Method for the analysis of contribution of sliding and hopping to a facilitated diffusion of DNA-binding protein: Application to in vivo data

M. Tabaka, K. Burdzy, and R. Hołyst

Phys. Rev. E, 2015, 92, 022721

DNA-binding protein searches for its target, a specific site on DNA, by means of diffusion. The search process consists of many recurrent steps of one-dimensional diffusion (sliding) along the DNA chain and three-dimensional diffusion (hopping) after dissociation of a protein from the DNA chain. Here we propose a computational method that allows extracting the contribution of sliding and hopping to the search process in vivo from the measurements of the kinetics of the target search by the lac repressor in Escherichia coli [P. Hammar et al., Science 336, 1595 (2012)]. The method combines lattice Monte Carlo simulations with the Brownian excursion theory and includes explicitly steric constraints for hopping due to the helical structure of DNA. The simulation results including all experimental data reveal that the in vivo target search is dominated by sliding. The short-range hopping to the same base pair interrupts one-dimensional sliding while long-range hopping does not contribute significantly to the kinetics of the search of the target in vivo.

Application of Europium Multiwalled Carbon Nanotubes as Novel Luminophores in an Electrochemiluminescent Aptasensor for Thrombin Using Multiple Amplification Strategies

Dan Wu, Xia Xin, Xuehui Pang, M. Pietraszkiewicz, R. Hołyst, Xian′ge Sun, and Qin Wei

ACS Appl. Mater. Interfaces 2015, 7, 23, 12663–12670

A novel electrochemiluminescent (ECL) aptasensor was proposed for the determination of thrombin (TB) using exonuclease-catalyzed target recycling and hybridization chain reaction (HCR) to amplify the signal. The capture probe was immobilized on an Au-GS-modified electrode through a Au–S bond. Subsequently, the hybrid between the capture probe and the complementary thrombin binding aptamer (TBA) was aimed at obtaining double-stranded DNA (dsDNA). The interaction between TB and its aptamer led to the dissociation of dsDNA because TB has a higher affinity to TBA than the complementary strands. In the presence of exonuclease, aptamer was selectively digested and TB could be released for target recycling. Extended dsDNA was formed through HCR of the capture probe and two hairpin DNA strands (NH2-DNA1 and NH2-DNA1). Then, numerous europium multiwalled carbon nanotubes (Eu-MWCNTs) could be introduced through amidation reaction between NH2-terminated DNA strands and carboxyl groups on the Eu-MWCNTs, resulting in an increased ECL signal. The multiple amplification strategies, including the amplification of analyte recycling and HCR, and high ECL efficiency of Eu-MWCNTs lead to a wide linear range (1.0 × 10–12–5.0 × 10–9 mol/L) and a low detection limit (0.23 pmol/L). The method was applied to serum sample analysis with satisfactory results.

Sterilization of polydimethylsiloxane surface with Chinese herb extract: a new antibiotic mechanism of chlorogenic acid

Song Ren, Ming Wu, Jiayu Guo, Wang Zhang, Xiaohan Liu, Lili Sun, Robert Hołyst, Sen Hou, Yongchun Fang and Xizeng Feng

Scientific Reports volume, 2015, 5, 10464

Coating of polydimethylsiloxane (PDMS) surface with a traditional Chinese herb extract chlorogenic acid (CA) solves the contemporary problem of sterilization of PDMS surface. The E. coli grows slower and has a higher death rate on the CA-coated PDMS surfaces. A smoother morphology of these E. coli cell wall is observed by atomic force microscopy (AFM). Unlike the reported mechanism, where CA inhibits bacterial growth by damaging the cell membrane in the bulk solution, we find the CA-coated PDMS surface also decreases the stiffness of the cell wall. A decrease in the Young’s modulus of the cell wall from 3 to 0.8 MPa is reported. Unexpectedly, the CA effect on the swarming ability and the biofilm stability of the bacteria can be still observed, even after they have been removed from the CA environment, indicating a decrease in their resistance to antibiotics for a prolonged time. The CA-coated PDMS surface shows better antibiotic effect against three types of both Gram-positive and Gran-negative bacteria than the gentamicin-coated PDMS surface. Coating of CA on PDMS surface not only solves the problem of sterilization of PDMS surface, but also shines light on the application of Chinese traditional herbs in scientific research.

Go with the flow

P. Garstecki and R. Hołyst

Nature Physics, 2015, 11, 305–306

The article focuses on a research paper on an experiment in which evenly spaced water droplets was generated by using a microfluidic device by Tsevi Beatus and colleagues in a 2006 issue of the journal “Nature Physics.” Topics discussed include observance of unusual dispersion relations following a spectral analysis of the collective vibrations of droplets, impact of long-range hydrodynamic interactions on droplets in microfluidics, and role of model systems in physics.

Gold–Oxoborate Nanocomposites and Their Biomedical Applications

K. Wybrańska, J. Paczesny, K. Serejko, K. Sura, K. Włodyga, I. Dzięcielewski, S. T. Jones, A. Śliwa, I. Wybrańska, R. Hołyst, O. A. Scherman and M. Fiałkowski

ACS Appl. Mater. Interfaces 2015, 7, 7, 3931–3939

A novel inorganic nanocomposite material, called BOA, which has the form of small building blocks composed of gold nanoparticles embedded in a polyoxoborate matrix, is presented. It is demonstrated that cotton wool decorated with the BOA nanocomposite displays strong antibacterial activity toward both Gram-positive and -negative bacteria strains. Importantly, the modified cotton does not release any toxic substances, and the bacteria are killed upon contact with the fibers coated with the BOA. Toxicity tests show that the nanocomposite–in spite of its antiseptic properties–is harmless for mammalian cells. The presented method of surface modification utilizes mild, environmentally friendly fabrication conditions. Thus, it offers a facile approach to obtain durable nontoxic antiseptic coatings for biomedical applications.

A method for rapid screening of interactions of pharmacologically active compounds with albumin

A. Majcher, A. Lewandrowska, F. Herold, J. Stefanowicz, T. Słowiński, A. P. Mazurek, S. A.Wieczorek and R. Hołyst

Analytica Chimica Acta, 2015, 855, 51-59

We determine the association constants for ligand–protein complex formation using the flow injection method. We carry out the measurements at high flow rates (F = 1 mL min−1) of a carrier phase. Therefore, determination of the association constant takes only a few minutes. Injection of 1 nM of the ligand (10 μL of 1 μM concentration of the ligand solution) is sufficient for a single measurement. This method is tested and verified for a number of complexes of selected drugs (cefaclor, etodolac, sulindac) with albumin (BSA). We obtain K = 4.45 × 103 M−1 for cefaclor, K = 1.00 × 105 M−1 for etodolac and K = 1.03 × 105 M−1 for sulindac in agreement with the literature data. We also determine the association constants of 20 newly synthesized 3β- and 3α-aminotropane derivatives with potential antipsychotic activity – ligands of 5-HT1A, 5-HT2A and D2 receptors with the albumin. Results of the studies reported here indicate that potential antipsychotic drugs bind weakly to the transporter protein (BSA) with ≈ 102–103 M−1. Our method allows measuring K in a wide range of values (102–109 M−1). This range depends only on the solubility of the ligand and sensitivity of the detector.

A molecular dynamics test of the Hertz–Knudsen equation for evaporating liquids

R. Hołyst, M. Litniewski and D. Jakubczyk

Soft Matter, 2015,11, 7201-7206

The precise determination of evaporation flux from liquid surfaces gives control over evaporation-driven self-assembly in soft matter systems. The Hertz–Knudsen (HK) equation is commonly used to predict evaporation flux. This equation states that the flux is proportional to the difference between the pressure in the system and the equilibrium pressure for liquid/vapor coexistence. We applied molecular dynamics (MD) simulations of one component Lennard-Jones (LJ) fluid to test the HK equation for a wide range of thermodynamic parameters covering more than one order of magnitude in the values of flux. The flux determined in the simulations was 3.6 times larger than that computed from the HK equation. However, the flux was constant over time while the pressures in the HK equation exhibited strong fluctuations during simulations. This observation suggests that the HK equation may not appropriately grasp the physical mechanism of evaporation. We discuss this issue in the context of momentum flux during evaporation and mechanical equilibrium in this process. Most probably the process of evaporation is driven by a tiny difference between the liquid pressure and the gas pressure. This difference is equal to the momentum flux i.e. momentum carried by the molecules leaving the surface of the liquid during evaporation. The average velocity in the evaporation flux is very small (two to three orders of magnitude smaller than the typical velocity of LJ atoms). Therefore the distribution of velocities of LJ atoms does not deviate from the Maxwell–Boltzmann distribution, even in the interfacial region.

Hollow microtubes made of carbon, boron and gold: novel semiconducting nanocomposite material for applications in electrochemistry and temperature sensing

J. Paczesny, K. Wybrańska, J. Niedziółka-Jönsson, E. Roźniecka, M. Wadowska, P. Zawal, I. Malka, I. Dzięcielewski, D. Prochowicz, R. Hołyst and M. Fiałkowski

RSC Adv., 2015,5, 64083-64090

Carbon based nanocomposites have recently been intensively investigated as a new class of functional hybrid materials. Here, we present a procedure to obtain a new nanocomposite material made of carbon, boron and gold for applications in electrochemistry and electronics. The presented fabrication protocol uses cellulose fibers as a template that is first modified with an inorganic nanocomposite material consisting of gold nanoparticles (AuNPs) embedded in a polyoxoborate matrix, and then is subjected to the process of thermal decomposition. The as obtained material has a form of tubes with a diameter of a couple of micrometers that are composed of carbonized cellulose coated with the polyoxoborate–AuNP nanocomposite. This inorganic shell, which covers the outer surface of the carbon microtubes, serves as a scaffold that makes the structure stable. The obtained material exhibits electrical properties of a semiconductor with the width of the band gap of about 0.6 eV, and forms Schottky contact with a metal electrode. We show that the new material is suitable for preparation of the NCT-type thermistor. We also demonstrate application of the new nanocomposite in electrochemistry for modification of the surface of a working electrode. Experiments carried out with three exemplary redox probes show that the electrochemical performance of the modified electrode depends greatly on the amount of AuNPs in the nanocomposite.

Manipulation of multiple-responsive fluorescent supramolecular materials based on the inclusion complexation of cyclodextrins with Tyloxapol

J. Shen, J. Pang, T. Kalwarczyk, R. Hołyst, Xia Xin, G. Xu, X. Luan and Y. Yang

J. Mater. Chem. C, 2015, 3, 8104-8113

A fluorescent supramolecular hydrogel was prepared by α-cyclodextrin (α-CD) and Tyloxapol, which can be considered as an oligomer of the nonionic surfactant polyoxyethylene tert-octylphenyl ether (Triton X-100, TX-100) with a polymerization degree below 7. For comparison, both Tyloxapol and TX-100 were selected to form hydrogels with α-CD to get more information about the interaction between different types of surfactants and cyclodextrin. These hydrogels have been thoroughly characterized using various techniques including phase behavior observation, transmission electron microscopy (TEM), field emission scanning electron microscopy (FE-SEM), fluorescence spectra, fluorescence microscopy observations, Fourier transform infrared (FT-IR) spectroscopy, 1H NMR, 2D 1H-1H ROESY NMR, small-angle X-ray scattering (SAXS), X-ray diffraction (XRD) and rheological measurements. The hydrogels of α-CD/Tyloxapol are responsive to external stimuli including temperature, pH and guest molecules, and present gelation-induced quenching fluorescence emission properties. The reason for this phenomenon may be that Tyloxapol molecules come into the cavity of α-CD and form the inclusion complexes. Due to the high electron density of the narrow cavity of α-CD, it induces the shift of the electron on the benzene ring which can weaken the π–π interaction and lead to the fluorescence quenching. Moreover, the hydrogel formed by α-CD/Tyloxapol is highly responsive to the formaldehyde (HCHO). The addition of a small amount of HCHO can induce a gel-to-sol transition. Interestingly, once the gel transforms into solution, it becomes fluorescent. This makes the α-CD/Tyloxapol hydrogel a promising candidate for HCHO detection and removal in home furnishings to reduce indoor environmental pollutants.

Tracking structural transitions of bovine serum albumin in surfactant solutions by fluorescence correlation spectroscopy and fluorescence lifetime analysis

X. Zhang, A. Poniewierski, S. Hou, K. Sozański, A. Wisniewska, S. A. Wieczorek, T. Kalwarczyk, L. Sun, R. Hołyst

Soft Matter, 2015,11, 2512-2518

The structural dynamics of proteins is crucial to their biological functions. A precise and convenient method to determine the structural changes of a protein is still urgently needed. Herein, we employ fluorescence correlation spectroscopy (FCS) to track the structural transition of bovine serum albumin (BSA) in low concentrated cationic (cetyltrimethylammonium chloride, CTAC), anionic (sodium dodecyl sulfate, SDS), and nonionic (pentaethylene glycol monododecyl ether, C12E5 and octaethylene glycol monododecyl ether, C12E8) surfactant solutions. BSA is labelled with the fluorescence dye called ATTO-488 (ATTO-BSA) to obtain steady fluorescence signals for measurements. We find that the diffusion coefficient of BSA decreases abruptly with the surfactant concentration in ionic surfactant solutions at concentrations below the critical micelle concentration (CMC), while it is constant in nonionic surfactant solutions. According to the Stokes–Sutherland–Einstein equation, the hydrodynamic radius of BSA in ionic surfactant solutions amounts to ∼6.5 nm, which is 1.7 times larger than in pure water or in nonionic surfactant solutions (3.9 nm). The interaction between BSA and ionic surfactant monomers is believed to cause the structural transition of BSA. We confirm this proposal by observing a sudden shift of the fluorescence lifetime of ATTO-BSA, from 2.3 ns to ∼3.0 ns, in ionic surfactant solutions at the concentration below CMC. No change in the fluorescence lifetime is detected in nonionic surfactant solutions. Moreover, by using FCS we are also able to identify whether the structural change of protein results from its self-aggregation or unfolding.

Towards improved precision in the quantification of surface-enhanced Raman scattering (SERS) enhancement factors: a renewed approach

A. Sivanesan, W. Adamkiewicz, G. Kalaivani, A. Kamińska, J. Waluk, R. Hołyst, E. L. Izake

Analyst, 2015,140, 489-496

This paper demonstrates a renewed procedure for the quantification of surface-enhanced Raman scattering (SERS) enhancement factors with improved precision. The principle of this method relies on deducting the resonance Raman scattering (RRS) contribution from surface-enhanced resonance Raman scattering (SERRS) to end up with the surface enhancement (SERS) effect alone. We employed 1,8,15,22-tetraaminophthalocyanato-cobalt(II) (4α-CoIITAPc), a resonance Raman- and electrochemically redox-active chromophore, as a probe molecule for RRS and SERRS experiments. The number of 4α-CoIITAPc molecules contributing to RRS and SERRS phenomena on plasmon inactive glassy carbon (GC) and plasmon active GC/Au surfaces, respectively, has been precisely estimated by cyclic voltammetry experiments. Furthermore, the SERS substrate enhancement factor (SSEF) quantified by our approach is compared with the traditionally employed methods. We also demonstrate that the present approach of SSEF quantification can be applied for any kind of different SERS substrates by choosing an appropriate laser line and probe molecule.

Quantitative influence of macromolecular crowding on gene regulation kinetics

M. Tabaka, T. Kalwarczyk and R. Hołyst

Nucleic Acids Research, Volume 42, Issue 2, 2014, Pages 727–738

We introduce macromolecular crowding quantitatively into the model for kinetics of gene regulation in Escherichia coli. We analyse and compute the specific-site searching time for 180 known transcription factors (TFs) regulating 1300 operons. The time is between 160 s (e.g. for SoxS Mw = 12.91 kDa) and 1550 s (e.g. for PepA6 of Mw = 329.28 kDa). Diffusion coefficients for one-dimensional sliding are between forumla for large proteins up to forumla for small monomers or dimers. Three-dimensional diffusion coefficients in the cytoplasm are 2 orders of magnitude larger than 1D sliding coefficients, nevertheless the sliding enhances the binding rates of TF to specific sites by 1–2 orders of magnitude. The latter effect is due to ubiquitous non-specific binding. We compare the model to experimental data for LacI repressor and find that non-specific binding of the protein to DNA is activation- and not diffusion-limited. We show that the target location rate by LacI repressor is optimized with respect to microscopic rate constant for association to non-specific sites on DNA. We analyse the effect of oligomerization of TFs and DNA looping effects on searching kinetics. We show that optimal searching strategy depends on TF abundance.

Length-scale dependent transport properties of colloidal and protein solutions for prediction of crystal nucleation rates

T. Kalwarczyk, K. Sozanski, S. Jakiela, A. Wisniewska, E. Kalwarczyk, K. Kryszczuk, S. Hou and R. Holyst

Nanoscale, 2014, 6, 10340-10346

We propose a scaling equation describing transport properties (diffusion and viscosity) in the solutions of colloidal particles. We apply the equation to 23 different systems including colloids and proteins differing in size (range of diameters: 4 nm to 1 μm), and volume fractions (10−3–0.56). In solutions under study colloids/proteins interact via steric, hydrodynamic, van der Waals and/or electrostatic interactions. We implement contribution of those interactions into the scaling law. Finally we use our scaling law together with the literature values of the barrier for nucleation to predict crystal nucleation rates of hard-sphere like colloids. The resulting crystal nucleation rates agree with existing experimental data.

A depletion layer in polymer solutions at an interface oscillating at the subnano- to submicrometer scale

K. Sozanski, A. Wisniewska, T. Piasecki, K. Waszczuk, A. Ochab-Marcinek, T. Gotszalk and R. Holyst

Soft Matter, 2014, 10, 7762-7768

The mobility of segments of the polymer mesh in a solution determines the dynamic response of the depletion layer (DL) to mechanical stimuli. This phenomenon can be used to vastly decrease the local viscosity experienced by any device performing periodic motion at the nano- and microscale in complex liquids. We refined the vibrating quartz tuning fork (QTF) method to probe the viscosity of model aqueous solutions of polyethylene glycol, covering a broad range of molecular weights (3 kDa to 1 MDa) and QTF oscillation amplitudes (50 pm to 100 nm). For semidilute solutions of PEGs of high molecular weight, we found a drop of local viscosity, up to two orders of magnitude below the bulk value. We propose a simple explanation based on the motion of the depletion layer, strongly supported by rheometry and dynamic light scattering results. We show that it is possible to directly probe the viscosity of the DL and increase its thickness far above the equilibrium value. The key role is played by the rate of relaxation of the entangled system. The relevance of this paradigm ranges from the basic research on dynamics of entangled systems to design of energy-efficient nanomachines operating in a crowded environment.

A flexible fluorescence correlation spectroscopy based method for quantification of the DNA double labeling efficiency with precision control

S. Hou, M. Tabaka, L. Sun, P. Trochimczyk, T. Kaminski, T. Kalwarczyk, X Zhang and R. Holyst

Laser Physics Letters, Volume 11, Number 8

We developed a laser-based method to quantify the double labeling efficiency of double-stranded DNA (dsDNA) in a fluorescent dsDNA pool with fluorescence correlation spectroscopy (FCS). Though, for quantitative biochemistry, accurate measurement of this parameter is of critical importance, before our work it was almost impossible to quantify what percentage of DNA is doubly labeled with the same dye. The dsDNA is produced by annealing complementary single-stranded DNA (ssDNA) labeled with the same dye at 5′ end. Due to imperfect ssDNA labeling, the resulting dsDNA is a mixture of doubly labeled dsDNA, singly labeled dsDNA and unlabeled dsDNA. Our method allows the percentage of doubly labeled dsDNA in the total fluorescent dsDNA pool to be measured. In this method, we excite the imperfectly labeled dsDNA sample in a focal volume of <1 fL with a laser beam and correlate the fluctuations of the fluorescence signal to get the FCS autocorrelation curves; we express the amplitudes of the autocorrelation function as a function of the DNA labeling efficiency; we perform a comparative analysis of a dsDNA sample and a reference dsDNA sample, which is prepared by increasing the total dsDNA concentration c (> 1) times by adding unlabeled ssDNA during the annealing process. The method is flexible in that it allows for the selection of the reference sample and the c value can be adjusted as needed for a specific study. We express the precision of the method as a function of the ssDNA labeling efficiency or the dsDNA double labeling efficiency. The measurement precision can be controlled by changing the c value.

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