Sieving of double-stranded DNA during agarose gel electrophoresis

Spontaneous and Electrically Induced Anisotropy of Composite Agarose Gels

Agarose gels containing and not bacteriorhodopsin purple membranes (incorporated before gelling) manifest spontaneous optical anisotropy. The dependencies of the anisotropy on the agarose concentration and time have been studied. The rise in the anisotropy is explained by the predominant orientation of the agarose fibers during the gelling and subsequent deformation of the gel net. In the electric field, additional optical anisotropy rises, which is caused by the orientation of the membranes. A procedure has been developed to separate electrically induced and spontaneous anisotropy in composite gels. The isoelectric points and surface electric potential of bacteriorhodopsin trimer and purple membranes are calculated by the method of protein electrostatics to explain their electric asymmetry, which leads to perpendicular orientation in the direct electric field and longitudinal in the kilohertz sinusoidal field. The results allow for an increase in the separation capability of composite gels of electrophoresis for macromolecules with different sizes by applying an appropriate electric field to modulate the effective pore size.

Western Agarose Native GeELution (WANGEL) with beta-amyloid and tau: Novel method to elute proteins or peptides using native agarose gels followed by Lumipulse assay

Alzheimer´s disease is characterized by hyperphosphorylated tau neurofibrillary tangles and beta-amyloid plaques. Both molecules can be easily measured in human fluids or tissue extracts by immunoassays. However, the different molecular weight species can only be differentiated on Western Blot gels. Analysis of native proteins from polyacrylamide gels is also not well characterized. Hence, we developed a modified method to elute proteins or peptides from native agarose gels. Initially, full-length tau (60 kDa) and beta-amyloid(42) (4 kDa) were separated on a Western Blot gel and eluted from native agarose gels (WANGEL) using an elution system inside a polypropylene tube. The eluates were analyzed with the Lumipulse immunoassay. Both molecules were successfully eluted into 1% agarose gels to the cathode and were detected in the eluate. Additionally, tau was eluted from mouse cortical extracts, but was below the detection limit when eluted from human cerebrospinal fluid. Beta-amyloid(40) was eluted from CSF extracts and detected by Lumipulse. In cortical extracts taken from transgenic mice (APP_SweDI) beta-amyloid(42) was detectable as a native peptide and small oligomeric aggregates. Taken together, our novel WANGEL method enables fast, easy and cheap elution of protein/peptides from polyacrylamide/agarose gels with a subsequent analysis by Lumipulse immunoassay.

Three bullet points:•

Beta-amyloid and tau are major hallmarks in Alzheimer´s disease and are established cerebrospinal fluid biomarkers.

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Lumipulse is a method to measure beta-amyloid and tau in cerebrospinal fluid in the pg/mL range.

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Western Blot and our novel combined native agarose method (WANGEL) allows an easy and fast determination of the molecular size in combination with Lumipulse.

Highly Stable, Nondestructive, and Simple Visualization of Latent Blood Fingerprints Based on Covalent Bonding Between the Fluorescent Conjugated Polymer and Proteins in Blood

Latent blood fingerprints (LBFPs) can provide critical information of foul play and help identify the suspects at violent crime scenes. The current methods for LBFP visualization are still not satisfactory because of the low sensitivity or complicated protocol. This study demonstrates a simple and effective LBFP visualization strategy by integrating a new amphiphilic fluorescent amino-functionalized conjugated polymer with the cotton-pad developing protocol. LBFPs on various substrates are visualized by simply covering them with the polymer solution-soaked cotton pads. The images display clear fingerprint patterns, ridge details, and sweat pores, even on very challenging substrates such as painted wood and multicolored can. The gray value analysis confirms semiquantitatively the enhancement of the contrast between ridges and furrows. Even LBFPs with various contaminations or aged for more than 600 days are effectively developed and visualized. The developed fingerprint images show superior stability over long storage time and against solvent washing. Moreover, the polymer causes no degradation of DNAs in the blood, suggesting the possibility of further DNA profiling and identification after development. The mechanistic investigation suggests that the formation of positive or inverted images can be attributed to the synergistic effects from the affinity between polymer and blood, and the affinity betwen polymer and substrate, as well as the slight quenching of polymer fluorescence by blood. Furthermore, the covalent bonding between the protonated primary amino group and proteins in blood endows the stability of the developed fingerprints. The result rationalizes the molecular design of the fluorescent polymer and sheds new light on the future strategies to effective LBFP visualization in practical applications.

Electromobility of plasmid DNA in tumor tissues during electric field-mediated gene delivery

Interstitial transport is a crucial step in plasmid DNA-based gene therapy. However, interstitial diffusion of large nucleic acids is prohibitively slow. Therefore, we proposed to facilitate interstitial transport of DNA via pulsed electric fields. To test the feasibility of this approach to gene delivery, we developed an ex vivo technique to quantify the magnitude of DNA movement due to pulsed electric fields in two tumor tissues: B16.F10 (a mouse melanoma) and 4T1 (a mouse mammary carcinoma). When the pulse duration and strength were 50 ms and 233 V/cm, respectively, we found that the average plasmid DNA movements per 10 pulses were 1.47 microm and 0.35 microm in B16.F10 and 4T1 tumors, respectively. The average plasmid DNA movements could be approximately tripled, ie to reach 3.69 microm and 1.01 microm, respectively, when the pulse strength was increased to 465 V/cm. The plasmid DNA mobility was correlated with the tumor collagen content, which was approximately eight times greater in 4T1 than in B16.F10 tumors. These data suggest that electric field can be a powerful driving force for improving interstitial transport of DNA during gene delivery.

A computer simulation accounting for dissimilar electrophoretic behavior between two similarly curved DNA fragments due to a difference in arc-length

Arc-shaped bent DNA fragments of the same predicted planar curvature but differing in length by 20% were compared in regard to their mobilities in 3 to 10% polyacrylamide. The longer (155 bp) fragment is retarded far more severely than the shorter (124 bp) fragment. The effect of gel concentration in promoting the retardation is far more pronounced for the 155 bp than for the 124 bp fragment. Moreover, a temperature change from 25 degrees C to 4 degrees C does not substantially affect the gel concentration dependent mobility of the 124 bp fragment while it increases the retardation of the 155 bp fragment greatly. The strong increase in retardation brought about by a mere 20% increase in the length of the arc was accounted for by a simple computer simulation of gel electrophoresis which considered the rate of passage of arc-shaped objects through a two-dimensional array of disc-shaped obstacles. Since the simulation relies exclusively on geometric factors, its success in predicting the behavior of the 124 and 155 bp DNA fragments suggests that geometric factors are largely responsible for their electrophoretic properties. The simulation can account for the strong temperature effect on the retardation of a model of the 155 bp DNA in polyacrylamide gels by showing that a decreased degree of random motion has a profound effect on the modeled 155 bp particle, but not on the modeled 124 bp DNA.

Comparison of properties of agarose for electrophoresis of DNA

Agarose as a medium for separation of DNA was first introduced in 1962 and since the early 1970s agarose submarine gel electrophoresis has been synonymous with separations of DNA molecules larger than 1 kilobase pair (kb). The large pore size, low electroendosmosis and strength of the matrix have advantages over other media such as polyacrylamide for many applications. The variety of grades of agarose, developed by chemical manipulation of the substitutions on the agarose polymer, provides a range of matrices for separation of DNA molecules from a few base pairs (bp) to over 5 megabase pairs (Mb) in length. The introduction of low-melting-temperature agarose has revolutionised the extraction and manipulation of chromosome-sized molecules. On the other hand, the demand for analysis of very small quantities of DNA will most likely lead to the increasing importance of capillary electrophoresis. Many theories have been propounded to explain the electrophoretic migration of DNA in agarose. The most popular of these has been reptation theory but none can account for all of the reported anomalies in migration. However, anomalous migration has been exploited to study DNA structure, topology and catenation. An example of the use of two-dimensional electrophoresis to demonstrate the complexity of DNA migration through agarose is given. Generally, for molecules smaller than 50 kb, electrophoretic separation is a function of length. By alternately electrophoresing DNA in two different directions, molecules as large as 5.7 Mb have been effectively separated, although with such large molecules DNA structure as well as size may determine migration. In the case of separations of chromosomes from the intestinal protozoan, Giardia duodenalis, for example, a discrepancy of 1 Mb in the size of one chromosome, with an apparent size of 0.7-2.0 Mb, depended on the boundary conditions of separation. Major challenges for the molecular biologist are separation of larger chromosomal sized molecules, greater number of samples and smaller formats. Towards this challenge computer-aided technology is a key component in the control of electrophoresis parameters and analysis.

DNA electrophoresis in microlithographic arrays

We have used optical microlithography to fabricate capped quasi-two-dimensional obstacle courses in SiO2. We report here observations using epifluorescence microscopy of the electrophoresis and length fractionation of large DNA molecules confined in arrays. Simple reptation theory, based on the work of deGennes, predicts that at low electric fields the electrophoretic mobility of a polymer of length L much greater than the persistence length p scales inversely with L (ref. 2). But elongation of the coil in the matrix at sufficiently strong electric fields results in a length-independent electrophoretic mobility. The application of suitably timed pulsed electric fields restores the fractionating power of gels for long molecules but the protocols of pulsed-field electrophoresis are semi-empirical because the complex and ill-understood gel matrix plays a critical role in fractionation. Microlithographically constructed obstacle arrays, with their low dimensionality, small volume and extremely reproducible topography, will make it possible to understand the motion and fractionation of large polymer molecules in complex but well characterized topologies.

Apparatus for gel electrophoresis with continuous monitoring of individual DNA molecules by video epifluorescence microscopy

Apparatus for gel electrophoresis with continuous scanning by video epifluorescence microscopy was constructed and applied to measurements on individual DNA molecules in the size range of several hundred kilobase pairs. The gel electrophoresis apparatus comprises a horizontal glass cell and several commercially available components--an epifluorescence microscope, an image intensifier, two video cameras, a monitor, videotape recorder and voltmeter. Data in the form of videotapes can be subsequently analyzed on a computer graphics work station.

Free mobility determination by electrophoresis in polyacrylamide containing agarose at a nonrestrictive concentration

In the determination of the free mobility, related to the surface net charge, by quantitative gel electrophoresis, the previous arbitrary extrapolation of Ferguson plots from the lowest gel concentrations that give a mechanically stable gel to 0% T has recently been replaced by measurement of mobilities across that concentration range, using the addition of 0.5% agarose to polyacrylamide at the various low concentrations in application to a DNA fragment 155 bp in size (Orbán, L. et al., in preparation). The present study applies that approach to several proteins and DNA fragments smaller than 1300 bp, using 0.4% agarose in polyacrylamide gels of varying concentration. The intercepts of the plots with the mobility axis provide experimental data by which the free mobility in polyacrylamide gel electrophoresis can be estimated for molecules not significantly retarded in their migration at the agarose concentration admixed to polyacrylamide. Across the gel concentration range below 3% T, in the presence of agarose, the Ferguson plots of proteins and DNA fragments are convex. It was shown by mass spectrometry that this convex curvature of the plots in the mixed polymer is not significantly due to low polymerization efficiency in the concentration range of liquid polyacrylamide (below 3%T).

Information on DNA conformation derived from the Ferguson plot of DNA fragments of up to 9 kb in size, using polyacrylamide gel electrophoresis in a discontinuous buffer system

The Ferguson plot in polyacrylamide gel electrophoresis (PAGE)(15%CDATD, moving boundary electrophoresis buffer system operative at pH 8.9, 4 degrees C, 8 mA/cm2 of gel) of DNA fragments up to 9.4 kb in size was found to exhibit a linear segment at polyacrylamide concentrations starting at 3% T and undergoing a gradual transition into a concave segment at higher gel concentrations, confirming previous findings by Stellwagen. The larger the DNA, and the higher the gel concentration, the less extended the linear and the more extended the concave segment of the plot. The lowest % T of the linear range for DNA in polyacrylamide remains unknown since mobilities at nongelling concentrations below 3% T have not as yet been measured. As previously suggested, the transition from the linear to the concave segment corresponds to that from the randomly oriented DNA to the anisotropically stretched, "reptating" DNA. For a DNA of 9.4 kb in size, the end of the linear range of the Ferguson plot can be extended from 3.5 to 5% T when 15% DATD rather than 2.5% Bis is used to crosslink the polyacrylamide. Increasing the temperature of PAGE from 4 degrees C to 25 and 50 degrees C widens the linear segment progressively, indicating an increasingly random orientation with rising temperature. When current density is increased from 8 to 40 mA/cm2, the concave curvature of the Ferguson plot of DNA 1 to 9.4 kb in size decreases, suggesting a transition from a "reptating" to a randomly distributed molecule, due to increased Joule heat.(ABSTRACT TRUNCATED AT 250 WORDS)