Pavel Ulbrich

Carboxylic Carbon Quantum Dots as a Fluorescent Sensing Platform for DNA Detection

The demand for simple, sensitive, affordable, and selective DNA biosensors is ubiquitous, due to the important role that DNA detection performs in the areas of disease diagnostics, environment monitoring, and food safety. A novel application of carboxylic carbon quantum dots (cCQD) is highlighted in this study. Herein, cCQD function as a nanoquencher in the detection of nucleic acid based on a homogeneous fluorescent assay. To that purpose, the performance of two types of cCQD, namely, citric acid QD and malic acid QD, is evaluated. The principle behind the sensing of nucleic acid lies in the different propensity of single-stranded DNA and double-stranded DNA to adsorb onto the surface of cCQD. For both types of cCQD, a superior range of detection of at least 3 orders of magnitude is achieved, and the potential to distinguish single-base mismatch is also exhibited. These findings are anticipated to provide valuable insights on the employment of cCQD for the fabrication of future DNA biosensors.

Conserved and Variable Features of Gag Structure and Arrangement in Immature Retrovirus Particles

ABSTRACT The assembly of retroviruses is driven by oligomerization of the Gag polyprotein. We have used cryo-electron tomography together with subtomogram averaging to describe the three-dimensional structure of in vitro-assembled Gag particles from human immunodeficiency virus, Mason-Pfizer monkey virus, and Rous sarcoma virus. These represent three different retroviral genera: the lentiviruses, betaretroviruses and alpharetroviruses. Comparison of the three structures reveals the features of the supramolecular organization of Gag that are conserved between genera and therefore reflect general principles of Gag-Gag interactions and the features that are specific to certain genera. All three Gag proteins assemble to form approximately spherical hexameric lattices with irregular defects. In all three genera, the N-terminal domain of CA is arranged in hexameric rings around large holes. Where the rings meet, 2-fold densities, assigned to the C-terminal domain of CA, extend between adjacent rings, and link together at the 6-fold symmetry axis with a density, which extends toward the center of the particle into the nucleic acid layer. Although this general arrangement is conserved, differences can be seen throughout the CA and spacer peptide regions. These differences can be related to sequence differences among the genera. We conclude that the arrangement of the structural domains of CA is well conserved across genera, whereas the relationship between CA, the spacer peptide region, and the nucleic acid is more specific to each genus.

Distinct Roles for Nucleic Acid in In Vitro Assembly of Purified Mason-Pfizer Monkey Virus CANC Proteins

ABSTRACT In contrast to other retroviruses, Mason-Pfizer monkey virus (M-PMV) assembles immature capsids in the cytoplasm. We have compared the ability of minimal assembly-competent domains from M-PMV and human immunodeficiency virus type 1 (HIV-1) to assemble in vitro into virus-like particles in the presence and absence of nucleic acids. A fusion protein comprised of the capsid and nucleocapsid domains of Gag (CANC) and its N-terminally modified mutant (ΔProCANC) were used to mimic the assembly of the viral core and immature particles, respectively. In contrast to HIV-1, where CANC assembled efficiently into cylindrical structures, the same domains of M-PMV were assembly incompetent. The addition of RNA or oligonucleotides did not complement this defect. In contrast, the M-PMV ΔProCANC molecule was able to assemble into spherical particles, while that of HIV-1 formed both spheres and cylinders. For M-PMV, the addition of purified RNA increased the efficiency with which ΔProCANC formed spherical particles both in terms of the overall amount and the numbers of completed spheres. The amount of RNA incorporated was determined, and for both rRNA and MS2-RNA, quantities similar to that of genomic RNA were encapsidated. Oligonucleotides also stimulated assembly; however, they were incorporated into ΔProCANC spherical particles in trace amounts that could not serve as a stoichiometric structural component for assembly. Thus, oligonucleotides may, through a transient interaction, induce conformational changes that facilitate assembly, while longer RNAs appear to facilitate the complete assembly of spherical particles.

In Vitro Assembly of Virus-Like Particles of a Gammaretrovirus, the Murine Leukemia Virus XMRV

ABSTRACT Immature retroviral particles are assembled by self-association of the structural polyprotein precursor Gag. During maturation the Gag polyprotein is proteolytically cleaved, yielding mature structural proteins, matrix (MA), capsid (CA), and nucleocapsid (NC), that reassemble into a mature viral particle. Proteolytic cleavage causes the N terminus of CA to fold back to form a β-hairpin, anchored by an internal salt bridge between the N-terminal proline and the inner aspartate. Using an in vitro assembly system of capsid-nucleocapsid protein (CANC), we studied the formation of virus-like particles (VLP) of a gammaretrovirus, the xenotropic murine leukemia virus (MLV)-related virus (XMRV). We show here that, unlike other retroviruses, XMRV CA and CANC do not assemble tubular particles characteristic of mature assembly. The prevention of β-hairpin formation by the deletion of either the N-terminal proline or 10 initial amino acids enabled the assembly of ΔProCANC or Δ10CANC into immature-like spherical particles. Detailed three-dimensional (3D) structural analysis of these particles revealed that below a disordered N-terminal CA layer, the C terminus of CA assembles a typical immature lattice, which is linked by rod-like densities with the RNP.

Purification of proteins containing zinc finger domains using immobilized metal ion affinity chromatography

Heterologous proteins are frequently purified by immobilized metal ion affinity chromatography (IMAC) based on their modification with a hexa-histidine affinity tag (His-tag). The terminal His-tag can, however, alter functional properties of the tagged protein. Numerous strategies for the tag removal have been developed including chemical treatment and insertion of protease target sequences in the protein sequence. Instead of using these approaches, we took an advantage of natural interaction of zinc finger domains with metal ions to purify functionally similar retroviral proteins from two different retroviruses. We found that these proteins exhibited significantly different affinities to the immobilized metal ions, despite that both contain the same type of zinc finger motif (i.e., CCHC). While zinc finger proteins may differ in biochemical properties, the multitude of IMAC platforms should allow relatively simple yet specific method for their isolation in native state.

Light-activated polymethylmethacrylate nanofibers with antibacterial activity

The creation of an antibacterial material with triggerable properties enables us to avoid the overuse or misuse of antibacterial substances and, thus, prevent the emergence of resistant bacterial strains. As a potential light-activated antibacterial material, polymethylmethacrylate (PMMA) nanofibers doped with silver nanoparticles (AgNPs) and meso-tetraphenylporphyrin (TPP) were prepared by electrospinning. TPP was chosen as an effectively reactive oxygen species (ROS) producer. Antibacterial tests on Staphylococcus epidermidis (S. epidermidis) and Enterococcus faecalis (E. faecalis) showed the excellent light-triggerable antibacterial activity of the doped materials. Upon light irradiation at the wavelength corresponding to the TPP absorption peak (405nm), antibacterial activity dramatically increased, mostly due to the release of AgNPs from the polymer matrix. Furthermore, under prolonged light irradiation, the AgNPs/TPP/PMMA nanofibers, displayed enhanced longevity and photothermal stability. Thus, our results suggest that the proposed material is a promising option for the photodynamic inactivation of bacteria.

Thermo-responsive adhesion properties of composite hydrogel microcapsules

The present work describes the synthesis and characterisation of thermo-responsive microcapsules consisting of poly-N-isopropylacrylamide (PNIPAM) hydrogel, hydrophilic citrate-stabilized super-paramagnetic iron oxide nanoparticles (SPIONs) that perform the function of a local heat source and hydrophobic nanoparticles (either SiO2 or oleic acid-coated SPIONs) that stabilize the microcapsule surface. The microcapsules have been synthesized by the inverse Pickering emulsion polymerisation method. The effect of iron oxide concentration in the hydrogel on the shape, size, shrinkage ratio and heating rate of the microcapsules has been systematically investigated. The adhesion properties of the composite microcapsules towards a range of substrates have been characterised in a microfluidic flow cell and it was found that the temperature-induced change of the microcapsule size is an effective way of controlling adhesion. The induction heating of the embedded SPIONs makes it possible to control adhesion remotely in environments where macroscopic heating is not possible.

Temperature-responsive PLLA/PNIPAM nanofibers for switchable release

Smart antimicrobial materials with on-demand drug release are highly desired for biomedical applications. Herein, we report about temperature-responsive poly(N-isopropylacrylamide) (PNIPAM) nanospheres doped with crystal violet (CV) and incorporated into the poly-l-lactide (PLLA) nanofibers. The nanofibers were prepared by electrospinning, using different initial polymers ratios. The morphology of the nanofibers and polymers distribution in the nanofibers were characterized by scanning electron microscopy (SEM) and atomic force microscopy (AFM). The interaction between PNIPAM and PLLA in the nanofibers was studied by Fourier transform infrared spectroscopy (FTIR) and its effect on the PNIPAM phase transition was also investigated. It was shown that by the changing of the environmental temperature across the lower critical solution temperature (LCST) of PNIPAM, the switchable wettability and controlled CV release can be achieved. The temperature-dependent release kinetics of CV from polymer nanofibers was investigated by ultraviolet-visible spectroscopy (UV-Vis). The temperature-responsive release of antibacterial CV was also tested for triggering of antibacterial activity, which was examined on Staphylococcus epidermidis (S. epidermidis) and Escherichia coli (E. coli). Thus, the proposed material is promising value for controllable drug-release.

Nanoscaled porphyrinic metal–organic frameworks: photosensitizer delivery systems for photodynamic therapy

The photocytotoxic activity of porphyrin-containing materials including metal-organic frameworks (MOFs) has attracted ever increasing interest. We have developed a simple synthesis of hexagonal PCN-222/MOF-545 nanoparticles, which are powerful in inducing reactive oxygen species-mediated apoptosis of cancer cells upon visible light irradiation. The extent of the cytotoxic effect well correlates with the nanoparticle size and structural instability. High phototoxicity of the presented nanoparticles and their deactivation within several hours open up the door to possible applications in cancer therapy.

One-step preparation of antimicrobial silver nanoparticles in polymer matrix

Simple one-step procedure for in situ preparation of silver nanoparticles (AgNPs) in the polymer thin films is described. Nanoparticles (NPs) were prepared by reaction of N-methyl pyrrolidone with silver salt in semi-dry polymer film and characterized by transmission electron microscopy, XPS, and UV–Vis spectroscopy techniques. Direct synthesis of NPs in polymer has several advantages; even though it avoids time-consuming NPs mixing with polymer matrix, uniform silver distribution in polymethylmethacrylate (PMMA) films is achieved without necessity of additional stabilization. The influence of the silver concentration, reaction temperature and time on reaction conversion rate, and the size and size-distribution of the AgNPs was investigated. Polymer films doped with AgNPs were tested for their antibacterial activity on Gram-negative bacteria. Antimicrobial properties of AgNPs/PMMA films were found to be depended on NPs concentration, their size and distribution. Proposed one-step synthesis of functional polymer containing AgNPs is environmentally friendly, experimentally simple and extremely quick. It opens up new possibilities in development of antimicrobial coatings with medical and sanitation applications.