Aggregation of some water-soluble derivatives of chitin in aqueous solutions: Role of the degree of acetylation and effect of hydrogen bond breaker

By dynamic light scattering in combination with fluorescence spectroscopy and TEM it was shown that aggregation in aqueous solutions is inherent not only to chitosan, but also to two other water-soluble derivatives of chitin: O-carboxymethylchitin and di-N,N-carboxymethylchitosan. Aggregation is observed even for the samples without N-acetyl-d-glucosamine units, which remain upon incomplete chemical modification of chitin, indicating that specific interactions between residual chitin repeat units cannot be the main reason for the aggregation. At the same time, 7 M urea weakens the aggregation, thus testifying that hydrogen bonding and/or hydrophobic interactions are partially responsible for this phenomenon. The incomplete disruption of aggregates in 7 M urea may arise from crystallization of junction zones between different macromolecules, which makes some hydrogen bonds inaccessible for urea or too stable for breaking by this agent.     

Colorimetric assay for sensitive poly(styrene sulfonate) quantification in a template directed polyelectrolyte-assembling process

Template directed Layer-by-layer (LbL) technology recently moved into the center of scientific attention, particularly as a versatile tool for bioencapsulation purposes. Its major advantages can be found in the striking simplicity of tuning wall properties and the complete control over layer thickness and permeability. Yet, for the most commonly applied pair of polyelectrolytes, poly(allylamine) hydrochloride (PAH) and poly(styrene sulfonate) sodium salt (PSS), the mandatory control of the successful deposition on plane and colloidal surfaces is currently only attainable by means of sophisticated and expensive equipment. Here we describe an alternative quantification method based on a simple colorimetric assay using the Bradford reagent, a cost-effective commercially available dye, and standard laboratory technical devices. The binding of the dye to PSS causes a distinct shift of the absorption maximum from 465 to 680 nm, providing a method for spectral quantification of submicrogram amounts of dissolved PSS during LbL coating with significant accuracy and excellent reproducibility. The method was successfully employed to quantify accurate polyelectrolyte loadings on several particles that have a general importance as LbL templates. Thus, this method can be recommended as standard laboratory technique for control of LbL encapsulation and will considerably broaden the applicability of this promising technology in biotechnology.     

A molecular dynamics simulation study of polyamine– and sodium–DNA. Interplay between polyamine binding and DNA structure

Four different molecular dynamics (MD) simulations have been performed for infinitely long ordered DNA molecules with different counterions, namely the two natural polyamines spermidine(3+) (Spd³⁺) and putrescine(2+) (Put²⁺), the synthetic polyamine diaminopropane(2+) (DAP²⁺), and the simple monovalent cation Na⁺. All systems comprised a periodical hexagonal cell with three identical DNA decamers, 15 water molecules per nucleotide, and counterions balancing the DNA charge. The simulation setup mimics the DNA state in oriented DNA fibers, previously studied using NMR and other experimental methods. In this paper the interplay between polyamine binding and local DNA structure is analyzed by investigating how and if the minor groove width of DNA depends on the presence and dynamics of the counterions. The results of the MD simulations reveal principal differences in the polyamine–DNA interactions between the natural [spermine(4+), Spd³⁺, Put²⁺] and the synthetic (DAP²⁺) polyamines.Abbreviations DAP diaminopropane - DDD Drew–Dickerson dodecamer - MD molecular dynamics - Put putrescine - RDF radial distribution function - Spd spermidine - Spm spermine     

Labelfree fully electronic nucleic acid detection system based on a field-effect transistor device

The labelfree detection of nucleic acid sequences is one of the modern attempts to develop quick, cheap and miniaturised hand-held devices for the future genetic testing in biotechnology and medical diagnostics. We present an approach to detect the hybridisation of DNA sequences using electrolyte-oxide-semiconductor field-effect transistors (EOSFETs) with micrometer dimensions. These semiconductor devices are sensitive to electrical charge variations that occur at the surface/electrolyte interface, i.e. upon hybridisation of oligonucleotides with complementary single-stranded (ss) oligonucleotides, which are immobilised on the oxide surface of the transistor gate. This method allows direct, time-resolved and in situ detection of specific nucleic acid binding events without any labelling. We focus on the detection mechanism of our sensors by using oppositely charged polyelectrolytes (PAH and PSS) subsequently attached to the transistor structures. Our results indicate that the sensor output is charge sensitive and distance dependent from the gate surface, which pinpoints the need for very defined surface chemistry at the device surface. The hybridisation of natural 19 base-pair sequences has been successfully detected with the sensors. In combination with nano-transistors a PCR free detection system might be feasible in future.     

Computer Modelling Studies on the Mechanism of Action of Ribonuclease T1

Abstract

The mechanism of action of ribonuclease (RNase) T₁ is still a matter of considerable debate as the results of x-ray, 2-D nmr and site-directed mutagenesis studies disagree regarding the role of the catalytically important residues. Hence computer modelling studies were carried out by energy minimisation of the complexes of RNase T₁ and some of its mutants (His40Ala, His40Lys, and Glu58Ala) with the substrate guanyl cytosine (GpC), and of native RNase T₁ with the reaction intermediate guanosine 2′, 3′-cyclic phosphate (G>p). The puckering of the guanosine ribose moiety in the minimum energy conformer of the RNase T₁ - GpC (substrate) complex was found to be O4′-endo and not C3′-endo as in the RNase T₁ - 3′-guanylic acid (inhibitor/product) complex. A possible scheme for the mechanism of action of RNase T₁ has been proposed on the basis of the arrangement of the catalytically important amino acid residues His40, Glu58, Arg77, and His92 around the guanosine ribose and the phosphate moiety in the RNase T₁ - GpC and RNase T₁ - G>p complexes. In this scheme, Glu58 serves as the general base group and His92 as the general acid group in the transphosphorylation step. His40 may be essential for stabilising the negatively charged phosphate moiety in the enzyme-transition state complex.     

Removal of enzymatic and fermentation inhibitory compounds from biomass slurries for enhanced biorefinery process efficiencies

Within the biorefinery paradigm, many non-monomeric sugar compounds have been shown to be inhibitory to enzymes and microbial organisms that are used for hydrolysis and fermentation. Here, two novel separation technologies, polyelectrolyte polymer adsorption and resin-wafer electrodeionization (RW-EDI), have been evaluated to detoxify a dilute acid pretreated biomass slurry. Results showed that detoxification of a dilute acid pretreated ponderosa pine slurry by sequential polyelectrolyte and RW-EDI treatments was very promising, with significant removal of acetic acid, 5-hydroxymethyl furfural, and furfural (up to 77%, 60%, and 74% removed, respectively) along with >97% removal of sulfuric acid. Removal of these compounds increased the cellulose conversion to 94% and elevated the hydrolysis rate to 0.69 g glucose/L/h. When using Saccharomyces cerevisiae D₅A for fermentation of detoxified slurry, the process achieved 99% of the maximum theoretical ethanol yield and an ethanol production rate nearly five-times faster than untreated slurry.     

Hydrodynamic and molecular characteristics of polyelectrolyte complexes between sodium dextransulfate and chitosan hydrochloride

Hydrodynamic and molecular characteristics of particles of polyelectrolyte complexes (PEC) between sodium dextransulfate and chitosan hydrochloride were studied by various physicochemical methods (high-rate sedimentation, viscosimetry, turbidimetry, and diffusion). As was shown, the complex formation is accompanied by increase in the average sizes with simultaneous changes in the shape of the particles of the investigated PEC. According to the proposed polycomplexes model, side by side aggregation of the taken macromolecules could cause disordering of adjacent helical parts of polyanion-matrix that facilitates the formation of sphere-like polycomplexes particles.     

Novel cellulose-based polyelectrolytes synthesized via the click reaction

Novel polyelectrolytes were prepared by conversion of 6-azido-6-deoxycellulose with acetylenedicarboxylic acid dimethyl ester and subsequent saponification. Up to 62% of the azide moieties were converted. The reaction was completed within 48 h using 2 moles of acetylenedicarboxylic acid dimethyl ester per mole of modified anhydroglucose unit. FTIR and NMR spectroscopy were applied to elucidate the molecular structure of the polymers. The polymer degradation was acceptable during this two-step reaction. The resulting biopolymer derivatives were water soluble and reduced the surface tension on water significantly. Moreover, they form ionotropic gels with multivalent metal ions.     

Kinetics and mechanisms of depolymerization of alginate and chitosan in aqueous solution

The kinetics and mechanisms of depolymerization of aqueous chitosan and alginate solutions at elevated temperatures have been investigated. Chitosan salts of different degree of acetylation (F_A), type of counterions (-glutamate, -chloride) and degree of purity were studied. One commercially available highly purified sodium alginate sample with high content of guluronic acid (G) was also studied. Furthermore, the influence of oxygen, H⁺ and OH⁻ ions on the initial depolymerization rates was investigated. Depolymerization kinetics was followed by measuring the time courses of the apparent viscosity and the intrinsic viscosity. The initial rate constants for depolymerization were determined from the intrinsic viscosity data converted to a quantity proportional to the fraction of bonds broken. The activation energies of the chitosan chloride and chitosan glutamate solutions with pH close to 5 and the same degree of acetylation, F_A = 0.14, were determined from the initial rate constants to be 76 ± 13 kJ/mol and 80 ± 11 kJ/mol, respectively.The results reported herein suggest that the stability of aqueous chitosan and alginate solutions at pH values 5–8 will be influenced by oxidative–reductive depolymerization (ORD) as the primary mechanism as long as transition metal ions are presented in the samples. Acid – and alkaline depolymerization will be the primary mechanisms for highly purified samples.