Adsorption Behavior Of DNA Research Articles

Studies of the interactions mechanism between DNA and silica surfaces by Isothermal Titration Calorimetry

DNA and RNA (or miRNA) are potential biomarkers that could be applied to the diagnosis and treatment of diseases as liquid biopsy toward precision medicine. However, the quantitative detections of the nucleic acid from the liquid sample will be dependent on a well-defined and qualified nucleic acid extraction as sample preparation for the detections/measurements. For nucleic acid extraction, most of the commercial kits rely on silica adsorption as one of the major steps for purification. Unfortunately, the lack of knowledge of the binding mechanism of using silica as an adsorbent for nucleic acids limits the improvements and applications. This study is aiming to explore the adsorption mechanism by adsorption isotherm measurements and thermodynamics information obtained by isothermal titration calorimetry (ITC). This work demonstrates that the mechanistic aspects underlying the adsorption behaviors of DNA with mesoporous silica particles in aqueous solution. We changed the binding parameters, such as pH values, ionic strength, and types of salt and concentrations. We established the adsorption isotherms and measured the binding enthalpy and entropy by ITC at any given binding condition. The elucidated mechanism could provide a better binding condition design for nucleic acid purification and liquid biopsy applications in detection and data transferability.

Modulation of membrane properties by DNA in liposomes: A spectroscopic study.

Liposome mediated DNA transport possesses a number of preventing diseases in clinical trials, thus, the study of interaction between DNA and liposomes has become a hot research direction. In this paper, the adsorption behavior of DNA onto two representative lipids had been studied by the fluorescence spectrum measurement, Ultraviolet absorption spectrum and Langmuir-Blodgett technology. The results of fluorescence spectrum measurement indicated that the fluorescence liposomes were quenched statically by DNA at all three temperatures. Thermodynamic analysis displayed that the intermolecular forces between DNA and liposomes were van der Waals forces and Hydrogen bonding. The experimental results of Ultraviolet absorption spectrum and Langmuir-Blodgett technology further verified these mechanisms. This work provides useful theoretical basis for the development of novel DNA delivery materials.

Adsorption behavior of DNA on phosphatidylcholine at the air-water interface

In this paper, the adsorption behavior of DNA on 1,2-dipalmitoyl-sn-glycero-3- phosphocholine (DPPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) mixed lipid monolayers had been studied at the air-water interface through the surface pressure-area curves (π-A), adsorption curves (π/π0-t), excess mean area (∆Aexc), excess Gibbs free energy (∆Gex) and the atomic force microscopy (AFM). π-A isotherms showed that the curves moved to larger mean molecular area after DNA added into subphase, however, the curves shifted to smaller mean molecular area when the concentration of DNA was higher than 1.2 μg/mL. The result of adsorption curves indicated that DNA molecules were spread by combining with polar head groups of lipids except the concentration of DNA was 0.4 μg/mL. ∆Aexc and ∆Gex demonstrated that DNA enlarged the interval between DPPC and POPC, and the strongest position happened at the concentration of DNA was 1.2 μg/mL. These phenomena might be the steric hindrance between DNA molecules. Morphology of surface observed by AFM was agreement with the results above, which verified our conclusion from a more intuitive aspect. This work provides useful theoretical basis for the development of novel DNA delivery materials.

Adsorption behaviors of DNA by modified magnetic nanoparticles: Effect of spacer and salt

Abstract The isolation of nucleic acid is an essential operation before biochemical and diagnostic processes. Here the adsorption of plasmid DNA and salmon sperm DNA on amine magnetic nanoparticles coated with ligand acridine orange was investigated. Spacers such as 6-bromohexanoic acid, 4-bromobutyric acid, and 2-bromoacetic acid were used to facilitate connection between the magnetic nanoparticles and acridine orange. We carried out adsorption mechanism with a study of adsorption isotherm and adsorption kinetics to find out the strong evidence for the influence of electrostatic and intercalating forces which enhance the DNA separation efficiency. The modified magnetic nanoparticles (MNPs) were characterized using TEM, SQUID, Zeta potential and FTIR. The maximum adsorption capacity of acridine orange modified MNPs using the 6-bromohexanoic acid as the spacer for plasmid DNA was found to be 181.1 μg mg−1. The addition of 0.5 M CaCl2 in the solution could further enhance the adsorption capacity to 335.8 μg mg−1. The adsorption isotherms and kinetics fitted well to the Langmuir model and the pseudo-first-order model. The acridine orange modified MNPs exhibited very short equilibrium time (2 min) for the adsorption of plasmid DNA and salmon sperm DNA. The facile method could facilitate the development of simple and fast separation of nucleic acid.

Polyethyleneimine–iron phosphate nanocomposite as a promising adsorbent for the isolation of DNA

A polyethyleneimine (PEI)–iron phosphate (FePO4) nanocomposite is prepared by immobilization of PEI onto the surface of FePO4 nanoparticles via electrostatic interaction. The obtained PEI–FePO4 nanocomposites are spherical with a size centered in ca. 100nm. They provide a novel adsorbent for the solid-phase extraction of DNA from complex sample matrices. At pH 4, 50μgmL−1 of DNA (salmon sperm DNA sodium salt) in 1.0mL aqueous solution are quantitatively adsorbed (100%) by 2mg of the PEI–FePO4 nanocomposites, and meanwhile the coexisting albumin at a same concentration level is not retained, demonstrating the favorable selectivity of the nanocomposites to DNA against proteins. The adsorption behaviors of DNA onto the PEI–FePO4 nanocomposites fit Langmuir model, corresponding to an adsorption capacity of 61.88mgg−1. The adsorbed DNA could be readily recovered by using a 0.04molL−1 Britton–Robinson (BR) buffer at pH 10, resulting in a recovery of 85%. The nanocomposites have been further used for the isolation of DNA from a series of real sample matrices, including synthetic λ-DNA sample, human whole blood and Escherichia coli cell lysate. The extraction efficiency and the purity of the recovered DNA are at least comparable to those achieved by using the reported sorbent materials or commercial kits. In addition, the DNAs isolated from human whole blood and E. coli cell lysate are of high quality, which have been further demonstrated by using them as templates for successful PCR amplifications.

Adsorption behavior of DNA onto a cationic surfactant monolayer at the air–water interface

This communication reports the adsorption of DNA to the preformed Langmuir monolayer of cationic surfactant Octadecylamine (ODA) at the air–water interface and thereby formation of ODA/DNA complex monolayer at the interface. Effect of concentration of DNA in the subphase as well as subphase pH on the adsorption of DNA onto ODA monolayer assemblies have been studied by monitoring the change in surface pressure of ODA/DNA complex monolayer as a function of time. The complex monolayer was also transferred onto solid substrate to prepare ODA/DNA Langmuir–Blodgett films which were analyzed by UV–vis absorption, ATR–FTIR spectroscopic techniques. The most significant observations is that the extent of interactions between ODA and DNA at the air–water interface increases with increasing concentration of DNA in the subphase and also subphase pH. At higher pH, hydrophobic interaction dominates over electrostatic interaction between DNA and ODA in the aqueous subphase. DNA immobilized in the backbone of ODA lies almost flat or extended onto solid substrate at neutral pH whereas, they lie aggregated and compacted coil rather than flat when adsorbed from high pH namely, 11.5 of the subphase. This was confirmed by atomic force microscopy of these complex LB films onto solid substrate.

Unusual DNA Structures Formed on Bare Highly Oriented Pyrolytic Graphite Surfaces Studied by Atomic Force Microscopy

It is important to know the detailed DNA structure on carbonaceous surfaces for further application of DNA-functionalized carbonaceous materials in diverse research areas. In this study, the topographic and structural characteristics of the separated single DNA molecules and their assembly on highly oriented pyrolytic graphite (HOPG) surfaces have been investigated by atomic force microscopy (AFM). AFM results indicate that both circular and linear DNA molecules tend to form hexagonal patterns along with some unusual structures that include node, protrusion, cruciform, parallel single-stranded DNA (ssDNA), and compact zigzag. Furthermore, parallel ssDNA patterns and their crossed structures have been obtained under high-temperature conditions. Our AFM results reveal that a bare HOPG surface can induce DNA molecules to form various unusual structures. This finding is helpful for understanding the adsorption behavior of DNA on other carbonaceous surfaces such as carbon nanotubes and graphene. In addition, the hexagonal DNA patterns in this study are similar to those formed on the alkylamine-modified HOPG surface, which implies that a bare HOPG, without any chemical modification, has a strong ability to align biomolecules. This study could expand our knowledge of the diversities of DNA structures and the aligning ability of carbonaceous surfaces.

Study on the Adsorption Mechanism of DNA with Mesoporous Silica Nanoparticles in Aqueous Solution

Among the numerous adsorption strategies for DNA adsorption into mesopores, the salt-solution-induced adsorption method has a great application potential in nucleic acids science; thus, it is important to understand the adsorption mechanism. This work demonstrates the mechanistic aspects underlying the adsorption behaviors of DNA with mesoporous silica nanoparticles (MSNs) in aqueous solution. The driving forces for the adsorption process can be categorized into three parts: the shielded electrostatic force, the dehydration effect, and the intermolecular hydrogen bonds. Compared to the adsorption behaviors of DNA with a solid silica nanosphere, we find some unique features for DNA adsorption into the mesopores, such as increasing the salt concentration or decreasing the pH value can promote DNA adsorption into the mesoporous silica. Further analysis indicates that the entrance of DNA into mesopores is probably controlled by the Debye length in solution and DNA can generate direct and indirect hydrogen bonds in the pores with different diameters. The following desorption study depicts that such types of hydrogen bonds result in different energy barriers for the desorption process. In summary, our study depicts the mechanism of DNA adsorption within mesopores in aqueous solution and sets the stage for formulating MSNs as carriers of nucleic acids.

Stereoselective Interaction between DNA and Stable Chiral Surfaces Modified with 1,2-Diphenylethylenediamine Enantiomers

This work described an interesting phenomenon of the stereoselective adsorption behaviors of DNA on stable chiral surfaces which were modified with 1,2-diphenylethylenediamine enantiomers on gold electrodes. The modification process and electrochemical characterization of the chiral surfaces were measured by cyclic voltammetry (CV). The stereoselective adsorption behaviors of DNA on the two chiral surfaces were investigated via atomic force microscopy (AFM), CV, electrochemical impedance spectroscopy (EIS) and quartz crystal microbalance (QCM). All results confirmed that (1R,2R)-1,2-diphenylethylenediamine modified surface had stronger interaction with DNA molecules than (1S,2S)-1,2-diphenylethylenediamine modified surface, and the chirality of the surfaces created an different effect on the morphology and adsorption quantity of DNA.

Characterization of chitosan nanofiber fabric by electrospray deposition: Electrokinetic and adsorption behavior

Cationic biopolymer nanofiber fabrics were prepared from a chitosan/poly(ethylene oxide) blend solution by electrospray deposition. Their electrokinetic properties and DNA adsorption behavior were analyzed as a function of pH. The zeta potential was determined from streaming potential/streaming current measurements. The adsorption of DNA onto the fabrics was investigated by spectrophotoscopy. The adsorption behavior of DNA correlated well with the electrokinetic properties of the fabrics. This revealed that the electrokinetic approach was a useful option for characterization of novel nanofiber assemblies made by the electrostatic spray process. In addition, these results provided fundamental information about chitosan nanofiber fabrics for both biomedical and analytical applications.

Adsorption of Duplex DNA on Mesoporous Silicas: Possibility of Inclusion of DNA into Their Mesopores

It is well known that a silica surface cannot adsorb duplex DNA in common aqueous solution (not chaotropic solution) because of the electrostatic repulsion of the silica surface and polyanionic DNA. However, we recently found that when duplex DNA in phosphoric acid form (or in acidic solution) was used, DNA was successfully adsorbed into mesoporous silicas even in low-salt aqueous solution. The adsorption behaviors of DNA into mesoporous silicas were influenced by the pore diameter sizes. Mesoporous silicas with 2.80- or 3.82-nm peak pore diameters adsorbed DNA the best in diluted NaCl solution. Formation of the hydrogen bond between P(O)OH groups in DNA and adsorbed water, SiOH groups, or both on silica surfaces is regarded as a main factor in this adsorption. The coincidence of the pore sizes and DNA diameter realizes this unique adsorption promoted by the effect of encompassing DNA with the inner surface of mesoporous silica. Although there is no clear direct evidence for including duplex DNA in the mesopores yet, this adsorption technique is expected to provide a new tool for DNA science, because DNA in the pore size 2-5 nm in diameter has to be in unusual disentangled thread form.

Adsorption Behavior of DNA onto Self-assembled Monolayer Containing Intercalator

We synthesized an unsymmetric disulfide containing an anthryl group, which can form a self-assembled monolayer (SAM) on a gold surface, to immobilize DNA onto the gold surface through the intercalation between DNA and anthryl groups. A surface plasmon resonance (SPR) measurement indicates that the SAM can detect DNA efficiently at a liquid-solid interface.