Total intensity light scattering from short,optically anisotropic wormlike chains

Simple exact equations are derived for intensity light scattering from optically anisotropic wormlike chains in the absence of excluded volume. The results are valid at low scattering angles (q² 〈R²_G〉 ? 1) for all sormilke chains from rigid rods to random couils. The present work and an earlier theory [Nagai, K. (1972) Polym. J. 3 , 67–83] appear to be equivalent, although they were both derived using different methods. The present work is primarily concerned with short wormlike chains, since intensity light scattering from short fragments may provide valuable information about DNA flexibility. By using the results of this work to reanalyze some older light-scattering studies [Godfrey, J. E. & Eisenberg, H. (1976) Biophys. Chem. 5 , 301–318], it is shown that anisotropy corrections to polarized light-scattering measurements have been overcorrected in the past. It can be anticipated that future light-scattering experiments will determine the base-pair anisotropy.     

Light scattering from wormlike chains with excluded volume effects

This paper reports a calculation of the angular dependence of light scattering from wormlike chains with excluded volume effects. The Daniels distribution function, modified for excluded volume effects, is used to compute averages for scattering elements separated by contour lengths which are long with respect to the persistence length of the chain. An expansion in terms of exactly known moments of the distribution for the wormlike coil without excluded volume is used for short contour lengths. The results are applied to scattering from calf thymus (M = 18.1 × 10⁶) and T7 (M = 25.4 × 10⁶) DNA. It is demonstrated that the same values of excluded volume parameter (ε = 0.11) and statistical segment length (1/λ′ = 900 Å) which explain the sedimentation and viscosity behavior of DNA also account satisfactorily for the scattering behavior. Molecular weights and root-mean-square radii estimated by extrapolation from scattering data obtained in the angular region from 10° to 25° will be 5–10% too large for DNA of molecular weight 20 × 10⁶–30 × 10⁶.     

Optical Properties and Light Climate in Lake Verevi

The optical properties and light climate during the ice-free period in the highly stratified Lake Verevi (Estonia) have been studied together with other lakes in same region since 1994. The upper water layer above the thermocline belongs to class “moderate” by optical classification of Estonian lakes but can turn “turbid” (concentration of chlorophyll a up to 73 mg m⁻³ and total suspended matter up to 13.2 g m⁻³) during late summer blooms. In the blue part of the spectrum, light is mainly attenuated by dissolved organic matter and in red part notably scattering but also absorption by phytoplanktonic pigments effect the spectral distribution of underwater light. Consequently, the underwater light is of greenish-yellow color (550–650 nm). Rapid change in optical properties occurs with an increase of all optically active substances close to thermocline (2.5–6 m). Optical measurements are often hampered beneath this layer so that modeling of the depth distribution of the diffuse attenuation coefficient is an useful compliment to field measurements. K_d,PAR ranges from 0.8 to 2.9 m⁻¹ in the surface layer, and model results suggest that it may be up to 5.8 m⁻¹ in the optically dense layer. This forms a barrier for light penetration into the hypolimnion.     

Glucose biosensor based on nano-SiO2 and “unprotected” Pt nanoclusters

The “unprotected” Pt nanoclusters (average size 2 nm) mixed with the nanoscale SiO₂ particles (average size 13 nm) were used as a glucose oxidase immobilization carrier to fabricate the amperometric glucose biosensor. The bioactivity of glucose oxidase (GOx) immobilized on the composite was maintained and the as-prepared biosensor demonstrated high sensitivity (3.85 μA mM⁻¹) and good stability in glucose solution. The Pt–SiO₂ biosensor showed a detection limit of 1.5 μM with a linear range from 0.27 to 4.08 mM. In addition, the biosensor can be operated under wide pH range (pH 4.9–7.5) without great changes in its sensitivity. Cyclic voltammetry measurements showed a mixed controlled electrode reaction.     

Global conformation analysis of irradiated xyloglucans

Xyloglucan isolated and purified from tamarind seed was subjected to various degrees of γ-irradiation treatments, from 10 to 70 kGy, monitored for radiation damage and then studied using a new combined hydrodynamic approach with regards to conformation and flexibility. Radiation products were analysed with regard to molecular weight (weight average) M_w from size exclusion chromatography coupled to multi-angle laser light scattering (SEC–MALLs), intrinsic viscosity [η] and sedimentation coefficient s^o_20,w. Sedimentation coefficient distributions and elution profiles from SEC–MALLs confirmed the unimodal nature of the molecular weight distribution for each sample in solution. The chain flexibility was then investigated in terms of the persistence length, L_p of the equivalent worm-like chain model. The traditional Bushin–Bohdanecky (intrinsic viscosity) and Yamakawa–Fujii (sedimentation coefficient) relations were used separately then combined together by minimisation of a target function according to a recently published procedure [Ortega, A., & García de la Torre, J. (2007). Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility. Biomacromolecules, 8, 2464–2475 [see also Ortega, A. Metodologías computacionales para propiedades en disolución de macromoléculas rígidas y flexibles. Ph.D. Dissertation, Universidad de Murcia, 2005]] and yielded an estimate for L_p in the range 4–9 nm using floated and fixed mass per unit length analysis protocols and “point” global analysis: irradiated xyloglucans behave as flexible structures in common with pressure/heat treated materials.     

Intramolecular disorder and its relation to mesophase structure in lipid/water mixtures

NMR spin-half pair dipolar echo measurements are reported for the lamellar (dispersions and multibilayer stacks) and hexagonal phases of potassium palmitate/²H₂O mixtures. In the lamellar L_β and L_γ (gel) phases the alkyl chains are rigid and perfectly ordered, while in the lamellar L_α and hexagonal phases they are flexible and disordered. In particular, the measurements show that in the fluid lamellar L_α phase the chain is “bent” at the C₉–C₁₀ segment; but is “straight” in the hexagonal phase.     

Effect of alkylated and intercalated DNA on the generation of superoxide anion by riboflavin

Superoxide anion (O ₂ ^.– ) was photogenerated upon illumination of riboflavin in fluorescent light. The rate of O ₂ ^.– formation was stimulated by double stranded DNA but not by denatured DNA or RNA. Depurinated DNA, which was predominantly depleted in guanine residues, did not exhibit the stimulatory effect, indicating an interaction of riboflavin, or active oxygen species derived from it, with guanine bases. Also, the stimulation of O ₂ ^.– photogeneration was not observed with ethidium bromide but was seen with proflavin-intercalated DNA. Since ethidium bromide intercalates preferentially between purines and pyrimidines, and proflavin prefers dA-dT rich sites, these results were interpreted to suggest that the interaction of riboflavin with DNA is mainly with GC or CG base pairs.     

Novel alginates prepared by independent control of chain stiffness and distribution of G-residues: Structure and gelling properties

The study of alginate hydrogels is of increasing interest, given their potential applications as biomaterials for tissue engineering and for encapsulating drugs and living cells. In this study, we present a new strategy for tailoring alginates on the basis of homopolymeric mannuronan, where the chain stiffness and the content of G-residues could be varied independently. Partial periodate oxidation (0–8%) followed by borohydride reduction, introducing flexible linkages through C2–C3 cleavage and ring opening, was combined with in vitro epimerization, introducing either alternating (MG) sequences (in the case of enzyme AlgE4) or G-blocks (in the case of enzyme AlgE6). Both enzymes are recombinantly expressed from Azotobacter vinelandii. Two strategies were followed: (a) oxidation/reduction followed by epimerization (b) epimerization to 90% G followed by oxidation/reduction. The resulting alginates were characterised by NMR spectroscopy and size-exclusion chromatography (SEC) with multi angular laser light scattering (MALLS) and viscosity detectors. Gels were prepared using the ‘internal setting’ method with either 10 mM or 20 mM Ca²⁺ present, and studied by small-strain oscillatory measurements. It was found that periodate oxidation, in the range P₀ = 0.02–0.06, had a pronounced influence on the gelling properties. The decrease in dynamic storage modulus (G′) could mainly be attributed to increased local flexibility and not only a decrease in G-block lengths as a consequence of oxidation. The new alginate gels are easily degradable in a mild acidic environment and the degradation is easier to control than gels made of unoxidized alginate.     

Physiological acclimation to light in Chara intermedia nodes

In this study we investigated the ability of Chara intermedia to acclimate to different irradiances (i.e. “low-light” (LL): 20–30 μmol photons m⁻² s⁻¹ and “high-light” (HL): 180–200 μmol photons m⁻² s⁻¹) and light qualities (white, yellow and green), using morphological, photosynthesis, chlorophyll fluorescence and pigment analysis.Relative growth rates increased with increasing irradiance from 0.016 ± 0.003 (LL) to 0.024 ± 0.005 (HL) g g⁻¹ d⁻¹ fresh weight and were independent of light quality. A growth-based branch orientation towards high-light functioning as a mechanism to protect the plant from excessive light was confirmed. It was shown that the receptor responsible for the morphological reaction is sensitive to blue-light.C. intermedia showed higher oxygen evolution (up to 10.5 (HL) vs. 4.5 (LL) nmol O₂ mg Chl⁻¹ s⁻¹), photochemical and energy-dependent Chl fluorescence quenching and a lower Fv/Fm after acclimation to HL. With respect to qP, the acclimation of the photosynthetic apparatus depended on light quality and needed the blue part of the spectrum for full development. In addition, pigment composition was influenced by light and the Chl a/Car and Antheraxanthin (A) + Zeaxanthin (Z)/Violaxanthin (V) + A + Z (DES) ratios revealed the expected acclimation behaviour in favour of carotenoid protection under HL (i.e. decrease of Chl a/Car from 3.41 ± 0.48 to 2.30 ± 0.35 and increase of DES from 0.39 ± 0.05 to 0.87 ± 0.03), while the Chl a/Chl b ratios were not significantly affected. Furthermore it was shown that morphological light acclimation mechanisms influence the extent of the physiological modifications.     

Interaction of Topotecan,DNA Topoisomerase I Inhibitor,with Double-Stranded Polydeoxyribonucleotides. 2. Formation of Topotecan–DNA Complex Containing Several DNA Molecules

This study is a continuation of a series of papers dealing with topotecan interaction with double-stranded polydeoxyribonucleotides. We showed earlier that topotecan molecules form dimers in solution at concentration above 10^–5(per base pair). Topotecan interaction with calf thymus DNA in solutions of low ionic strength was studied by fluorescence, circular dichroism, and linear flow dichroism. The data obtained indicate that topotecan forms two types of complex with DNA, DNA molecules combining with each other during formation of one of these complexes. The association constant of two topotecan-filled DNA molecules with each other was estimated at 10⁴M^–1(per base pair) in 1 mM sodium cacodylate buffer, pH 6.8, at 20°C. A possibility of modulation of DNA topoisomerase I activity by topotecan due to complexation with several sites of a supercoiled DNA molecule is discussed.     

Molecular aspects on the interaction of isatin-3-isonicotinylhydrazone to deoxyribonucleic acid: model for intercalative drug-DNA binding

Isatin-3-isonicotinylhydrazone was synthesized and characterized. The interaction of native calf thymus DNA with isatin-3-isonicotinylhydrazone (IINH) in 10 mM Tris–HCl aqueous solutions at neutral pH 7.4 has been investigated by spectrophotometric, circular dichroism (CD), melting temperature (T _m ), spectrofluorimetric, and viscometric techniques. It is found that IINH molecules could intercalate between base pairs of DNA as are evidenced by: hypochromism in UV absorption band of IINH, induced CD spectral changes, sharp increase in specific viscosity of DNA, and increase in the fluorescence of methylene blue (MB)-DNA solutions in the presence of increasing amounts of IINH, which indicates that it is able to release the intercalated MB completely. The binding constants of IINH–DNA complex at four different temperatures (277, 288, 298, and 310 K) were calculated to be 4.7 × 10⁴, 2.2 × 10⁴, 1.75 × 10⁴ and 1.1 × 10⁴ M⁻¹, respectively. Furthermore, the enthalpy and entropy of the reaction between IINH and CT-DNA showed that the reaction is enthalpy-favored and entropy- disfavored (∆H = −30.187 kJ mol⁻¹; ∆S = −20.46 J mol⁻¹K⁻¹) which are other evidences to indicate the IINH is able to be intercalated in the DNA base pairs.     

New insights for using self-assembly materials to improve the detection stability in label-free DNA-chip and immuno-sensors

This paper examines reliable advancements in low-cost DNA- and immuno-chips. Capacitance detection was successfully chosen to develop label-free bio-chips. Probe immobilization was rigorously investigated in order to obtain reliable capacitance measurements. Protein probes immobilized by using usual alkanethiols or thiolated ssDNA probes directly immobilized on gold do not allow sufficient stable capacitance measurements. New alkanethiols improved with ethylene–glycol function are shown in this paper to be more suitable materials for capacitive bio-chip development. Atomic Force Microscopy, Quartz Crystal Microbalance, and Capacitance Measurements were used to demonstrate that ethylene–glycol alkanethiols allow high time stability, smaller errors in detection, and improved ideal behaviour of the sensing surfaces. Measured capacitance is in the range of 8–11 nF/mm² for antibody layers and close to 6 nF/mm² for DNA probes. It is in the range of 10–12 nF/mm² and of 4–6 nF/mm² for antigen and DNA detection, respectively. The percentage error in detection is highly improved and it is in the range of 11–37% and of 0,23–0,82% for antigen and DNA, respectively. The reproducibility is also improved and it is close to 0,44% for single spot measurements on ethylene–glycol alkanethiols. A molecular theory attributing these improvements to water molecules strongly coordinated by ethylene–glycol functional groups and to solution ions not entering into probe films is finally proposed.     

Macromolecular conformation of chitosan in dilute solution: A new global hydrodynamic approach

Chitosans of different molar masses were prepared by storing freshly prepared samples for up to 6 months at either 4, 25 or 40 °C. The weight-average molar masses, M_w and intrinsic viscosities, [η] were then measured using size exclusion chromatography coupled to multi-angle laser light scattering (SEC-MALLS) and a “rolling ball” viscometer, respectively.The solution conformation of chitosan was then estimated from:

(a) the Mark–Houwink–Kuhn–Sakurada (MHKS) power law relationship [η] = kM_w^a and

(b) the persistence length, L_p calculated from a new approach based on equivalent radii [Ortega, A., & Garcia de la Torre, J. (2007). Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility. Biomacromolecules, 8, 2464–2475].

Both the MHKS power law exponent (a = 0.95 ± 0.01) and the persistence length (L_p = 16 ± 2 nm) are consistent with a semi-flexible rod type (or stiff coil) conformation for all 33 chitosans studied. A semi-flexible rod conformation was further supported by the Wales–van Holde ratio, the translational frictional ratio and sedimentation conformation zoning.     

DNA-binding geometry dependent energy transfer from 4′,6-diamidino-2-phenylindole to cationic porphyrins

The circular and linear dichroism (CD and LD) spectral properties of the meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP)–DNA complex at a [porphyrin]/[DNA] ratio below 0.015 showed that TMPyP intercalates between DNA base pairs. Contrarily, when cis–bis(N-methylpyridinium-4-yl)porphyrin (BMPyP) is associated with DNA, no CD spectrum was induced and a bisignate LD spectrum was observed. These spectral properties of both the TMPyP and BMPyP were essentially retained when the minor groove of the DNA was saturated with 4′,6-diamidino-2-phenylindole (DAPI). The fluorescence of the DNA-bound DAPI was effectively quenched by BMPyP and TMPyP. The quenching by BMPyP can be described through a pure static mechanism while TMPyP quenching produced an upward bending curve in the Stern–Volmer plot. Quenching efficiency was by far greater than predicted by the “sphere of action model”, suggesting that the DNA provides some additional processes for an effective energy transfer.     

Variance of Writhe for Wormlike DNA Rings with Excluded Volume

Abstract

We have calculated the variance of the equilibrium distribution of a circular wormlike polymer chain over the writhing number, <((Wr)² )>, with allowance for the excluded volume effects. Within this model the <((Wr)² )> value is a function of the number of Kuhn statistical segments, n, and the chain diameter, d measured in Kuhn statistical lengths, b. Simulated DNA chains varied from 200 to 10,000 base pairs and the d value varied from 0.02 to 0.2. Theory predicts a considerable ionic strength dependence of the DNA superhelix energy as a consequence of the change in the DNA diameter. A comparison with the available experimental data has yielded an estimate of the DNA torsional rigidity, the Kuhn statistical length, and the effective diameter of the double helix under conditions of the complete screening of the DNA electrostatic potential.     

Water relations and CO2 exchange of the terrestrial lichen Teloschistes capensis in the Namib fog desert: Measurements during two seasons in the field and under controlled conditions

Although the coastal zone of the Central Namib Desert (Namibia) has negligible rainfall, frequent fog, dew and high air humidity support a luxurious lichen flora. Large areas of soil crust communities are dominated by the multibranched, fruticose Teloschistes capensis interspersed by a (still indeterminable) Ramalina species. In earlier communications, based on field measurements in autumn, we began the analysis of functional mechanisms that allow these lichens to exist under the special conditions of a fog desert. We have extended this work by monitoring lichen CO₂ exchange and water relations in spring and by experiments under controlled conditions.In both seasons, nocturnal hydration, by fog and/or dew, activated dark respiration of the lichens which was followed, after sunrise, by a short period of positive net photosynthesis (NP) that continued until metabolic inactivation occurred from desiccation. Dry thalli of T. capensis were able to reactivate NP through water vapour uptake alone, beginning at an air relative humidity of 82%, i.e. at a water potential of −26.3 MPa; the moisture compensation point during desiccation was at 13% thallus water content (WC, dry weight related). Optimal WC for photosynthesis was around 100%, and both species showed a large and extended suprasaturation depression of CO₂ assimilation. Light response showed “sun-plant” characteristics with saturation >1000 μmol m⁻² s⁻¹ photosynthetically active photon flux density (PPFD). However, due to rapid desiccation, the combination of light saturation with optimal WC very rarely occurred under field conditions. Light compensation point after sunrise was highly dependent on actual WC: at low hydration, it amounted to only ca. 10 μmol m⁻² s⁻¹ PPFD so that even the smallest levels of hydration could be used for carbon gain before desiccation took place again. This phenomenon was probably due to a hydration gradient in the thallus branches during transient moistening so that the outer photobiont layer was favoured in contrast to the internal mycobiont which remained dry longer and did not contribute respiratory CO₂ loss. Fully hydrated thalli had light compensation points around 50 μmol m⁻² s⁻¹ PPFD. Extended desiccation of 1–3 days had no impact on the magnitude and recovery of photosynthesis but, imposed desiccation of 10 days reduced NP in lab and field experiments and caused an extended period of recovery. “Resaturation respiration” was not detected in the field data, although it was present after experimental moistening of dry thalli.In spring, the higher fog frequency and intensity increased maximal nocturnal WC, maximal attained NP as well as integrated daily carbon income (ΣNP) compared to the autumn measurements. NP_max and ΣNP depended on maximal nocturnal WC with a saturation-type response. In terms of carbon gain both species seem to be optimally adapted to nocturnal moistening up to 160% WC and were not able to make use of higher degrees of hydration, a feature that might well influence their habitat selection.Maximal daily carbon-related ΣNP for T. capensis was 4.6 mg_C (g_C)⁻¹ day⁻¹. A rough estimate of the annual (projected) area-related carbon balance (photosynthetic income minus respiratory losses) based on published fog and dew frequencies and personal observations was 15–34 mg_C m⁻² yr⁻¹.     

The Production of Miniantibodies Against Human Granulocyte Colony-Stimulating Factor Using the Murine scFv Combinatory Library

To develop a phage display of single-chain antibodies (scFv), fractions of total cell DNA and RNA were obtained from splenocytes of naive mice. The DNA fragments encoding variable regions of light and heavy immunoglobulin chains were amplified and isolated using primers specific to the conservative regions of these genes. The construction of the library was based on the principle of stochastic combining the DNA fragments encoding the light and heavy antibody chains with the DNA linker, whose structure corresponded to the (Gly₄Ser)₃ sequence. The scFv library was constructed using the E. coli TG1 strain and the phagemid vector pHEN1. The repertoire of the library exceeded 5 × 10⁷ independent recombinant clones. The clones producing antibodies to human granulocyte colony-stimulating factor were isolated. The affinity constants of the resulting scFv were in the range of 2 × 10⁴ to 1.8 × 10⁷ M^–1.     

Physicochemical properties and antitumor activities for sulfated derivatives of lentinan

Five fractions of lentinan, a β-(1→3)-d-glucan bearing β-(1→6)-d-glucopyranosyl branches, were treated with chlorosulfonic acid for 90 min at 60 °C in pyridine medium to synthesize water-soluble sulfated derivatives having the substitution degree of 1.44–1.76. The ¹³C NMR spectra of the sulfated β-glucans indicated that the C-6 position was preferentially substituted by the sulfate groups. The values of the weight-average molecular weight (M_w), radius of gyration (), and intrinsic viscosity ([η]) of the sulfated lentinan fractions were determined by size-exclusion chromatography with multi-angle laser light scattering (SEC–MALLS) and viscometry in 0.15 M aq NaCl at 25 °C, respectively. The dependence of [η] on M_w for the sulfated lentinan was found to be [η] = 8.93 × 10⁻³ (mL/g) in 0.15 M aq NaCl (for M_w ranging from 14.6 × 10⁴ to 50.4 × 10⁴). On the basis of the Yamakawa–Fujii–Yoshizaki (YFY) theory, the conformational parameters of the sulfated lentinan were calculated as 950 nm⁻¹ for the molar mass per unit contour length (M_L), 4.8 nm for the persistence length (q), and 13.9 for the characteristic ratio (C_∞), indicating relatively extended single flexible chains in solution. The sulfated glucan fractions exhibited in vitro antiproliferative activities against sarcoma 180 (S-180) cells, and their inhibition ratios were lower than that of the triple-helix lentinan, but higher than that for the one with single random-coil lentinan chains.     

A selective resonance scattering assay for immunoglobulin G using Cu(II)-ascorbic acid-immunonanogold reaction

In sodium acetate–acetic acid buffer solution, Au, Ag, Pt, Pd, Fe₃O₄, and Cu₂O nanoparticles have catalytic enhancement effect on the reduction of Cu²⁺ by ascorbic acid to form large copper particles that exhibit a strong resonance scattering peak at 610 nm. Those nanocatalytic reactions were studied by the resonance scattering spectral technique, and smaller nanogold exhibited stronger catalytic enhancement effect in pH 4.2 sodium acetate–acetic acid buffer solution. The resonance scattering intensity at 610 nm increased linearly with the concentrations of 0.02 to 1.60, 0.040 to 1.20, and 0.12 to 4.70 nM nanogold in sizes of 5, 10, and 15 nm with detection limits of 0.010, 0.030, and 0.10 nM, respectively. An immunonanogold-catalytic resonance scattering bioassay was established, combining the immunonanogold-catalytic effect on CuSO₄–ascorbic acid reaction with the resonance scattering detection technique. As a model, 0.03 to 7.5 ng ml⁻¹ immunoglobulin G can be assayed by this immunonanogold-catalytic resonance scattering bioassay with a detection limit of 0.015 ng ml⁻¹.     

Preparation and characterization of self-assembled nanoparticles of the novel carboxymethyl pachyman-deoxycholic acid conjugates

Various novel carboxymethyl pachyman-deoxycholic acid conjugates (CMPD) were synthesized using carboxymethylated pachyman (CMP) as a hydrophilic segment and Deoxycholic Acid (DOCA) as a hydrophobic segment. The degree of DOCA substitution (DS) in CMPD conjugates, which was determined by elemental analysis, can reach to 30.0, 49.2, or 54.9 DOCA groups per hundred sugar residues of CMP. Structural characteristics of these CMPD conjugates were investigated by using ¹H NMR, dynamic light scattering, zeta potential, transmission electron microscopy (TEM) and fluorescence spectroscopy. The CMPD conjugates provided apparently smaller monodispersed self-aggregates in water, with mean diameters decreasing with increasing of DOCA DS in the range of 98–158 nm. Zeta potentials of the CMPD self-aggregated nanoparticles indicated that the nanoparticles were covered with negatively charged CMP shells. TEM images demonstrated that the nanoparticles were spherical in shape. The critical aggregation concentration (cac) of the CMPD nanoparticles (1.55 × 10⁻²–5.89 × 10⁻³ mg/mL) was comparatively low which implies that the CMPD self-assembled nanoparticles form at low concentration in aqueous solution.