Optimized DNA hybridization detection on nanocolloidal particles by dielectrophoresis

Oligonucleotides of varying surface coverage are functionalized onto the surface of 100 nm silica particles and the corresponding hybridization reaction with target ssDNA is studied using dielectrophoresis (DEP). The measured DEP cross‐over frequency (cof) is found to be sensitive to the oligonucleotide surface conformation. Zeta potential and particle size measurements suggest that at low oligo surface concentrations, non‐specific binding of oligo to the particle surface prevents efficient hybridization. At high surface coverage, steric hindrance due to the fully stretched, tightly packed oligo conformation prevents diffusion of DNA molecules to the particle surface. The optimum surface coverage exists at intermediate coverage where the particle is found to be the least electrically conductive, and hence exhibits the lowest measured cof. A simple DEP cof measurement hence allows one to determine the optimal oligo surface coverage for increased hybridization efficiency and detection sensitivity.     

Effects of dielectrophoresis on thrombogenesis in human whole blood

Thrombogenesis (blood clot formation) is a major barrier to the development of biomedical devices that interface with blood. Although state‐of‐the‐art chemically and pharmacologically mediated clot mitigation strategies are effective, some limitations of such approaches include depletion of active agents, or adverse reactions in patients. Increased clotting protein adsorption and platelet adhesion, which occur when artificial surfaces are exposed to blood result in enhanced clot formation on artificial surfaces. It is hypothesized that repelling proteins and platelets using dielectrophoresis (DEP), a contact‐free particle manipulation technique, will reduce clot formation in biomedical devices. In this paper, the effect of DEP on thrombogenesis in human blood is investigated. Undiluted whole blood from human donors is pumped through microchannels at a physiological shear rate (400 s ⁻¹). Experiments are performed by applying 0 V, 0.5 V_rms , 2 V_rms , and 3 V_rms to electrodes in the channel. Clot formation is observed to decrease in experiments in which DEP electrodes are active (average of 6% coverage @ 0V reduced to 0.08% coverage @ 3 V_rms ). Repulsion is more effective at higher voltages. DEP causes a quantifiable reduction in microscopic and macroscopic clot formation in PDMS microchannels.     

Metabolic viability of Escherichia coli trapped by dielectrophoresis in microfluidics

The spatial and temporal control of biological species is essential in complex microfluidic biosystems. In addition, if the biological species is a cell, microfluidic handling must ensure that the cell's metabolic viability is maintained. The use of DEP for cell manipulation in microfluidics has many advantages because it is remote and fast, and the voltages required for cell trapping scale well with miniaturization. In this paper, the conditions for bacterial cell (Escherichia coli) trapping using a quadrupole electrode configuration in a PDMS microfluidic channel were developed both for stagnant and for in‐flow fluidic situations. The effect of the electrical conductivity of the fluid, the applied electric field and frequency, and the fluid‐flow velocity were studied. A dynamic exchange between captured and free‐flowing cells during DEP trapping was demonstrated. The metabolic activity of trapped cells was confirmed by using E. coli cells genetically engineered to express green fluorescent protein under the control of an inducible promoter. Noninduced cells trapped by negative DEP and positive DEP were able to express green fluorescent protein minutes after the inducer was inserted in the microchannel system immediately after DEP trapping. Longer times of trapping prior to exposure to the inducer indicated first a degradation of the cell metabolic activity and finally cell death.     

Intracellular potassium under osmotic stress determines the dielectrophoresis cross‐over frequency of murine myeloma cells in the MHz range

Dielectrophoresis (DEP) has been widely studied for its potential as a biomarker‐free method of sorting and characterizing cells based upon their dielectric properties. Most studies have employed voltage signals from ∼1 kHz to no higher than ∼30 MHz. Within this range a transition from negative to positive DEP can be observed at the cross‐over frequency f_x01. The value of f_x01 is determined by the conductivity of the suspending medium, as well as the size and shape of the cell and the dielectric properties (capacitance, conductivity) of its plasma membrane. In this work DEP measurements were performed up to 400 MHz, where the transition from positive to negative DEP can be observed at a higher cross‐over frequency f_x02. SP2/O murine myeloma cells were suspended in buffer media of different osmolarities and measurements taken of cell volume, f_x01 and f_x02. Potassium‐binding benzofuran isophthalate (PBFI), a potassium‐sensitive fluorophore, and flow cytometry was employed to monitor relative changes in intracellular potassium concentration. In agreement with theory, it was found that f_x02 is independent of the cell parameters that control f_x01 and is predominantly determined by intracellular conductivity. In particular, the value of f_x02 is highly correlated to that of the intracellular potassium concentration.     

Mapping alternating current electroosmotic flow at the dielectrophoresis crossover frequency of a colloidal probe

AC electroosmotic (ACEO) flow above the gap between coplanar electrodes is mapped by the measurement of Stokes forces on an optically trapped polystyrene colloidal particle. E²‐dependent forces on the probe particle are selected by amplitude modulation (AM) of the ACEO electric field (E) and lock‐in detection at twice the AM frequency. E²‐dependent DEP of the probe is eliminated by driving the ACEO at the probe's DEP crossover frequency. The location‐independent DEP crossover frequency is determined, in a separate experiment, as the limiting frequency of zero horizontal force as the probe is moved toward the midpoint between the electrodes. The ACEO velocity field, uncoupled from probe DEP effects, was mapped in the region 1–9 μm above a 28 μm gap between the electrodes. By use of variously sized probes, each at its DEP crossover frequency, the frequency dependence of the ACEO flow was determined at a point 3 μm above the electrode gap and 4 μm from an electrode tip. At this location the ACEO flow was maximal at ～117 kHz for a low salt solution. This optical trapping method, by eliminating DEP forces on the probe, provides unambiguous mapping of the ACEO velocity field.     

Photochemistry and Photobiology of the Spore Photoproduct: A 50‐Year Journey

Fifty years ago, a new thymine dimer was discovered as the dominant DNA photolesion in UV‐irradiated bacterial spores [Donnellan, J. E. & Setlow R. B. (1965) Science, 149, 308–310], which was later named the spore photoproduct (SP). Formation of SP is due to the unique environment in the spore core that features low hydration levels favoring an A‐DNA conformation, high levels of calcium dipicolinate that acts as a photosensitizer, and DNA saturation with small, acid‐soluble proteins that alters DNA structure and reduces side reactions. In vitro studies reveal that any of these factors alone can promote SP formation; however, SP formation is usually accompanied by the production of other DNA photolesions. Therefore, the nearly exclusive SP formation in spores is due to the combined effects of these three factors. Spore photoproduct photoreaction is proved to occur via a unique H‐atom transfer mechanism between the two involved thymine residues. Successful incorporation of SP into an oligonucleotide has been achieved via organic synthesis, which enables structural studies that reveal minor conformational changes in the SP‐containing DNA. Here, we review the progress on SP photochemistry and photobiology in the past 50 years, which indicates a very rich SP photobiology that may exist beyond endospores.     

Diethylphosphonate‐containing benzoxazine compound as a thermally latent catalyst and a reactive property modifier for polybenzoxazine‐based resins

A diethylphosphonate‐containing benzoxazine compound (DEP‐Bz) to be used as a multi‐functional reaction agent for preparation of high performance polybenzoxazine thermosetting resins has been reported. The chemical structure of DEP‐Bz has been characterized with FTIR, ¹H NMR, and elemental analysis. The phosphonate groups of DEP‐Bz could convert into phosphonic acid groups which could catalyze the ring‐opening addition reaction of benzoxazines, to demonstrate the thermally latent catalytic effect of DEP‐Bz on the polymerization of benzoxazine compounds. Moreover, DEP‐Bz could also serve as a reactive‐type modifier for polybenzoxazines and other thermosets. DEP‐Bz modified polybenzoxazine resins have shown relatively low reaction temperature (about 190 °C), high mechanical strength with a storage modulus of about 3.0 GPa, and high flame retardancy with a limit oxygen index of about 32. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013 , 51, 3523–3530     

Bringing It All Together: Coupling Excision Repair to the DNA Damage Checkpoint

Nucleotide excision repair and the ATR‐mediated DNA damage checkpoint are two critical cellular responses to the genotoxic stress induced by ultraviolet (UV) light and are important for cancer prevention. In vivo genetic data indicate that these global responses are coupled. Aziz Sancar et al. developed an in vitro coupled repair‐checkpoint system to analyze the basic steps of these DNA damage stress responses in a biochemically defined system. The minimum set of factors essential for repair‐checkpoint coupling include damaged DNA, the excision repair factors (XPA, XPC, XPF‐ERCC1, XPG, TFIIH, RPA), the 5′‐3′ exonuclease EXO1, and the damage checkpoint proteins ATR‐ATRIP and TopBP1. This coupled repair‐checkpoint system was used to demonstrate that the ~30 nucleotide single‐stranded DNA (ssDNA) gap generated by nucleotide excision repair is enlarged by EXO1 and bound by RPA to generate the signal that activates ATR.     

Synthesis,Characterization, and Repair of a Flexible O6‐2′‐Deoxyguanosine‐alkylene‐O6‐2′‐deoxyguanosine Intrastrand Cross‐Link

Oligonucleotides tethered by an alkylene linkage between the O⁶‐atoms of two consecutive 2′‐deoxyguanosines, which lack a phosphodiester linkage between these residues, have been synthesized as a model system of intrastrand cross‐linked (IaCL) DNA. UV thermal denaturation studies of duplexes formed between these butylene‐ and heptylene‐linked oligonucleotides with their complementary DNA sequences revealed about 20 °C reduction in stability relative to the unmodified duplex. Circular dichroism spectra of the model IaCL duplexes displayed a signature characteristic of B‐form DNA, suggesting minimal global perturbations are induced by the lesion. The model IaCL containing duplexes were investigated as substrates of O⁶‐alkylguanine DNA alkyltransferase (AGT) proteins from human and E. coli (Ada‐C and OGT). Human AGT was found to repair both model IaCL duplexes with greater efficiency towards the heptylene versus butylene analog adding to our knowledge of substrates this protein can repair.     

Efficient complexation of pyrrole-bridged dizinc(II) bisporphyrin with fluorescent probe pyrene: synthesis, structure, and photoinduced singlet-singlet energy transfer

A diethylpyrrole‐bridged dizinc(II) bisporphyrin (Zn₂DEP) is reported that encapsulates fluorescent probe pyrene molecules through strong π–π interactions, which can relay information about the chemical environment in the interior of the host–guest supramolecular assembly. X‐ray structures of both Zn₂DEP and the encapsulated pyrene complex are reported, which provides a rare opportunity to investigate the structural changes upon guest binding. A comparative structural analysis demonstrated the exceptional ability of this bisporphyrin platform to open its binding pocket for pyrene encapsulation by a vertical displacement of more than 2.45 Å, although both Zn₂DEP and the pyrene complex have nearly parallel porphyrin ring orientations. The ¹H NMR spectrum of the encapsulated pyrene complex in solution shows the upfield shifts of the pyrene protons due to a strong ring current effect, which demonstrates the retention of the solid‐state structure in solution. To further assess the extent to which pyrene guests remain encapsulated in solution, a known fluorescence quencher, dimethylaniline, was added to the host–guest assembly, which shows no exciplex formation for days in nonpolar solvents. Thus, the assembly also retained the structural integrity in solution for a long time. The association constant (K_asso) for such a complexation process in solution was observed to be 1.78×10⁵ M ^?2 for 1:2 binding. Steady‐state fluorescence and lifetime studies indicate significant photoinduced singlet–singlet energy transformation from the excited state of pyrene to zinc bisporphyrin.     

Synthesis of bis-indole carboxamides as G-quadruplex stabilizing and inducing ligands

The design and synthesis of a series of bis‐indole carboxamides with varying amine containing side chains as G‐quadruplex DNA stabilising small molecules are reported. Their interactions with quadruplexes have been evaluated by means of Förster resonance energy transfer (FRET) melting analysis, UV/Vis spectroscopy, circular dichroism spectroscopy and molecular modelling studies. FRET analysis indicates that these ligands exhibit significant selectivity for quadruplex over duplex DNA, and the position of the carboxamide side chains is of paramount importance in G‐quadruplex stabilisation. UV/Vis titration studies reveal that bis‐indole ligands bind tightly to quadruplexes and show a three‐ to fivefold preference for c‐kit2 over h‐telo quadruplex DNA. CD studies revealed that bis‐indole carboxamide with a central pyridine ring induces the formation of a single, antiparallel, conformation of the h‐telo quadruplex in the presence and absence of added salt. The chirality of h‐telo quadruplex was transferred to the achiral ligand (induced CD) and the formation of a preferred atropisomer was observed.     

On‐line separation of bacterial cells by carbon‐electrode dielectrophoresis

Dielectrophoresis (DEP) represents a powerful approach to manipulate and study living cells. Hitherto, several approaches have used 2‐D DEP chips. With the aim to increase sample volume, in this study we used a 3‐D carbon‐electrode DEP chip to trap and release bacterial cells. A continuous flow was used to plug an Escherichia coli cell suspension first, to retain cells by positive DEP, and thereafter to recover them by washing with peptone water washing solution. This approach allows one not only to analyze DEP behavior of living cells within the chip, but also to further recover fractions containing DEP‐trapped cells. Bacterial concentration and flow rate appeared as critical parameters influencing the separation capacity of the chip. Evidence is presented demonstrating that the setup developed in this study can be used to separate different types of bacterial cells.     

Protein dielectrophoresis: Key dielectric parameters and evolving theory

Globular proteins exhibit dielectrophoresis (DEP) responses in experiments where the applied field gradient factor ∇E² appears far too small, according to standard DEP theory, to overcome dispersive forces associated with the thermal energy kT of disorder. To address this a DEP force equation is proposed that replaces a previous empirical relationship between the macroscopic and microscopic forms of the Clausius–Mossotti factor. This equation relates the DEP response of a protein directly to the dielectric increment δε⁺ and decrement δε⁻ that characterize its β-dispersion at radio frequencies, and also indirectly to its intrinsic dipole moment by way of providing a measure of the protein's effective volume. A parameter Γ_pw, taken as a measure of cross-correlated dipole interactions between the protein and its water molecules of hydration, is included in this equation. For 9 of the 12 proteins, for which an evaluation can presently be made, Γ_pw has a value of ≈4600 ± 120. These conclusions follow an analysis of the failure of macroscopic dielectric mixture (effective medium) theories to predict the dielectric properties of solvated proteins. The implication of a polarizability greatly exceeding the intrinsic value for a protein might reflect the formation of relaxor ferroelectric nanodomains in its hydration shell.     

Evidence from Circular Dichroism and from Melting Behavior for Helix‐Inducing Complexation of a Designed β3‐Pentadecapeptide with DNA Duplexes. Preliminary Communication

Inspired by naturally occurring DNA‐binding proteins and their artificial α‐peptidic mimics reported to date, a research project was initiated aiming at creating a new class of β‐peptides capable of binding to and ultimately regulating the functions of DNA. As an initial foray, a β³‐pentadecapeptide 1 , which bears H‐bonding Asn side chains and positively charged Lys side chains, was designed and synthesized on the solid support. DNA‐Complexation studies by means of circular dichroism and DNA‐melting‐temperature measurements revealed the first preliminary indications that support the existence of ordered interactions between β‐peptides and DNA.     

DNA Binding and Cleavage Activity of cis‐Cobalt Aromatic Oxime Complexes and Its Pyridine/imidazole Adducts

cis‐Cobalt complexes with salicycaldoxime(SAO), (Z)‐1‐(2‐hydroxyphenyl)ethanonoxime (HEO), (Z)‐1‐(2,5‐dihydroxyphenyl)ethanonoxime (DEO), (Z)‐1‐(2,5‐dihydroxyphenyl)(phenyl)methanonoxime (DPO) and their adducts with pyridine (Py) and imidazole (Im) were synthesized and characterized by elemental analysis, magnetic susceptibility, UV‐Vis and IR spectra. The electrochemical studies were carried by cyclic voltammeter, the peak potential separation and formal potential of complexes were independent of sweep rate or scan rate (ν) indicating a quasi reversible one‐electron redox process. Absorption studies and thermal denature studies revealed that each of these octahedral complexes is an avid binder of calf thymus DNA. The apparent binding constants for mixed ligand complexes are in order of ～10³‐10³ M^?1. Based on the data obtained in the DNA binding studies a partial intercalative mode of binding is suggested for these complexes. The nucleolytic cleavage activity of parent complexes and their pyridine adduct were carried out on double stranded pBR322 circular plasmid DNA by using a gel electrophoresis experiment in the presence and absence of oxidant (H₂O₂). All the metal complexes show enhanced cleavage activity in presence of oxidant. The hydrolytic cleavage of DNA of Co(DEO)₂ and Co(DPO)₂ is evidenced from the control experiments showing discernable cleavage inhibition in the presence of the hydroxyl radical inhibitor DMSO and EDTA.     

Insulator‐based dielectrophoresis combined with the isomotive AC electric field and applied to single cell analysis

We developed an insulator‐based dielectrophoretic (iDEP) creek‐gap device that enables the isomotive movement of cells and that is suitable for determining their DEP properties. In the iDEP creek‐gap device, a pair of planar insulators forming a single fan‐shaped channel allows the induction of the isomotive iDEP force on cells. Hence, the cells’ behavior is characterized by straight motion at constant velocity in the longitudinal direction of the channel. Operation of the device was demonstrated using human breast epithelial cells (MCF10A) by applying an AC voltage of V_pp = 34 V peak‐to‐peak and frequencies of 200 kHz and 50 MHz to the device. Subsequently, the magnitude of DEP forces and the real part of the ClausiusMossotti (CM) factor, Re(β), were deduced from the measured cell velocity. The values of Re(β) were 0.14 ± 0.01 for the frequency of 200 kHz and ?0.12 ± 0.01 for 50 MHz. These results demonstrated that the DEP properties of the cells could be extracted over a wide field frequency range. Therefore, the proposed iDEP creek‐gap device was found to be applicable to cell analysis.     

Photocaged Quinone Methide Crosslinkers for Light‐Controlled Chemical Crosslinking of Protein–Protein and Protein–DNA Complexes

Small‐molecule crosslinkers are invaluable for probing biomolecular interactions and for crosslinking mass spectrometry. Existing chemical crosslinkers target only a small selection of amino acids, while conventional photo‐crosslinkers target almost all residues non‐specifically, complicating data analysis. Herein, we report photocaged quinone methide (PQM)‐based crosslinkers that target nine nucleophilic residues through Michael addition, including Gln, Arg, and Asn, which are inaccessible to existing chemical crosslinkers. PQM crosslinkers were used in vitro, in Escherichia coli, and in mammalian cells to crosslink dimeric proteins and endogenous membrane receptors. The heterobifunctional crosslinker NHQM could crosslink proteins to DNA, for which few crosslinkers exist. The photoactivatable reactivity of these crosslinkers and their ability to target multiple amino acids will enhance the use of chemical crosslinking for studies of protein–protein and protein–DNA networks and for structural biology.     

NMR elucidation of monomer–dimer transition and conformational heterogeneity in histone‐like DNA binding protein of Helicobacter pylori

Helicobacter pylori (H. pylori) colonizes under harsh acidic/oxidative stress conditions of human gastrointestinal tract and can survive there for infinitely longer durations of host life. The bacterium expresses several harbinger proteins to facilitate its persistent colonization under such conditions. One such protein in H. pylori is histone‐like DNA binding protein (Hup), which in its homo‐dimeric form binds to DNA to perform various DNA dependent cellular activities. Further, it also plays an important role in protecting the genomic DNA from oxidative stress and acidic denaturation. Legitimately, if the binding of Hup to DNA is suppressed, it will directly impact on the survival of the bacterium, thus making Hup a potential therapeutic target for developing new anti‐H. pylori agents. However, to inhibit the binding of Hup to DNA, it is necessary to gain detailed insights into the molecular and structural basis of Hup‐dimerization and its binding mechanism to DNA. As a first step in this direction, we report here the nuclear magnetic resonance (NMR) assignments and structural features of Hup at pH 6.0. The study revealed the occurrence of dynamic equilibrium between its monomer and dimer conformations. The dynamic equilibrium was found to shifting towards dimer both at low temperature and low pH; whereas DNA binding studies evidenced that the protein binds to DNA in its dimeric form. These preliminary investigations correlate very well with the diverse functionality of protein and will form the basis for future studies aiming to develop novel anti‐H. pylori agents employing structure‐based‐rational drug discovery approach.     

Dielectrophoretic trapping of multilayer DNA origami nanostructures and DNA origami‐induced local destruction of silicon dioxide

DNA origami is a widely used method for fabrication of custom‐shaped nanostructures. However, to utilize such structures, one needs to controllably position them on nanoscale. Here we demonstrate how different types of 3D scaffolded multilayer origamis can be accurately anchored to lithographically fabricated nanoelectrodes on a silicon dioxide substrate by DEP. Straight brick‐like origami structures, constructed both in square (SQL) and honeycomb lattices, as well as curved “C”‐shaped and angular “L”‐shaped origamis were trapped with nanoscale precision and single‐structure accuracy. We show that the positioning and immobilization of all these structures can be realized with or without thiol‐linkers. In general, structural deformations of the origami during the DEP trapping are highly dependent on the shape and the construction of the structure. The SQL brick turned out to be the most robust structure under the high DEP forces, and accordingly, its single‐structure trapping yield was also highest. In addition, the electrical conductivity of single immobilized plain brick‐like structures was characterized. The electrical measurements revealed that the conductivity is negligible (insulating behavior). However, we observed that the trapping process of the SQL brick equipped with thiol‐linkers tended to induce an etched “nanocanyon” in the silicon dioxide substrate. The nanocanyon was formed exactly between the electrodes, that is, at the location of the DEP‐trapped origami. The results show that the demonstrated DEP‐trapping technique can be readily exploited in assembling and arranging complex multilayered origami geometries. In addition, DNA origamis could be utilized in DEP‐assisted deformation of the substrates onto which they are attached.