Anomalous electrophoretic migration of short oligodeoxynucleotides labelled with 5′‐terminal Cy5 dyes

By using a fluorescent exonuclease assay, we reported unusual electrophoretic mobility of 5′‐indocarbo‐cyanine 5 (5′‐Cy5) labelled DNA fragments in denaturing polyacrylamide gels. Incubation time and enzyme concentration were two parameters involved in the formation of 5′‐Cy5‐labelled degradation products, while the structure of the substrate was slightly interfering. Replacement of positively charged 5′‐Cy5‐labelled DNA oligonucleotides (DNA oligos) by electrically neutral 5′‐carboxyfluorescein (5′‐FAM) labelled DNA oligos abolished the anomalous migration pattern of degradation products. MS analysis demonstrated that anomalously migrating products were in fact 5′‐labelled DNA fragments ranging from 1 to 8 nucleotides. Longer 5′‐Cy5‐labelled DNA fragments migrated at the expected position. Altogether, these data highlighted, for the first time, the influence of the mass/charge ratio of 5′‐Cy5‐labelled DNA oligos on their electrophoretic mobility. Although obtained by performing 3′ to 5′ exonuclease assays with the family B DNA polymerase from Pyrococcus abyssi, these observations represent a major concern in DNA technology involving most DNA degrading enzymes.     

Interaction identification of Zif268 and TATAZF proteins with GC‐/AT‐rich DNA sequence: A theoretical study

Molecular dynamics (MD) simulations for Zif268 (a zinc‐finger‐protein binding specifically to the GC‐rich DNA)‐d(A₁G₂C₃G₄T₅G₆G₇G₈C₉A₁₀C₁₁)₂ and TATA_ZF (a zinc‐finger‐protein recognizing the AT‐rich DNA)‐d(A₁C₂G₃C₄T₅A₆T₇A₈A₉A₁₀A₁₁G₁₂G₁₃)₂ complexes have been performed for investigating the DNA binding affinities and specific recognitions of zinc fingers to GC‐rich and AT‐rich DNA sequences. The binding free energies for the two systems have been further analyzed by using the molecular mechanics Poisson‐Boltzmann surface area (MM‐PBSA) method. The calculations of the binding free energies reveal that the affinity energy of Zif268‐DNA complex is larger than that of TATA_ZF‐DNA one. The affinity between the zinc‐finger‐protein and DNA is mainly driven by more favorable van‐der‐Waals and nonpolar/solvation interactions in both complexes. However, the affinity energy difference of the two binding systems is mainly caused by the difference of van‐der‐Waals interactions and entropy components. The decomposition analysis of MM‐PBSA free energies on each residue of the proteins predicts that the interactions between the residues with the positive charges and DNA favor the binding process; while the interactions between the residues with the negative charges and DNA behave in the opposite way. The interhydrogen‐bonds at the protein‐DNA interface and the induced intrafinger hydrogen bonds between the residues of protein for the Zif268‐DNA complex have been identified at some key contact sites. However, only the interhydrogen‐bonds between the residues of protein and DNA for TATA_ZF‐DNA complex have been found. The interactions of hydrogen‐bonds, electrostatistics and van‐der‐Waals type at some new contact sites have been identified. Moreover, the recognition characteristics of the two studied zinc‐finger‐proteins have also been discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Efficient DNA Condensation Induced by Ruthenium(II) Complexes of a Bipyridine‐Functionalized Molecular Clip Ligand

Complexes of the type [Ru(bxbg)₂(N‐N)]²⁺, where N‐N denotes 2,2′‐bipyridine (bpy) ( 1 ), 1,10‐phenanthroline (phen) ( 2 ), dipyrido[3,2‐d:2′,3‐f] quinoxaline (dpq) ( 3 ), and dipyrido[3,2‐a:2′,3′‐c]phenazine (dppz) ( 4 ), incorporating bis(o‐xylene)bipyridine‐glycoluril (bxbg) as an ancillary “molecular clip” ligand, have been synthesized and characterized. These ruthenium(II) complexes of bis(o‐xylene)bipyridine‐glycoluril self‐associate in water through specific molecular recognition processes to form polycationic arrays. These arrays containing electrostatic binders as well as intercalator ligands at micromolar doses rapidly condense free DNA into globular nanoparticles of various sizes. The DNA condensation induced by these complexes has been investigated by electrophoretic mobility assay, dynamic light scattering, and transmission electron microscopy. The cellular uptake of complex–DNA condensates and the low cytotoxicity of these complexes satisfy the requirements of a gene vector.     

High‐resolution quantification by charge‐dominant electrophoretic mobility shift of quantum dots

Conjugation of biomolecules to colloidal nanoparticles, such as quantum dots (QDs), often leads to change in mobility. We discover that linking DNA molecules to quantum dots alters their surface charge density without significantly increasing the hydrodynamic radius, causing a prominent shift in electrophoretic mobility. In this study, a high‐resolution molecular quantification method named quantification by QDs electrophoretic mobility shift (qQEMS) is developed based on the charge‐dominant transformation that closely associates DNA quantity to QDs electrophoretic mobility. The versatility of qQEMS is demonstrated by a number of quantification assays in which DNA molecules functioned as enzyme substrates, target‐specific probes, and competitive charge carriers. qQEMS shows a great potential as a generic and versatile quantification platform for a wide range of applications.     

Characterization of complexes between phenethylamine enantiomers and β‐cyclodextrin derivatives by capillary electrophoresis—Determination of binding constants and complex mobilities

To optimize chiral separation conditions and to improve the knowledge of enantioseparation, it is important to know the binding constants K between analytes and cyclodextrins and the electrophoretic mobilities of the temporarily formed analyte‐cyclodextrin‐complexes. K values for complexes between eight phenethylamine enantiomers, namely ephedrine, pseudoephedrine, methylephedrine and norephedrine, and four different β‐cyclodextrin derivatives were determined by affinity capillary electrophoresis. The binding constants were calculated from the electrophoretic mobility values of the phenethylamine enantiomers at increasing concentrations of cyclodextrins in running buffer. Three different linear plotting methods (x ‐reciprocal, y ‐reciprocal, double reciprocal) and nonlinear regression were used for the determination of binding constants with β‐cyclodextrin, (2‐hydroxypropyl)‐β‐cyclodextrin, methyl‐β‐cyclodextrin and 6‐O‐α‐maltosyl‐β‐cyclodextrin. The cyclodextrin concentration in a 50 mM phosphate buffer pH 3.0 was varied from 0 to 12 mM. To investigate the influence of the binding constant values on the enantioseparation the observed electrophoretic selectivities were compared with the obtained K values and the calculated enantiomer‐cyclodextrin‐complex mobilities. The different electrophoretic mobilities of the temporarily formed complexes were crucial factors for the migration order and enantioseparation of ephedrine derivatives. To verify the apparent binding constants determined by capillary electrophoresis, a titration process using ephedrine enantiomers and β‐cyclodextrin was carried out. Furthermore, the isothermal titration calorimetry measurements gave information about the thermal properties of the complexes.     

Electric migration of α‐hemolysin in supported n‐bilayers: A model for transmembrane protein microelectrophoresis

Proteome analysis involves separating proteins as a preliminary step toward their characterization. This paper reports on the translational migration of a model transmembrane protein (α‐hemolysin) in supported n‐bilayers (n, the number of bilayers, varies from 1 to around 500 bilayers) when an electric field parallel to the membrane plane is applied. The migration changes in direction as the charge on the protein changes its sign. Its electrophoretic mobility is shown to depend on size and charge. The electrophoretic mobility varies as 1/R², with R the equivalent geometric radius of the embedded part of the protein. Measuring mobilities at differing pH in our system enables us to determine the pI and the charge of the protein. Establishing all these variations points to the feasibility of electrophoretic transport of a charged object in this medium and is a first step toward electrophoretic separation of membrane proteins in n‐bilayer systems.     

CE detection of N‐(3‐dimethylaminopropyl)‐N‐carbodiimide/N‐hydroxysuccinimide‐coupled proteins after homo‐ and hetero‐crosslinking reactions

Protein–protein conjugates formed by carbodiimide crosslinking reactions have been analyzed for the first time using CE. Lysozyme and BSA were chosen as model proteins to study the efficacy of N‐(3‐dimethylaminopropyl)‐N‐ethylcarbodiimide and N‐hydroxysuccinimide as crosslinkers. Detection of the molecular mass increase was checked by SDS‐PAGE. Commercially available, PVA‐coated capillaries showed appropriate selection, while phospho‐deactivated and dynamic PVA‐coated capillaries did not give suitable resolution. CE was found to be an efficient tool to characterize homo‐ (lysozyme–lysozyme) and hetero‐ (lysozyme–BSA) protein coupling by suitable variations of electrophoretic mobilities.     

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.     

ACE applied to the quantitative characterization of benzo‐18‐crown‐6‐ether binding with alkali metal ions in a methanol–water solvent system

ACE was applied to the quantitative evaluation of noncovalent binding interactions between benzo‐18‐crown‐6‐ether (B18C6) and several alkali metal ions, Li⁺, Na⁺, K⁺, Rb⁺ and Cs⁺, in a mixed binary solvent system, methanol–water (50/50 v/v). The apparent binding (stability) constants (K_b) of B18C6–alkali metal ion complexes in the hydro‐organic medium above were determined from the dependence of the effective electrophoretic mobility of B18C6 on the concentration of alkali metal ions in the BGE using a nonlinear regression analysis. Before regression analysis, the mobilities measured by ACE at ambient temperature and variable ionic strength of the BGE were corrected by a new procedure to the reference temperature, 25°C, and the constant ionic strength, 10 mM . In the 50% v/v methanol–water solvent system, like in pure methanol, B18C6 formed the strongest complex with potassium ion (log K_b=2.89±0.17), the weakest complex with cesium ion (log K_b=2.04±0.20), and no complexation was observed between B18C6 and the lithium ion. In the mixed methanol–water solvent system, the binding constants of the complexes above were found to be about two orders lower than in methanol and about one order higher than in water.     

Determination of ζ‐potential,charge, and number of organic ligands on the surface of water soluble quantum dots by capillary electrophoresis

The number of charges and/or organic ligands covalently attached to the surface of CdTe quantum dot nanoparticles has been determined from their electrophoretic mobilities measured in capillaries filled with free electrolyte buffers. Three sizes of water soluble CdTe quantum dots with 3‐mercaptopropionic and thioglycolic acids as surface ligands were prepared. Their electrophoretic mobilities in different pH and ionic strength values of separation buffers were measured by capillary electrophoresis with laser induced fluorescence detection. The ζ‐potentials determined from electrophoretic mobilities using analytical solution of Henry function proposed by Ohshima were in the range from ?30 to ?100 mV. Charges of QDs were calculated from ζ‐potentials. As a result, numbers of organic ligands bonded to QDs surface were determined to be 13, 14, and 15 for the sizes of 3.1, 3.5, and 3.9 nm, respectively. The dissociation constants of organic ligands bonded on QDs surfaces estimated from the dependence of QDs charge on pH of the separation buffer were 7.8 and 7.9 for 3‐mercaptopropionic acid and 6.9 for thioglycolic acid.     

Direct Detection of DNA and DNA‐Ligand Interaction by Impedance Spectroscopy

In this work we present an impedimetric detection system for DNA‐ligand interactions. The sensor system consists of thiol‐modified single‐stranded DNA chemisorbed to gold. Impedance measurements in the presence of the redox system ferri‐/ferrocyanide show an increase in charge transfer resistance (R_ct) after hybridisation of a complementary target. Different amounts of capture strands, used for gold electrode modification, result in surface coverages between 3 and 15 pmol/cm² ssDNA. The relative change in R_ct upon hybridisation increases with increasing amount of capture probe on the electrode from 1.5‐ to 4.5‐fold. Impedimetric detection of binding events of a metal‐intercalator ([Ru(phen)₃]²⁺) and a groove binder (spermine) to double‐stranded DNA is demonstrated. Binding of [Ru(phen)₃]²⁺ and spermine exhibits a decrease in charge transfer resistance. Here, the ligand’s interaction leads to electrostatic shielding of the negatively charged DNA backbone. The impedance changes have been evaluated in dependence on the concentration of both DNA binders. Furthermore, the association of a single‐stranded binding protein (SSBP) is found to cause an increase in charge transfer resistance only when incubated with single‐stranded DNA. The specific binding of an anti‐dsDNA antibody to the dsDNA‐modified electrode surface decreases in contrast the interfacial impedance.     

Complexes of cationic block copolymer micelles with DNA: histone/DNA complex mimetics

The formation of complexes between cationic polymeric micelles of PS-b-PQ2VP amphiphilic block copolymers and DNA molecules in aqueous solutions is investigated at pH = 7. The physicochemical characteristics of the "polyplexes" at different DNA/polymer ratios were characterized in terms of mass, size and charge using static, dynamic and electrophoretic light scattering and AFM. The complexes are spherical and assume their maximum size and mass around the charge stoichiometric ratio. After addition of increased amounts of salt in the solutions, partial dissociation of the systems was observed. The present systems can be considered as mimetics of histone/DNA complexes formed under physiological conditions in living cells.     

4, 5-二氮芴-9-酮Cu(II)、Co(II)多核配合物的合成，晶体结构及DNA结合作用初探

合成了两个4, 5-二氮芴-9-酮Cu(II)、Co(II)的多核配合物[Cu2(CH3COO)4(H2O) 2]·2dafo 1 和 [(μ2-O)2-Co3(dafo)6] (ClO3)2·H2O 2 (dafo=4,5-diazafluoren-9-one) 并且对它们进行了元素分析,红外以及紫外光谱的表征,同时测定了配合物的晶体结构。用紫外光谱,发射光谱和循环伏安三种方法初步研究了配合物1和2与DNA的结合作用,结果表明,配合物1和2与DNA的结合为以插入作用为主 。     

MALDI‐MS detection of noncovalent interactions of single stranded DNA with Escherichia coli single‐stranded DNA‐binding protein

The Escherichia coli single‐stranded DNA binding protein (SSB) selectively binds single‐stranded (ss) DNA and participates in the process of DNA replication, recombination and repair. Different binding modes have previously been observed in SSB?ssDNA complexes, due to the four potential binding sites of SSB. Here, chemical cross‐linking, combined with high‐mass matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry (MS), is used to determine the stoichiometry of the SSB?ssDNA complex. SSB forms a stable homotetramer in solution, but only the monomeric species (m/z 19 100) can be detected with standard MALDI‐MS. With chemical cross‐linking, the quaternary structure of SSB is conserved, and the tetramer (m/z 79 500) was observed. We found that ssDNA also functions as a stabilizer to conserve the quaternary structure of SSB, as evidenced by the detection of a SSB?ssDNA complex at m/z 94 200 even in the absence of chemical cross‐linking. The stability of the SSB?ssDNA complex with MALDI strongly depends on the length and strand of oligonucleotides and the stoichiometry of the SSB?ssDNA complex, which could be attributed to electrostatic interactions that are enhanced in the gas phase. The key factor affecting the stoichiometry of the SSB?ssDNA complex is how ssDNA binds to SSB, rather than the protein‐to‐DNA ratio. This further suggests that detection of the complex by MALDI is a result of specific binding, and not due to non‐specific aggregation in the MALDI plume. Copyright © 2012 John Wiley & Sons, Ltd.     

Effect of divalent metal ions on DNA studied by capillary electrophoresis

Divalent metal ions, such as Zn(2+), Co(2+), and Ni(2+), are capable of incorporating into DNA under certain conditions to form complexes termed M-DNA. To better understand the effects of these cations on DNA we used capillary electrophoresis (CE). The presence of these metal ions in a typical genotyping buffer led to broad peaks with low fluorescence intensities. In addition, some of the metal-complexed DNA molecules had different electrophoretic mobilities than their normal DNA counterparts. It is likely that the mobility shifts observed in the electropherograms of these affected fragments are due to the divalent cations causing structural changes in the single-stranded DNA. However, as can be seen from the resulting peak shapes, the structure, charge, and/or mass changes due to metal binding are not conserved among all of the DNA fragments. The extent of both peak-broadening and mobility shifts were found to be dependent on the metal cation and its concentration, the length of time that the DNA sample existed in formamide prior to injection into the capillary, and also the fragment size and sequence. These results suggest that the presence of metal ions might be responsible for the poor CE performance that occurs when genotyping certain kinds of DNA samples.     

P4VP and oligo(phenylenevinylene)‐perylenebisimide mixed donor‐acceptor supramolecular comb polymer complexes with improved charge carrier mobility

Random donor‐acceptor (D‐A) supramolecular comb polymers were formed when hydroxyl functionalized donor and acceptor small molecules based on Oligo(phenylenevinylene) (named OPVCN‐OH ) and Perylenebisimide (named UPBI‐PDP ), respectively, were complexed with Poly(4‐vinyl pyridine) (P4VP). A series of random D‐A supramolecular comb polymers were formed by varying the ratios of UPBI‐PDP and OPVCN‐OH with P4VP. A 100% P4VP‐donor polymer complex [ P4VP(OPV_1.00 )] and a 100% P4VP‐acceptor polymer complex [ P4VP(UPBI_1.00 )] were also synthesized and characterized. Complex formation was confirmed by FT‐IR and ¹H NMR spectroscopy. Solid state structural studies carried out using small angle X‐ray scattering and wide angle X‐ray diffraction experiments revealed altered packing of the D and A molecules in the complexes. Transmission electron microscopy images showed lamellar structures in the < 10 nm scale for the P4VP(OPV_1.00 ), P4VP(UPBI_1.00 ), and mixed P4VP (D‐A) complexes. The effect of the nanoscopic D‐A self‐assembly on the bulk mobility of the materials was probed using SCLC measurements. The mixed D‐A random complexes exhibited ambipolar charge transport characteristics with higher values for the average bulk hole mobility estimate. P4VP(OPV_0.25 + UPBI_0.75) exhibited an average hole mobility in the order of 10^?2cm² V^?1 s^?1 and electron mobility 10^?5cm² V^?1 s^?1. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 2403–2412     

Stabilizing labile DNA–protein complexes in polyacrylamide gels

The electrophoretic mobility‐shift assay (EMSA) is one of the most popular tools in molecular biology for measuring DNA–protein interactions. EMSA, as standardly practiced today, works well for complexes with association binding constants K_a>10⁹ M^?1 under normal conditions of salt and pH. Many DNA–protein complexes are not stable enough so that they dissociate while moving through the gel matrix giving smeared bands that are difficult to quantitate reliably. In this work we demonstrate that the addition of the osmolyte triethylene glycol to polyacrylamide gels dramatically stabilizes labile restriction endonuclease EcoRI complexes with nonspecific DNA sequences enabling quantitation of binding using EMSA. The significant improvement of the technique resulting from the addition of osmolytes to the gel matrix greatly extends the range of binding constants of protein–DNA complexes that can be investigated using this widely used assay. Extension of this approach to other techniques used for separating bound and free components such as gel chromatography and CE is straightforward.     

Electrophoretic mobility of duplex DNA cross‐linked by mechlorethamine at a cytosine–cytosine mismatch pair

The common nitrogen mustard, mechlorethamine, can form a covalent cross‐link between the two bases of a cytosine–cytosine mismatch pair within a DNA duplex. The cross‐linked species can be readily separated from DNA monoadducts and unreacted strands using denaturing polyacrylamide gel electrophoresis. Here, using DNA 19 mer duplexes that are mechlorethamine cross‐linked at a C₄–C₃₅, C₇–C₃₂, C₁₀–C₂₉, or C₁₃–C₂₆ mismatch pair, we show that the denaturing polyacrylamide gel electrophoresis mobility of the cross‐linked species is particularly sensitive to the proximity of the C–C cross‐link to the duplex end. Species that are cross‐linked at a C₄–C₃₅ mismatch have greater mobilities than those cross‐linked at C₇–C₃₂ or C₁₃–C₂₆, and the species with a central C₁₀–C₂₉ cross‐link have the lowest mobility. The mobility is also dependent on the proximity of the cross‐link to a 5′‐³²P‐phosphate or a 5′‐fluorescein label. We interpret these results in terms of the conformational properties of the cross‐linked species in the denaturing gel. The results are consistent with the retention of partial duplex character at the end proximal to the cross‐link, with an influence on the mobility of the GC/AT ratio proximal to the cross‐link and at the duplex end, and a small but discernible effect of the label.     

Unravelling the Correlation between Charge Mobility and Cocrystallization in Rod–Rod Block Copolymers for High‐Performance Field‐Effect Transistors

Cocrystallization involving two or more components aggregating into cocrystals allows the preparation of materials with markedly improved charge mobility. This approach however, is little explored in all‐conjugated block copolymers (BCPs). Herein, we report the first investigation into the correlation between cocrystals and charge mobility in a series of new all‐conjugated BCPs: poly(3‐butylthiophene)‐b‐poly(3‐hexylselenophene) (P3BT‐b‐P3HS) for high‐performance field‐effect transistors. These rationally synthesized rod–rod BCPs self‐assemble into cocrystals with high charge mobilities. Upon one‐step thermal annealing, their charge mobilities decrease slightly despite their increased crystallinities. After two‐step thermal annealing, P3BT‐b‐P3HS (P3BT/P3HS=2:1) and (1:1) cocrystals disappear and phase separation occurs, leading to greatly decreased charge mobilities. In contrast, P3BT‐b‐P3HS (1:2) retains its cocrystalline structure and its charge mobility.     

Antibacterial Activities and Nuclease Properties of Two New Ternary Copper(II) Complexes with 2‐(4′‐Thiazolyl)‐benzimidazole and 2,2′‐Bipyridine/1,10‐phenanthroline

Two new complexes: [Cu(TBZ)(bipy)Cl]Cl·H₂O ( 1 ) and [Cu(TBZ)(phen)Cl]Cl·H₂O ( 2 ) [TBZ=2‐(4′‐thiazolyl)‐ benzimidazole, phen=1,10‐phenanthroline and bipy=2,2′‐bipyridine] have been synthesized and characterized by elemental analysis, molar conductivity, IR, and UV‐vis methods. Complex 2 , structurally characterized by single‐crystal X‐ray crystallography, crystallizes in the monoclinic space group P2₁/c in a unit cell of a=0.85257(12) nm, b=2.5358(4) nm, c=1.15151(13) nm, β=118.721(8)°, V=2.183.2(5) nm³, Z=4, D_c=1.624 g·cm⁻³, µ=1.367 mm⁻¹. The complexes, free ligands and chloride copper(II) salt were each tested for their ability to inhibit the growth of two gram‐positive (B. subtilis and S. aureus) and two gram‐negative (Salmonella and E. coli) bacteria. The complexes showed good antibacterial activities against the microorganisms. The interaction between the complexes and calf thymus DNA in aqueous solution was investigated adopting electronic absorption spectroscopy, fluorescence spectroscopy, viscosity measurements and cyclic voltammetry. Results suggest that the two complexes can bind to DNA by intercalative mode. In addition, the result of agarose gel electrophoresis suggested that the complexes can cleave the plasmid DNA at physiological pH and room temperature. Mechanistic studies with different inhibiting reagents reveal that hydroxyl radicals, and a singlet oxygen‐like copper‐oxo species are all involved in the DNA scission process mediated by the complexes.