Peter Mojzeš

Polymorphism of human telomeric quadruplex structure controlled by DNA concentration: a Raman study

DNA concentration has been recently suggested to be the reason why different arrangements are revealed for K+-stabilized human telomere quadruplexes by experimental methods requiring DNA concentrations differing by orders of magnitude. As Raman spectroscopy can be applied to DNA samples ranging from those accessible by absorption and CD spectroscopies up to extremely concentrated solutions, gels and even crystals; it has been used here to clarify polymorphism of a core human telomeric sequence G3(TTAG3)3 in the presence of K+ and Na+ ions throughout wide range of DNA concentrations. We demonstrate that the K+-structure of G3(TTAG3)3 at low DNA concentration is close to the antiparallel fold of Na+-stabilized quadruplex. On the increase of G3(TTAG3)3 concentration, a gradual transition from antiparallel to intramolecular parallel arrangement was observed, but only for thermodynamically equilibrated K+-stabilized samples. The transition is synergically supported by increased K+ concentration. However, even for extremely high G3(TTAG3)3 and K+ concentrations, an intramolecular antiparallel quadruplex is spontaneously formed from desalted non-quadruplex single-strand after addition of K+ ions. Thermal destabilization or long dwell time are necessary to induce interquadruplex transition. On the contrary, Na+-stabilized G3(TTAG3)3 retains its antiparallel folding regardless of the extremely high DNA and/or Na+ concentrations, thermal destabilization or annealing.

Charge Transport in DNA Oligonucleotides with Various Base-Pairing Patterns

We combined various experimental (scanning tunneling microscopy and Raman spectroscopy) and theoretical (density functional theory and molecular dynamics) approaches to study the relationships between the base-pairing patterns and the charge transfer properties in DNA 32-mer duplexes that may be relevant for identification and repair of defects in base pairing of the genetic DNA and for DNA use in nanotechnologies. Studied were two fully Watson-Crick (W-C)-paired duplexes, one mismatched (containing three non-W-C pairs), and three with base pairs chemically removed. The results show that the charge transport varies strongly between these duplexes. The conductivity of the mismatched duplex is considerably lower than that of the W-C-paired one despite the fact that their structural integrities and thermal stabilities are comparable. Structurally and thermally much less stable abasic duplexes have still lower conductivity but not markedly different from the mismatched duplex. All duplexes are likely to conduct by the hole mechanism, and water orbitals increase the charge transport probability.

Testing anionic spacers by SERRS (surface-enhanced resonance Raman scattering) of a cationic free-base porphyrin in systems with laser-ablated Ag colloids

Abstract Thiopheneacetic acid and several thiol-based anionic species were tested as prospective spacers between the surface of Ag colloidal particles (prepared by laser ablation) and a chromophoric cationic adsorbate. Time-evolution of the SERRS signal of a cationic free base porphyrin, 5,10,15,20-tetrakis(1-methyl-4-pyridiniumyl)porphine (H 2 TMPyP) attached to the surface of laser-ablated Ag colloidal particles modified by adsorption of either 3-thiopheneacetic acid or a thiol-based anionic species was measured on 2 h time-scale and analyzed. While H 2 TMPyP adsorbed on bare surfaces of laser-ablated Ag colloidal particles is rapidly converted into AgTMPyP surface complex (spectrally identical with its synthetic analogue), denaturation of the native structure of the porphyrin by formation of the same AgTMPyP surface species was not observed upon adsorption on the modified colloidal surfaces. The native structure of H 2 TMPyP was fully preserved upon adsorption on Ag colloid modified by 3-thiopheneacetic acid and good quality SERRS spectra of H 2 TMPyP were obtained from Ag colloid/3-thiopheneacetic acid/H 2 TMPyP system. By contrast, none of the thiol-based spacers enabled to obtain SERRS spectrum of unperturbed H 2 TMPyP. Modification of Ag colloid by 3-mercaptopropionic acid, 2-mercaptoethanesulfonic acid, 2-mercaptoethanesulfonate and 3-mercaptopropanesulfonate did not prevent metalation of the porphyrin, however, it affected the structure of the resulting AgTMPyP surface complex, as witnessed by the difference of the characteristic marker bands (384, 1005, 1366 and 1566 cm −1 ) from those of synthetically prepared AgTMPyP. Modification of the colloid by mercaptoethanol prevents porphyrin metalation, however, it induces another kind of perturbation of the native structure of H 2 TMPyP.

The molecular force field of guanine and its deuterated species as determined from neutron inelastic scattering and resonance Raman measurements

Neutron inelastic scattering (NIS) spectra from polycrystalline samples and ultraviolet resonance Raman scattering (RRS) spectra from aqueous solutions of guanine and CS-deuterated and (N9, NI, C2-amino)-deuterated guanine are reported. These measurements allowed theoretical simulations of the vibrational wavenumbers and intensities of the NIS and RRS bands to be performed. Å valence force field enabled the normal mode wavenumbers, as well as the atomic displacements, to be calculated. The NIS intensities were simulated by considering multi-phonon interactions arising from the lattice mode couplings with the internal molecular vibrational modes. The RRS intensities were simulated within the framework of the so-called “small shift approximation”, by using the molecular bond-order changes induced by the electronic transition from the ground to the first electronic excited state. It is shown that NIS spectroscopy mainly provides information on the guanine out-of-plane modes of vibration, while RRS allows the in-plane stretching vibrational motions to be analyzed.

Probing strong optical fields in compact aggregates of silver nanoparticles by SERRS of protoporphyrin IX

TEM images and measurements of SERRS (surface-enhanced resonance Raman scattering) spectra as a function of the porphyrin concentrations in systems with unmodified and chloride-modified Ag nanoparticles and protoporphyrin IX (PPIX) are reported. TEM images have shown formation of compact aggregates in systems with chloride modified Ag nanoparticles, as opposed to systems with the unmodified particles constituted by isolated particles. SERRS spectra of PPIX as a function of PPIX concentration were measured and subjected to factor analysis. Two spectral components were identified and tentatively attributed to unperturbed PPIX and to Ag+ -PPIX surface species. Concentration value of the SERRS spectral detection limit of the latter species was determined to be nearly three orders of magnitude lower in the system with the compact aggregates than in the system with separated nanoparticles and achieves the value of 1 x 10(-10) M in a macrosampling Raman experiment. TEM images and SERRS-micro-Raman spectra of single compact aggregates of chloride-modified Ag nanoparticles incorporating PPIX molecules were acquired from a sample prepared by attachment of the aggregates to amine groups of derivatized, SiOx/formvar coated copper grids for TEM. The SERRS signal has shown large temporal fluctuations as well as variations from one aggregate to another. Within the signal fluctuations, a SERRS spectrum showing the characteristic bands of both SERRS spectral forms of PPIX and originating most probably from a few PPIX molecules located in hot spots in the interstices between the Ag nanoparticles, was obtained.

Lincomycin Biosynthesis Involves a Tyrosine Hydroxylating Heme Protein of an Unusual Enzyme Family

The gene lmbB2 of the lincomycin biosynthetic gene cluster of Streptomyces lincolnensis ATCC 25466 was shown to code for an unusual tyrosine hydroxylating enzyme involved in the biosynthetic pathway of this clinically important antibiotic. LmbB2 was expressed in Escherichia coli, purified near to homogeneity and shown to convert tyrosine to 3,4-dihydroxyphenylalanine (DOPA). In contrast to the well-known tyrosine hydroxylases (EC 1.14.16.2) and tyrosinases (EC 1.14.18.1), LmbB2 was identified as a heme protein. Mass spectrometry and Soret band-excited Raman spectroscopy of LmbB2 showed that LmbB2 contains heme b as prosthetic group. The CO-reduced differential absorption spectra of LmbB2 showed that the coordination of Fe was different from that of cytochrome P450 enzymes. LmbB2 exhibits sequence similarity to Orf13 of the anthramycin biosynthetic gene cluster, which has recently been classified as a heme peroxidase. Tyrosine hydroxylating activity of LmbB2 yielding DOPA in the presence of (6R)-5,6,7,8-tetrahydro-L-biopterin (BH4) was also observed. Reaction mechanism of this unique heme peroxidases family is discussed. Also, tyrosine hydroxylation was confirmed as the first step of the amino acid branch of the lincomycin biosynthesis.

Surface-enhanced resonance Raman spectroscopy of porphyrin and metalloporphyrin species in systems with Ag nanoparticles and their assemblies.

The advantages of systems with Ag nanoparticles and their assemblies for surface-enhanced resonance Raman scattering (SERRS) spectral investigation, detection and determination of porphyrin species are demonstrated. SERRS spectral detection limits of the testing porphyrin species (including porphyrin aggregates) in these systems are shown to be, on average, 10(2)-10(3) lower than detection limits by resonance Raman scattering (RRS). Systems with Ag nanoparticles modified by anionic organosulfur spacers enable us to obtain SERRS spectra of unperturbed cationic porphyrin species. In the case of thiopheneacetate-modified Ag particles prepared by laser ablation, no negative effect of the spacer on the spectral detection limit of the porphyrin was observed. Systems with isolated Ag nanoparticles allow for obtaining SERRS spectra of porphyrin species upon excitation into the Soret electronic absorption band which leads to at least a 10-fold decrease in the detection limit.

Characterization and surface-enhanced Raman spectral probing of silver hydrosols prepared by two-wavelength laser ablation and fragmentation

A four step Ag foil laser ablation-Ag nanoparticle fragmentation procedure in ultrapure water was carried out both under argon and in air. Pulses of a high power Nd/YAG laser were used for laser ablation (1064 nm) and for the three step Ag hydrosol treatment in the absence of Ag foil in the sequence 1064-532-1064 nm. Transmission electron microscopy (TEM) and surface plasmon (SP) extinction spectra provide evidence of Ag nanoparticle fragmentation in the second and third step of the procedure carried out under argon. While polydispersity of Ag hydrosol increases in the second step, both the polydispersity and the mean size of the nanoparticles are reduced in the third step. Qualitative and quantitative surface-enhanced Raman scattering (SERS)/surface-enhanced resonance Raman scattering (SERRS) spectral probing of systems with Ag hydrosols and the selected adsorbates at 514.5 nm excitation shows that Ag hydrosols obtained in the second step of the preparation procedure carried out in air are the most suitable substrates for SERS/SERRS experiments performed at this excitation wavelength.

Growth of algal biomass in laboratory and in large-scale algal photobioreactors in the temperate climate of western Germany

Growth of Chlorella vulgaris was characterized as a function of irradiance in a laboratory turbidostat (1L) and compared to batch growth in sunlit modules (5-25L) of the commercial NOVAgreen photobioreactor. The effects of variable sunlight and culture density were deconvoluted by a mathematical model. The analysis showed that algal growth was light-limited due to shading by external construction elements and due to light attenuation within the algal bags. The model was also used to predict maximum biomass productivity. The manipulative experiments and the model predictions were confronted with data from a production season of three large-scale photobioreactors: NOVAgreen (<36,000L), IGV (2,500-3,500L), and Phytolutions (28,000L). The analysis confirmed light-limitation in all three photobioreactors. An additional limitation of the biomass productivity was caused by the nitrogen starvation that was used to induce lipid accumulation. Reduction of shading and separation of biomass and lipid production are proposed for future optimization.

Spectroscopic investigation of nickel cation binding with adenine mononucleotides: stability and structure of the 1:2 complex with adenosine 5′-monophosphate

Abstract The interaction of Ni(II) ions with adenine mononucleotides (5′-AMP, 3′-AMP, 2′-AMP, 2′,3′-cAMP, 3′,5′-cAMP) was studied in aqueous solution using Raman spectroscopy and 13C and 31P NMR paramagnetic relaxation measurements. Macrochelate structures were observed to form for all non-cyclic AMPs, with increasing stability in the series: 3′-AMP < 2′-AMP < 5′-AMP. N7 of adenine was found to be the key site of the Ni(II)-adenine interaction for all non-cyclic AMPs. For 2′-AMP, an alternative binding to the pyrimidine ring may also exist. The dependence of Raman spectra on AMP and Ni(II) concentration confirmed the existence of a stable 1 : 2 Ni(II)-(5′-AMP) complex, besides the 1 : 1 complexes. In this complex, the adenine moieties of both 5′-AMP molecules are situated close to Ni(II), and their relative orientations with respect to the cation are very similar. The paramagnetic relaxation enhancements of the carbons indicate that the nickel ion is not located in the plane of the adenine units, but that the line connecting Ni(II) and N7 deviates strongly from the adenine planes. Phosphates are outer-sphere coordinated by the cation. Findings from both methods have led us to propose possible global architectures of the complex.