh, derived from static light scattering and dynamic light scattering experiments, respectively. The various nanogel samples studied included ones composed of lightly cross-linked N-isopropylacrylamide (NIPA) polymer, NIPA-based anionic or cationic copolymers, and amphoteric terpolymers. Polyelectrolyte complexes between anionic or cationic nanogels and oppositely charged polyions or nanogels having opposite charges were also studied. Most NIPA and NIPA-based polyelectrolyte nanogels in a swollen state had Rg/Rh values >0.775, which is the theoretically predicted value for a solid sphere. In a collapsed state, one may expect nanogel particles to be spherical in shape; however, this was not the case for a variety of nanogel samples, either with or without charges. These data were consistent with the idea that the surfaces of these nanogel particles were decorated with attached dangling chains. The Rg/Rh data from polyelectrolyte-nanogel complexes, however, indicated different structures from this. It was found that most of the polyelectrolyte-nanogel complex particles had Rg/Rh approximately 0.775. This suggested that the complexed nanogel particles were spherical in shape and that there were no dangling surface chains.     

A novel thermo-sensitive nanogel composing of poly(<Emphasis Type="Italic">N</Emphasis>-isopropylacrylamide) grafted onto alginate-modified graphene oxide for hydrophilic anticancer drug delivery

Nanogels have been demonstrated to be desirable for hydrophilic anticancer drug delivery. This study presents a novel nanogel consisting of sodium alginate-modified graphene oxide (SA-GO) and N-isopropylacrylamide (NIPAM) for sustained delivery of doxorubicin (DOX) drug. The PNIPAM/SA-GO nanogel was studied by various techniques including scanning electron microscopy, atomic force microscopy, dynamic light scattering, Fourier transform infrared spectroscopy, and thermo-gravimetric analysis. Subsequently, the thermo-responsive behavior of the PNIPAM/SA-GO nanogel was investigated by UV–Vis spectroscopy. DOX was successfully loaded into the PNIPAM/SA-GO nanogel in order to study entrapment efficiency and drug release behavior. Moreover, biocompatibility of the DOX-loaded PNIPAM/SA-GO nanogel was examined against Hella cells and was compared with free PNIPAM/SA-GO nanogel and DOX. This work offers that the nanogels could be developed further as an effective bioactive molecule delivery system.     

Interpenetrating polymer network (IPN) nanogels based on gelatin and poly(acrylic acid) by inverse miniemulsion technique: synthesis and characterization

Novel interpenetrating polymer network (IPN) nanogels composed of poly(acrylic acid) and gelatin were synthesised by one pot inverse miniemulsion (IME) technique. This is based on the concept of nanoreactor and cross-checked from template polymerization technique. Acrylic acid (AA) monomer stabilized around the gelatin macromolecules in each droplet was polymerized using ammonium persulfate (APS) and tetramethyl ethylene diamine (TEMED) in 1:5 molar ratio and cross-linked with N,N-methylene bisacrylamide (BIS) to form semi-IPN (sIPN) nanogels, which were sequentially cross-linked using glutaraldehyde (Glu) to form IPNs. Span 20, an FDA approved surfactant was employed for the formation of homopolymer, sIPN and IPN nanogels. Formation of stable gelatin-AA droplets were observed at 2% surfactant concentration. Dynamic light scattering (DLS) and scanning electron microscopy (SEM) studies of purified nanogels showed small, spherical IPN nanogels with an average diameter of 255 nm. In contrast, sIPN prepared using the same method gave nanogels of larger size. Fourier-transform infrared (FT-IR) spectroscopy, SEM, DLS, X-ray photoelectron spectroscopy (XPS) and zeta potential studies confirm the interpenetration of the two networks. Leaching of free PAA chains in sIPN upon dialysis against distilled water leads to porous nanogels. The non-uniform surface of IPN nanogels seen in transmission electron microscopy (TEM) images suggests the phase separation of two polymer networks. An increase of N/C ratio from 0.07 to 0.17 (from PAA gel to IPN) and O/C ratio from 0.22 to 0.37 (from gelatin gel to IPN) of the nanogels by XPS measurements showed that both polymer components at the nanogel surface are interpenetrated. These nanogels have tailoring properties in order to use them as high potential drug delivery vehicles for cancer targeting.     

Characterizing property distributions of polymeric nanogels by size-exclusion chromatography

Nanogels are highly branched, swellable polymer structures with average diameters between 1 and 100nm. Size-exclusion chromatography (SEC) fractionates materials in this size range, and it is commonly used to measure nanogel molar mass distributions. For many nanogel applications, it may be more important to calculate the particle size distribution from the SEC data than it is to calculate the molar mass distribution. Other useful nanogel property distributions include particle shape, area, and volume, as well as polymer volume fraction per particle. All can be obtained from multi-detector SEC data with proper calibration and data analysis methods. This work develops the basic equations for calculating several of these differential and cumulative property distributions and applies them to SEC data from the analysis of polymeric nanogels. The methods are analogous to those used to calculate the more familiar SEC molar mass distributions. Calibration methods and characteristics of the distributions are discussed, and the effects of detector noise and mismatched concentration and molar mass sensitive detector signals are examined.     

Impact of polymer hydrophobicity on the properties and performance of DNA sequencing matrices for capillary electrophoresis

To elucidate the impact of matrix chemical and physical properties on DNA sequencing separations by capillary electrophoresis (CE), we have synthesized, characterized and tested a controlled set of different polymer formulations for this application. Homopolymers of acrylamide and N,N-dimethylacrylamide (DMA) and copolymers of DMA and N,N-diethylacrylamide (DEA) were synthesized by free radical polymerization and purified. Polymer molar mass distributions were characterized by tandem gel permeation chromatography - laser light scattering. Polymers with different chemical compositions and similar molar mass distributions were selected and employed at the same concentration so that the variables of comparison between them were hydrophobicity and average coil size in aqueous solution. We find that the low-shear viscosities of 7% w/v polymer solutions decrease by orders of magnitude with increasing polymer hydrophobicity, while hydrophilic polymers exhibit more pronounced reductions in viscosity with increased shear. The performance of the different matrices for DNA sequencing was compared with the same sample under identical CE conditions. The longest read length was produced with linear polyacrylamide (LPA) while linear poly-N,N-dimethylacrylamide (PDMA) gave approximately 100 fewer readable bases. Read lengths with DMA/DEA copolymers were lower, and decreased with increasing DEA content. This study highlights the importance of polymer hydrophilicity for high-performance DNA sequencing matrices, through the formation of robust, highly-entangled polymer networks and the minimization of hydrophobic interactions between polymers and fluorescently-labeled DNA molecules. However, the results also show that more hydrophobic matrices offer much lower viscosities, enabling easier microchannel loading at low applied pressures.     

Nanogel engineering for new nanobiomaterials: from chaperoning engineering to biomedical applications

Nanosize hydrogels (nanogels) are polymer nanoparticles with three‐dimensional networks, formed by chemical and/or physical cross‐linking of polymer chains. Recently, various nanogels have been designed, with a particular focus on biomedical applications. In this review, we describe recent progress in the synthesis of nanogels and nanogel‐integrated hydrogels (nanogel cross‐linked gels) for drug‐delivery systems (DDS), regenerative medicine, and bioimaging. We also discuss chaperone‐like functions of physical cross‐linking nanogel (chaperoning engineering) and organic‐inorganic hybrid nanogels. © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Published online in Wiley InterScience ( www.interscience.wiley.com ) DOI 10.1002/tcr.201000008     

Biodegradable nanogels prepared by atom transfer radical polymerization as potential drug delivery carriers: synthesis, biodegradation, in vitro release, and bioconjugation

Stable biodegradable nanogels cross-linked with disulfide linkages were prepared by inverse miniemulsion atom transfer radical polymerization (ATRP). These nanogels could be used for targeted drug delivery scaffolds for biomedical applications. The nanogels had a uniformly cross-linked network, which can improve control over the release of encapsulated agents, and the nanogels biodegraded into water-soluble polymers in the presence of a biocompatible glutathione tripeptide, which is commonly found in cells. The biodegradation of nanogels can trigger the release of encapsulated molecules including rhodamine 6G, a fluorescent dye, and Doxorubicin (Dox), an anticancer drug, as well as facilitate the removal of empty vehicles. Results obtained from optical fluorescence microscope images and live/dead cytotoxicity assays of HeLa cancer cells suggested that the released Dox molecules penetrated cell membranes and therefore could suppress the growth of cancer cells. Further, OH-functionalized nanogels were prepared to demonstrate facile applicability toward bioconjugation with biotin. The number of biotin molecules in each nanogel was determined to be 142,000, and the formation of bioconjugates of nanogels with avidin was confirmed using optical fluorescence microscopy.     

Study of matrix and polymer substrate in MALDI-TOF mass spectrometry of DNA

Protein matrices such as 3,5-dimethoxy-4-hydroxycinnamic acid (sinapinic acid, SA) and a-cyano-4-hydroxycinnamic acid (CHCA) tend to yield homogeneous dried spots. However, well known MALDI matrices for single- and double-stranded DNA such as 3-hydroxy picolinic acid (HPA) and picolinic acid (PA) forms the crystals at the rim of their spots with uneven distribution of matrix and DNA. This inhomogeneous deposition of DNA-doped matrix crystals at the MALDI spot requires a search for sweet spots. It is important to obtain homogeneous MALDI spots that yield signals not only from the periphery but the entire spot for automated, high throughput MALDI-TOF analysis of short DNA fragments. We have investigated the characteristics of MALDI matrices for DNA and presented a method for improving the homogeneity of MALDI samples by using polymer substrates such as linear polyacrylamide (LPA), poly(ethylene oxide) (PEO), methyl cellulose (MC) and Nafion.     

Functionalized gold nanoparticles as additive to form polymer/metal composite matrix for improved DNA sequencing by capillary electrophoresis

A new matrix additive, poly (N,N-dimethylacrylamide)-functionalized gold nanoparticle (GNP-PDMA), was prepared by “grafting-to” approach, and then incorporated into quasi-interpenetrating network (quasi-IPN) composed of linear polyacrylamide (LPA, 3.3 MDa) and PDMA to form novel polymer/metal composite sieving matrix (quasi-IPN/GNP-PDMA) for DNA sequencing by capillary electrophoresis. Without complete optimization, quasi-IPN/GNP-PDMA yielded a readlength of 801 bases at 98% accuracy in about 64 min by using the ABI 310 Genetic Analyzer at 50 °C and 150 V/cm. Compared with previous quasi-IPN/GNPs, quasi-IPN/GNP-PDMA can further improve DNA sequencing performances. This is because the presence of GNP-PDMA can improve the compatibility of GNPs with the whole sequencing system, enhance the entanglement degree of networks, and increase the GNP concentration in system, which consequently lead to higher restriction and stability, higher apparent molecular weight (MW), and smaller pore size of the total sieving networks. Furthermore, the composite matrix was also compared with quasi-IPN containing higher-MW LPA and commercial POP-6. The results indicate that the composite matrix is a promising one for DNA sequencing to achieve full automation due to the separation provided with high resolution, speediness, excellent reproducibility, and easy loading in the presence of GNP-PDMA.     

Electrophoretic mobility of linear and star-branched DNA in semidilute polymer solutions

Electrophoresis of large linear T2 (162 kbp) and 3-arm star-branched (N(Arm) = 48.5 kbp) DNA in linear polyacrylamide (LPA) solutions above the overlap concentration c* has been investigated using a fluorescence visualization technique that allows both the conformation and mobility mu of the DNA to be determined. LPA solutions of moderate polydispersity index (PI approximately 1.7-2.1) and variable polymer molecular weight Mw (0.59-2.05 MDa) are used as the sieving media. In unentangled semidilute solutions (c* < c < c(e)), we find that the conformational dynamics of linear and star-branched DNA in electric fields are strikingly different; the former migrating in predominantly U- or I-shaped conformations, depending on electric field strength E, and the latter migrating in a squid-like profile with the star-arms outstretched in the direction opposite to E and dragging the branch point through the sieving medium. Despite these visual differences, mu for linear and star-branched DNA of comparable size are found to be nearly identical in semidilute, unentangled LPA solutions. For LPA concentrations above the entanglement threshold (c > c(e)), the conformation of migrating linear and star-shaped DNA manifest only subtle changes from their unentangled solution features, but mu for the stars decreases strongly with increasing LPA concentration and molecular weight, while mu for linear DNA becomes nearly independent of c and Mw. These findings are discussed in the context of current theories for electrophoresis of large polyelectrolytes.     

DNA Nanogels To Snare Carcinogens: A Bioinspired Generic Approach with High Efficiency

Polycyclic aromatic hydrocarbons (PAHs) are combustion‐related pollutants and are ubiquitous in the environment, including in sources of drinking water. Upon contact with DNA, stable PAH–DNA adducts form rapidly as the first step towards their toxic effects. In this work, we prepared hydrophilic DNA nanogels to exploit this generic complexation process as a biomimetic scavenging method. This approach relies on interaction between PAHs and the complete network that constitutes the water‐swollen nanogels, and is not restricted to interfacial adsorption. Up to 720 μg of PAH per gram of DNA nanogel are taken up, meaning that 1 mg of DNA nanogel is sufficient to purify a liter of water containing the critical PAH concentration for cancer risk (600 ng L^?1). As a result of short diffusion pathways, PAH uptake is rapid, reaching 50 % loading after 15 minutes. Beyond PAHs, DNA nanogels may be useful for the generic detoxification of water containing genotoxins, since most known molecules that strongly associate with DNA are mutagenic.     

DNA sequencing with hydrophilic and hydrophobic polymers at elevated column temperatures

Read length in DNA sequencing by capillary electrophoresis at elevated temperatures is shown to be greatly affected by the extent of hydrophobicity of the polymer separation matrix. At column temperatures of up to 80 degrees C, hydrophilic linear polyacrylamide (LPA) provides superior read length and separation speed compared to poly(N,N-dimethylacrylamide) (PDMA) and a 70:30 copolymer of N,N-dimethylacrylamide and N,N-diethylacrylamide (PDEA30). DNA-polymer and polymer intramolecular interactions are presumed to be a major cause of band broadening and the subsequent loss of separation efficiency with the more hydrophobic polymers at higher column temperatures. With LPA, these interactions were reduced, and a read length of 1000 bases at an optimum temperature of 70 degrees -75 degrees C was achieved in less than 59 min. By comparison, PDMA produced a read length of roughly 800 bases at 50 degrees C, which was close to the read length attained in LPA at the same temperature; however, the migration time was approximately 20% longer, mainly because of the higher polymer concentration required. At 60 degrees C, the maximum read length was 850 bases for PDMA, while at higher temperatures, read lengths for this polymer were substantially lower. With the copolymer DEA30, read length was 650 bases at the optimum temperature of 50 degrees C. Molecular masses of these polymers were determined by tandem gel permeation chromatography-multiangle laser light scattering method (GPC-MALLS). The results indicate that for long read, rapid DNA sequencing and analysis, hydrophilic polymers such as LPA provide the best overall performance.     

Electrophoretic dynamics of large DNA stars in polymer solutions and gels

We have developed a procedure for synthesizing large stable branched DNA structures that enables visualization via fluorescence microscopy. Using this procedure we have synthesized large DNA stars and observed their electrophoretic behavior in polymer solutions and gels. In dilute polyacrylamide solutions, the DNA stars move as random coils and appear to experience only brief collisions with the polymer chains in solution. The effect of polymer solution concentration on the electrophoretic mobility of stars in the dilute regime is found to be in good accord with predictions of the transient entanglement coupling (TEC) model. In semidilute polymer solutions, the star arms extend in the field direction and drag the core through the matrix. The star arms form several U-shaped conformations as they collide and engage with polyacrylamide chains. The U-shaped conformations occasionally evolve into J-shaped conformations as the star arms slide off the matrix chains they engage during electrophoretic migration. In concentrated polymer solutions, the arms of the star extend and form V-shaped structures with the core as the apex. The arms then pull the core through the matrix. These V-shaped conformations are much longer-lived than U-shaped ones and, unlike the latter, do not transform to J-shaped conformations. In polyacrylamide and agarose gels, where matrix entanglements are fixed, DNA stars become trapped when entanglements with matrix molecules prevent the core from being pulled through the matrix by the extended arms. This trapping was observed at all gel concentrations and electric fields studied.