Fluorescence Correlation Spectroscopy of the Binding of Nucleotide Excision Repair Protein XPC-hHr23B with DNA Substrates

The interaction of the nucleotide excision repair (NER) protein dimeric complex XPC-hHR23B, which is implicated in the DNA damage recognition step, with three Cy3.5 labeled 90-bp double-stranded DNA substrates (unmodified, with a central unpaired region, and cholesterol modified) and a 90-mer single-strand DNA was investigated in solution by fluorescence correlation spectroscopy. Autocorrelation functions obtained in the presence of an excess of protein show larger diffusion times (tau (d)) than for free DNA, indicating the presence of DNA-protein bound complexes. The fraction of DNA bound (theta), as a way to describe the percentage of protein bound to DNA, was directly estimated from FCS data. A significantly stronger binding capability for the cholesterol modified substrate (78% DNA bound) than for other double-stranded DNA substrates was observed, while the lowest affinity was found for the single-stranded DNA (27%). This is in accordance with a damage recognition role of the XPC protein. The similar affinity of XPC for undamaged and 'bubble' DNA substrates (58% and 55%, respectively) indicates that XPC does not specifically bind to this type of DNA substrate comprising a large (30-nt) central unpaired region.     

Encapsulation of a β-carboline in cucurbit[7]uril

Inclusion of a biological photosensitizer and prototype of β-carbolines, norharmane (NHM), into the cavity of cucurbit[7]uril (CB[7]) has been investigated for the first time, by using ¹H NMR and UV–visible spectroscopy, and ab initio calculations. Protonated NHM forms a very stable host–guest complex with CB[7] in aqueous solution, with a binding constant of (9.0 ± 0.5) × 10⁴ M^?1. The encapsulation of NHM into CB[7] has driven the prototropic equilibrium of NHM to protonated NHM (NHMH⁺) at neutral pH. A pH titration for the host–guest complex revealed a moderate shift of the acid–base equilibrium in the ground-state (from 7.2 to 7.9), which may be caused by the low polarity microenvironment of the CB[7] cavity. The CB[7] provides a binding pocket for the hydrophobic molecule, and the polar, carbonyl-lined portals offering an anchoring site for the positive charge of the cationic species NHMH⁺.     

Simultaneous saccharification and fermentation of pretreated wheat straw to ethanol with selected yeast strains and β-glucosidase supplementation

Previous shake flask and stirred tank evaluations of temperature tolerant (37–43°C) yeasts in simultaneous saccharification and fermentation (SSF) on Sigmacell-50 cellulose substrates to ethanol have identified several good microorganisms for further SSF studies (27). Of these, the glucose fermenting yeastCandida acidothermophilum, C. brassicae, Saccharomyces cerevisiae, S. uvarum, and a mixed culture of the cellobiose fermenting yeastBrettanomyces clausenii withS. cerevisiae as a control were chosen for shake flask SSF screening experiments with pretreated wheat straw. This study indicates that theSaccharomyces strainscerevisiae anduvarum, give very good performance at high cellulase loadings or when supplemented with Novo-188 β-glucosidase. In fact, with the higher enzyme loadings these yeast will give complete conversion of cellulose to ethanol. Yet at the lower, more economical enzyme loadings, the mixed culture ofBrettanomyces clausenii andS. cerevisiae performs better than any single yeast.

     

Evaluation of pretreated herbaceous crops for the simultaneous saccharification and fermentation process

Applied Biochemistry and Biotechnology - Three dilute acid pretreated herbaceous crops (Weeping lovegrass,Eragrotis curvula; Sericea lespedeza,Lespedeza cuneata; and switch-grass,Panicum virgatum)...     

Introduction to the Proceedings of the Fourteenth Symposium on Biotechnology for Fuels and Chemicals

Applied Biochemistry and Biotechnology -     

Introduction to the proceedings of the eleventh symposium on biotechnology for fuels and chemicals

Applied Biochemistry and Biotechnology -     

Synthetic approaches to bicyclic diazenium salts

Bicyclic diazenium salts have been prepared from α-chloroazo species via a Lewis acid-mediated intramolecular cycloaddition. An alternative, more direct, route to these salts by the reaction of hydrazones with dimethylsulfonium ditriflate is also described. Terminal olefins provided mixtures of fused and bridged bicyclic diazenium salts. The ratio of the fused and bridged species was observed to depend on the electronics of the N-aryl substituent, which is explained by considering a concerted asynchronous cycloaddition mechanism.     

Application of a depolymerization model for predicting thermochemical hydrolysis of hemicellulose

Literature data were collected and analyzed to guide selection of conditions for pretreatment by dilute acid and water-only hemicellulose hydrolysis, and the severity parameter was used to relate performance of different studies on a consistent basis and define attractive operating conditions. Experiments were then run to confirm performance with corn stover. Although substantially better hemicellulose sugar yields are observed when acid is added, costs would be reduced and processing operations simplified if less acid could be used while maintaining good yields, and understanding the relationship between operating conditions and yields would be invaluable to realizing this goal. However, existing models seldom include the oligomeric intermediates prevalent at lower acid levels, and the few studies that include such species do not account for the distribution of chain lengths during reaction. Therefore, the polymeric nature of hemicellulose was integrated into a kinetic model often used to describe the decomposition of synthetic polymers with the assumption that hemicellulose linkages are randomly broken during hydrolysis. Predictions of monomer yields were generally consistent with our pretreatment data, data reported in the literature, and predictions of other models, but the model tended to overpredict oligomer yields. These differences need to be resolved by gathering additional data and improving the model.