Effect of topological asymmetry on the electrophoretic mobility of branched DNA structures with and without single-base mismatches

The electrophoretic mobility of three-arm star DNA structures with varying degrees of branch length asymmetry has been investigated in polyacrylamide (PAA) hydrogels. We report the effect of single-base mismatches, adjacent to the branch point, on the mobility of branched DNA with three different arm lengths. Branched DNA structures were formed using wild-type and mutated fragments of the p53 tumor suppressor gene, which is believed to play an important role in cancer development. Branching was directed at the site of several previously characterized mutations in exon 7 of p53. At a given gel concentration, the mobility of branched DNA with fully complementary base pairing is found to increase as the degree of branch length asymmetry is increased. Ferguson analysis of the gel electrophoresis data leads to a retardation coefficient that is strongly dependent on topology. This finding can be explained in terms of a minimum molecular cross-section for each molecule. Specifically, we show that structures with the smallest molecular cross-section can access more pores in the gel, which leads to higher mobility. Our results can also be understood by considering the rotational diffusivity of branched DNA. Asymmetric DNA stars with higher calculated rotational diffusivities also have higher mobilities. When a mutated base is present in junctions with low degrees of branch length asymmetry, adjacent to the branch point, the mobility increases in comparison to the fully complementary molecules. The reason for this increased mobility is unclear, here, we propose that the mismatched base introduces additional flexibility to the arm containing the mutation leading to higher conformational freedom and enhanced mobility in gels. When a mismatched base is present in junctions with high degrees of branch length asymmetry, the opposite result is obtained. Here, the mutated species has a lower mobility. This result is argued to arise from incomplete hybridization and/or frayed ends. Finally, we have shown that by using two of the branch point oligonucleotides as probe molecules, mutations known to occur at specific sites can be detected through the mobility shift. If the sequences of the probe chains are changed in a controlled manner, the location and base of the mutant can also be determined.     

Effect of the matrix on DNA electrophoretic mobility

DNA electrophoretic mobilities are highly dependent on the nature of the matrix in which the separation takes place. This review describes the effect of the matrix on DNA separations in agarose gels, polyacrylamide gels and solutions containing entangled linear polymers, correlating the electrophoretic mobilities with information obtained from other types of studies. DNA mobilities in various sieving media are determined by the interplay of three factors: the relative size of the DNA molecule with respect to the effective pore size of the matrix, the effect of the electric field on the matrix, and specific interactions of DNA with the matrix during electrophoresis.     

Effect of matrix chain length on the electrophoretic mobility of large linear and branched DNA in polymer solutions

We study the effect of matrix chain molecular weight Mw and concentration c on the electrophoretic mobility micro of large linear and star-like, branched DNA in polymer solutions. Polyethylene oxide (PEO) with narrow molecular weight distributions form the main focus of this study. For PEO concentrations ranging from one half the overlap concentration, c*, to 3c*, the effective drag coefficient, zeta is identical with (mu0/mu) - 1, satisfies the following approximate scaling relationship, zeta approximately cMw(0.7). Here, mu0 is the electrophoretic mobility in free solution. While the concentration dependence is consistent with predictions from the transient entanglement coupling (TEC) model, the molecular weight dependence is significantly weaker. Although a similar dependence of mobility on Mw can be predicted when nonentangling collisions are the dominant source of drag, a model based on these collisions alone cannot reproduce the experimental observations. We also find that the architecture of large DNA does not affect either the concentration dependence or molecular weight dependence of the electrophoretic mobility.     

Time-resolved electrophoretic analysis of mobility shifts for dissociating DNA ligands

Intercalative binding of ligands to DNA can be demonstrated by helix unwinding, monitored by gel electrophoresis of supercoiled DNA, as electrophoretic mobility is sensitive to the topological DNA state. However, we show that an apparent lack of unwinding in an electrophoretic assay could be due to dissociation of the (intercalated) ligand during the analysis, rather than evidence for a nonintercalative mode of binding to DNA. Repetitive scanning during the electrophoresis ensures that release of the ligand during electrophoresis does not affect the measured degree of unwinding, based on the electrophoretic velocity being determined as a function of time. We use this assay to establish intercalation as a mode of binding to DNA for the cyanine dyes YO, YO-PRO as well as two enantiomeric forms of the ruthenium complexes [(phen)2 Ru(tatpp)Ru(phen)2]4+, and to support groove-binding for the new unsymmetrical cyanine dyes BOXTO and BOXTO-PRO. Groove-binding could be concluded from a lack of unwinding, because we could rule out that it is caused by release of the dye during the electrophoresis. The gel electrophoresis has the advantage over hydrodynamic techniques that much smaller sample amounts are required, and our time-resolved approach can be employed in all mobility-shift assays when applied to dissociating complexes.     

Conformation dependence of DNA electrophoretic mobility in a converging channel

The electrophoresis of λ‐DNA is observed in a microscale converging channel where the center‐of‐masses trajectories of DNA molecules are tracked to measure instantaneous electrophoretic (EP) mobilities of DNA molecules of various stretch lengths and conformations. Contrary to the usual assumption that DNA mobility is a constant, independent of field and DNA length in free solution, we find DNA EP mobility varies along the axis in the contracting geometry. We correlate this mobility variation with the local stretch and conformational changes of the DNA, which are induced by the electric field gradient produced by the contraction. A “shish‐kebab” model of a rigid polymer segment is developed, which consists of aligned spheres acting as charge and drag centers. The EP mobility of the shish‐kebab is obtained by determining the electrohydrodynamic interactions of aligned spheres driven by the electric field. Multiple shish‐kebabs are then connected end‐to‐end to form a freely jointed chain model for a flexible DNA chain. DNA EP mobility is finally obtained as an ensemble average over the shish‐kebab orientations that are biased to match the overall stretch of the DNA chain. Using physically reasonable parameters, the model agrees well with experimental results for the dependence of EP mobility on stretch and conformation. We find that the magnitude of the EP mobility increases with DNA stretch, and that this increase is more pronounced for folded conformations.     

Influence of arm length and number on star-shaped poly(2-isopropyl-2-oxazoline) aggregation in aqueous solutions near cloud point

Four-arm star-shaped poly(2-isopropyl-2-oxazolines) (PiPrOx₄) are synthesized by cationic polymerization on t-butylcalix[4]arene macroinitiator. The obtained samples differ by polymerization degree of arms N_PiPrOx = 9 and 25 and are characterized in chloroform. The behavior in aqueous solutions is studied by light scattering methods and compared with the results of investigation of eight-arm star with similar structure. Three types of particles are observed in solution of short-arm PiPrOx₄ at room temperature, whereas only two particle types are present in long-arm star solution. Arm shortening leads to widening of the phase transition interval. The arm number decreasing reduces the phase transition temperature by 1°C.     

A modified uridine for the synthesis of branched DNA

Branched DNA constructs have found wide application in DNA-based nanotechnology. Several reports describe the generation of branched DNA structures with variable numbers of arms to self-assemble with pre-designed architectures. Branched DNA is generated by using designed rigid crossover DNA molecules as building blocks. Alternatively, branched DNAs can also be generated by using synthetic branch points derived either from nucleoside or non-nucleoside building blocks. Herein, we report the synthesis of modified uridine derivatives as branching monomer for the synthesis of branched DNA and first studies of their self-assembling properties.     

The electrophoretic mobility of DNA fragments differing by a single 3′‐terminal nucleotide in an automated capillary DNA sequencer

The electrophoretic mobility of DNA fragments that differ by a single 3′‐terminal nucleotide was assessed by capillary electrophoresis. This was accomplished using dideoxy sequencing with a 5′‐fluorescently labelled primer to generate DNA fragments with 3′‐hydrogen ends. The resulting DNA fragments were electrophoresed on the ABI 3730 automated capillary sequencer, and the data were analysed with the GeneMapper software to determine the electrophoretic mobility differences on addition of a 3′‐terminal nucleotide. It was found that the 3′‐terminal nucleotide gave rise to different electrophoretic mobility profiles depending on the identity of the terminal nucleotide. The apparent electrophoretic mobility was (faster) –C > ?A > ?T > ?G (slower). The C‐terminated fragments were the fastest and the G‐terminated fragments the slowest, relative to other nucleotides. It was proposed that the terminal nucleotide effect was due to changes in partial net charges on the nucleotides that resulted in alterations in the electrophoretic mobility of the DNA fragments in the automated capillary DNA sequencer. Other alternative explanations are also discussed. Copyright © 2012 John Wiley & Sons, Ltd.     

Influence of saponin on the electric parameters and the electrophoretic mobility of erythrocytes

Structural changes in the membranes and charge changes on the cell surface of erythrocytes after saponin treatment were investigated by measuring the electric impedance of erythrocyte suspensions over the frequency range 0.5–20 MHz and the electrophoretic mobility of erythrocytes. From the characteristic time behaviour of the specific membrane capacitance calculated it can be concluded that two types of structure changes occur if saponin of a sufficiently high concentration acts. This is in good conformity with electron microscopic investigations. The electrophoretic mobility data show that the surface charge of erythrocytes decreases with saponin action. This effect allows a possible explanation for the observed increase in the conductivity inside and outside the cells.     

Hydrolysis of DNA by N-Phosphoryl Branched Peptide

A N-phosphoryl branched peptide (DIPP-Leu) ₂ -Lys-OCH ₃ was found to efficiently cleave double-strand DNA such as PUC19 and Lambda DNA at pH 8.5 in 100 mM Tris-HCl buffer. The T4 ligase experiment implied that the DNA cleavage occurs via a hydrolytic path.     

Gel electrophoretic mobility of single-stranded DNA: the two reptation field-dependent factors

The reptation model is the dominant theory in understanding the electrophoretic separation of single-stranded DNA molecules in gels or entangled polymer solutions. Recently, we showed that the Ogston and reptation regimes are separated by an entropic trapping regime at low field intensities. Here, we report the first comparison of the field-dependent part of the DNA mobility for both small and long reptating molecules. We show that both mobilities increase linearly with field intensity, with the mobility of the longer (comigrating) fragments increasing faster than that of the smaller ones. We compare our results to the predictions of the biased reptation model.     

Influence of cell-model boundary conditions on the conductivity and electrophoretic mobility of concentrated suspensions

In the last few years, different theoretical models and analytical approximations have been developed addressing the problem of the electrical conductivity of a concentrated colloidal suspension. Most of them are based on the cell model concept, and coincide in using Kuwabara's hydrodynamic boundary conditions, but there are different possible approaches to the electrostatic boundary conditions. We will call them Levine-Neale's (LN, they are Neumann type, that is they specify the gradient of the electrical potential at the boundary), and Shilov-Zharkikh's (SZ, Dirichlet type). The important point in our paper is that we show by direct numerical calculation that both approaches lead to identical evaluations of the conductivity of the suspensions if each of them is associated to its corresponding evaluation of the macroscopic electric field. The same agreement between the two calculations is reached for the case of electrophoretic mobility. Interestingly, there is no way to reach such identity if two possible choices are considered for the boundary conditions imposed to the field-induced perturbations in ionic concentrations on the cell boundary (r = b), deltan(i) (r = b). It is demonstrated that the conditions deltan(i)(b) = 0 lead to consistently larger conductivities and mobilities. A qualitative explanation is offered to this fact, based on the plausibility of counter-ion diffusion fluxes favoring both the electrical conduction and the motion of the particles.     

Synthesis and dilute solution properties of divinylbenzene-linked polystyrene stars with mixed arm lengths: Evidence for coupled stars

Sequential anionic polymerization of styrene and divinylbenzene (DVB) is known to lead to the formation of star-shaped polymers. This ‘arms-first’ method has been widely used and studied. It is known that this polymerization forms stars with anionically active cores. This article is concerned with the attempt to make asymmetric-star polymers utilizing these living carbanionic sites present in the core to form a second set of shorter arms growing out from the star core. The presence of remaining unreacted DVB within the core was found to cause the stars to couple to form linked double stars and other larger structures. Results from detailed dilute solution studies of the resulting polymers are reported. It was found that the results obtained from size exclusion chromatography for the double stars were flow rate dependent; only at low flow rates was a true size separation obtained. © 1997 John Wiley & Sons, Inc.     

Rapid electrophoretic recovery of DNA from dried blood spots

Large‐scale genetic screening of neonatal dried blood spots for episomal DNA has a great potential to lower patient mortality and morbidity through early diagnosis of primary immunodeficiencies. However, DNA extraction from the surface of dried blood spots remains one of the most time consuming, costly, and labor‐intensive parts of DNA analysis. In the present study, we developed and optimized a rapid methodology using only 50 V and heat to extract episomal DNA from dried blood spots prepared from diagnostic cord blood samples. This electric field DNA extraction is the first methodology to use an electric field to extract episomal DNA from a dried blood spot. This 25‐minute procedure has one of the lowest times for the extraction of episomal DNA found within the literature and this novel procedure not only negates the need for costly treatment and wash steps, but reduces the time of manual procedures by more than 30 min while retaining the 75–80% of the yield. Combined with real‐time PCR, this novel method of electric field extraction not only provides an effective tool for the large scale genetic analysis of neonates, but a key step forward in the simplification and standardization of diagnostic testing.     

Sequence‐specific nucleic acid mobility using a reversible block copolymer gel matrix and DNA amphiphiles (lipid‐DNA) in capillary and microfluidic electrophoretic separations

Reversible noncovalent but sequence‐dependent attachment of DNA to gels is shown to allow programmable mobility processing of DNA populations. The covalent attachment of DNA oligomers to polyacrylamide gels using acrydite‐modified oligonucleotides has enabled sequence‐specific mobility assays for DNA in gel electrophoresis: sequences binding to the immobilized DNA are delayed in their migration. Such a system has been used for example to construct complex DNA filters facilitating DNA computations. However, these gels are formed irreversibly and the choice of immobilized sequences is made once off during fabrication. In this work, we demonstrate the reversible self‐assembly of gels combined with amphiphilic DNA molecules, which exhibit hydrophobic hydrocarbon chains attached to the nucleobase. This amphiphilic DNA, which we term lipid‐DNA, is synthesized in advance and is blended into a block copolymer gel to induce sequence‐dependent DNA retention during electrophoresis. Furthermore, we demonstrate and characterize the programmable mobility shift of matching DNA in such reversible gels both in thin films and microchannels using microelectrode arrays. Such sequence selective separation may be employed to select nucleic acid sequences of similar length from a mixture via local electronics, a basic functionality that can be employed in novel electronic chemical cell designs and other DNA information‐processing systems.     

Estimation of the optimal electrophoretic temperature of DNA single-strand conformation polymorphism by DNA base composition

To explore the relation between DNA base composition and the optimal single-strand conformation polymorphism (SSCP) electrophoretic temperature (T(s)), we analyzed DNA base composition and T(s) of 24 DNA fragments from different genes and found that T(s) was positively correlative with the ratio of base C/base A. T(s) could be estimated by the formula T(s) = [80 x C/(A+1)]/[2.71 + [C/(A+1)]]. T(s) could be increased dramatically by the complementary sequences in both 5'-and 3'-ends of a DNA single-strand.     

Influence of electric field intensity, ionic strength, and migration distance on the mobility and diffusion in DNA surface electrophoresis

In order to increase the separation rate of surface electrophoresis while preserving the resolution for large DNA chains, e.g., genomic DNA, the mobility and diffusion of Lambda DNA chains adsorbed on flat silicon substrate under an applied electric field, as a function of migration distance, ionic strength, and field intensity, were studied using laser fluorescence microscope. The mobility was found to follow a power law with the field intensity beyond a certain threshold. The detected DNA peak width was shown to be constant with migration distance, slightly smaller with stronger field intensity, but significantly decreased with higher ionic strength. The molecular dynamics simulation demonstrated that the peak width was strongly related with the conformation of DNA chains adsorbed onto surface. The results also implied that there was no diffusion of DNA during migration on surface. Therefore, the Nernst-Einstein relation is not valid in the surface electrophoresis and the separation rate could be improved without losing resolution by decreasing separation distance, increasing buffer concentration, and field intensity. The results indicate the fast separation of genomic DNA chains by surface electrophoresis is possible.     

Effect of electric field switching on the electrophoretic mobility of single-stranded DNA molecules in polyacrylamide gels

We have examined the effects of pulsed electric fields on the separation of single-stranded DNA molecules in polyacrylamide sequencing gels. Using different electric field pulsing regimens, the mobilities of single-stranded DNA molecules can be retarded or increased as compared to conventional electrophoresis. These results indicated that pulsed field techniques can be applied to gel electrophoresis of small single-stranded DNA molecules.     

The use of poly(alkylene oxide)s to achieve fast and controlled photochromic switching in rigid matrices

We report a conjugation system for the enhancement of photochromic dye performance in rigid matrices using widely available, cheap, chemically robust and compatible polymeric starting materials, namely poly(propylene oxide) (PPO) and poly(1,2‐butylene oxide). Conjugation of these soft (low T_g) polymers to an indeno‐fused naphthopyran photochromic dye, in a telechelic geometry, gives access to a wide range of accelerated and tuned fade speeds (decoloration) via variation in molecular weight. The t_1/2 and t_3/4 fade speeds for PPO conjugates (polymer molecular weights ranging between ca. 425 and 2000) are accelerated by 35–58 and 51–76%, respectively, compared with the nonconjugated control dye. Longer oligomers provide faster decoloration approaching that obtained in solution. The stability of the polyethers allows functionalization using a wide variety of chemistries, including harsh acid catalyzed transformations, providing an overall facile synthesis of photochromic dye‐polymer conjugates in high yield and purity. In addition, these polymers give easy access to conjugates with star‐type architectures, which provide an even further improvement in performance compared with their linear counterparts with less conjugated polymer needed per dye to achieve a given fade speed. © 2012 Commonwealth of Australia. J Polym Sci Part A: Polym Chem, 2012