Clay-enhanced DNA separation in low-molecular-weight poly(N,N-dimethylacrylamide) solution by capillary electrophoresis

Atomic structure and surface defects at mineral-water interfaces probed by in situ atomic force microscopy

Atomic scale details of surface structure play a crucial role for solid-liquid interfaces. While macroscopic characterization techniques provide averaged information about bulk and interfaces, high resolution real space imaging reveals unique insights into the role of defects that are believed to dominate many aspects of surface chemistry and physics. Here, we use high resolution dynamic Atomic Force Microscopy (AFM) to visualize and characterize in ambient water the morphology and atomic scale structure of a variety of nanoparticles of common clay minerals adsorbed to flat solid surfaces. Atomically resolved images of the (001) basal planes are obtained on all materials investigated, namely gibbsite, kaolinite, illite, and Na-montmorillonite of both natural and synthetic origin. Next to regions of perfect crystallinity, we routinely observe extended regions of various types of defects on the surfaces, including vacancies of one or few atoms, vacancy islands, atomic steps, apparently disordered regions, as well as strongly adsorbed seemingly organic and inorganic species. While their exact nature is frequently difficult to identify, our observations clearly highlight the ubiquity of such defects and their relevance for the overall physical and chemical properties of clay nanoparticle-water interfaces.

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).

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.

Nanoparticle-filled capillary electrophoresis for the separation of long DNA molecules in the presence of hydrodynamic and electrokinetic forces

We report the analysis of long DNA molecules by nanoparticle-filled capillary electrophoresis (NFCE) under the influences of hydrodynamic and electrokinetic forces. The gold nanoparticle (GNP)/polymer composites (GNPPs) prepared from GNPs and poly(ethylene oxide) were filled in a capillary to act as separation matrices for DNA separation. The separations of lambda-DNA (0.12-23.1 kbp) and high-molecular-weight DNA markers (8.27-48.5 kbp) by NFCE, under an electric field of -140 V/cm and a hydrodynamic flow velocity of 554 microm/s, were accomplished within 5 min. To further investigate the separation mechanism, the migration of lambda-DNA was monitored in real time using a charge-coupled device (CCD) imaging system. The GNPPs provide greater retardation than do conventional polymer media when they are encountered during the electrophoretic process. The presence of interactions between the GNPPs and the DNA molecules is further supported by the fluorescence quenching of prelabeled lambda-DNA, which occurs through an energy transfer mechanism. Based on the results presented in this study, we suggest that the electric field, hydrodynamic flow, and GNPP concentration are the three main determinants of DNA separation in NFCE.

Nanomaterials and chip-based nanostructures for capillary electrophoretic separations of DNA

Capillary electrophoresis (CE) and microchip capillary electrophoresis (MCE) using polymer solutions are two of the most powerful techniques for the analysis of DNA. Problems, such as the difficulty of filling polymer solution to small separation channels, recovering DNA, and narrow separation size ranges, have put a pressure on developing new techniques for DNA analysis. In this review, we deal with DNA separation using chip-based nanostructures and nanomaterials in CE and MCE. On the basis of the dependence of the mobility of DNA molecules on the size and shape of nanostructures, several unique chip-based devices have been developed for the separation of DNA, particularly for long DNA molecules. Unlike conventional CE and MCE methods, sieving matrices are not required when using nanostructures. Filling extremely low-viscosity nanomaterials in the presence and absence of polymer solutions to small separation channels is an alternative for the separations of DNA from several base pairs (bp) to tens kbp. The advantages and shortages of the use of nanostructured devices and nanomaterials for DNA separation are carefully addressed with respect to speed, resolution, reproducibility, costs, and operation.

Advanced polymers for DNA separation

Recent research to improve matrices for DNA separation has resulted in the development of advanced polymers for use in capillary electrophoresis and, more generally, for electrophoresis in microchannels. To date, the most commonly used matrix is linear polyacrylamide (LPA). Unfortunately, the high-molecular weight LPA solutions required for achieving good resolution lead to very viscous solutions. Moreover, the coating ability of LPA is very poor. For these reasons, many research groups have developed low-viscosity matrices, which make microchannel filling easier, and self-coating matrices, which are able to reduce efficiently the electro-osmotic flow and the interaction of DNA with the capillary wall. To this purpose, thermo-adjustable viscosity polymers represent a very clever and interesting class of matrices.

Effects of metal ions on concentration of DNA in high-conductivity media by capillary electrophoresis

On-line concentration and separation of DNA prepared in low- or high-conductivity media has been demonstrated using poly(ethylene oxide) (PEO) solution in the presence of electroosmotic flow. DNA fragments migrating against EOF stacked at the boundary between the sample zone and PEO solutions, mainly because of sieving and increases in the viscosity. Unlike conventional methods, the large DNA fragments were detected earlier toward the cathode end in this study. The limit of detection (LOD) at a signal-to-noise ratio=3 for phiX174 RF DNA-Hae III digest prepared in 50 mM Tris-borate, pH 10.0, was down to 0.171 ng/ml, with an 860-fold improvement (compared to that obtained by 10-s injection at 25 V/cm) in the sensitivity, when injecting about 2.58 microl. By applying a short plug (2.3 cm) of 0.5 mM AgNO3 prepared in 1.5% PEO solution after sample injection, the analysis of up to 0.75 microl DNA prepared in phosphate-buffered saline (PBS) has been carried out without any tedious desalting processes. This results in an LOD of 6.86 ng/ml for the DNA sample and a 155-fold improvement in the sensitivity. Moreover, this method has allowed the analysis of 0.75 micro] of polymerase chain reaction products amplified after 18 cycles with good reproducibility.

Functional materials for microscale genomic and proteomic analyses

The design of functional materials for genomic and proteomic analyses in microscale systems has begun to mature, from materials designed for capillary-based electrophoresis systems to those tailored for microfluidic-based or 'chip-based' platforms. In particular, recent research has focused on evaluating different polymer chemistries for microchannel surface passivation and improved DNA separation matrix performance. Additionally, novel bioconjugate materials designed specifically for electrophoretic separations in microscale channels are facilitating new separation modalities.