Selective Alkylation of C‐Rich Bulge Motifs in Nucleic Acids by Quinone Methide Derivatives

A quinone methide precursor featuring a bis‐cyclen anchoring moiety has been synthesized and its capacity to alkylate oligonucleotide targets quantified in the presence and absence of divalent metal ions (Zn²⁺, Ni²⁺ and Cd²⁺). The oligonucleotides were designed for testing the sequence and secondary structure specificity of the reaction. Gel electrophoretic analysis revealed predominant alkylation of C‐rich bulges, regardless of the presence of divalent metal ions or even the bis‐cyclen anchor. This C‐selectivity appears to be an intrinsic property of the quinone methide electrophile as reflected by its reaction with an equimolar mixture of the 2′‐deoxynucleosides. Only dA‐N1 and dC‐N3 alkylation products were detected initially and only the dC adduct persisted for detection under conditions of the gel electrophoretic analysis.     

Probing small molecule binding to amyloid fibrils

Much effort has focussed in recent years on probing the interactions of small molecules with amyloid fibrils and other protein aggregates. Understanding and control of such interactions are important for the development of diagnostic and therapeutic strategies in situations where protein aggregation is associated with disease. In this perspective article we give an overview over the toolbox of biophysical methods for the study of such amyloid-small molecule interactions. We discuss in detail two recently developed techniques within this framework: linear dichroism, a promising extension of the more traditional spectroscopic techniques, and biosensing methods, where surface-bound amyloid fibrils are exposed to solutions of small molecules. Both techniques rely on the measurement of physical properties that are very directly linked to the binding of small molecules to amyloid aggregates and therefore provide an attractive route to probe these important interactions.     

Manipulation of Single‐Stranded DNA by Using an Artificial Site‐Selective DNA Cutter Composed of Cerium(IV)/EDTA and Phosphonate–Oligonucleotide Conjugates

An artificial site‐selective DNA cutter to hydrolyze single‐stranded DNA at a desired site was prepared from Ce^IV/ethylenediamintetraacetic acid (EDTA) and two ethylenediamine‐N,N,N′,N′‐tetrakis(methylenephosphonic acid)–oligonucleotide conjugates. By using this cutter, the sense strand of a blue fluorescent protein (BFP) gene was selectively cut at a predetermined site in the chromophore‐coding region. The upstream fragment obtained by the site‐selective scission was ligated with the downstream fragment of the closely related green fluorescent protein (GFP) gene so that the 5′‐ and 3′‐end portions of the chromophore came from the BFP fragment and the GFP fragment, respectively. The recombinant gene was successfully expressed in E. coli and the chimeric chromophore emitted green fluorescence as expected.     

Holomorphic functional calculus of Hodge-Dirac operators in L p

We study the boundedness of the H ^∞ functional calculus for differential operators acting in L ^p (R ⁿ ; C ^N ). For constant coefficients, we give simple conditions on the symbols implying such boundedness. For non-constant coefficients, we extend our recent results for the L ^p theory of the Kato square root problem to the more general framework of Hodge-Dirac operators with variable coefficients Π _B as treated in L ²(R ⁿ ; C ^N ) by Axelsson, Keith, and McIntosh. We obtain a characterization of the property that Π _B has a bounded H ^∞ functional calculus, in terms of randomized boundedness conditions of its resolvent. This allows us to deduce stability under small perturbations of this functional calculus.     

Measuring tablet porosity using multispectral imaging system

A multispectral imaging system with computer controlled light source of 16 light emitting diodes is applied for measuring of tablet porosity. The system is based on a subspace vector model of surface reflection. The measured spectral data are compressed on the stage of measurement and used directly for the discrimination of tablets with different porosity. The experimental results demonstrate that the multispectral imaging system is a potential method for tablet porosity measurement.     

Thermoluminescence study of persistent luminescence materials: Eu2+- and R3+-doped calcium aluminates, CaAl2O4:Eu2+,R3+

Thermoluminescence properties of the Eu2+-, R3+-doped calcium aluminate materials, CaAl2O4:Eu2+,R3+, were studied above room temperature. The trap depths were estimated with the aid of the preheating and initial rise methods. The seemingly simple glow curve of CaAl2O4:Eu2+ peaking at ca. 80 degrees C was found to correspond to several traps. The Nd3+ and Tm3+ ions, which enhance most the intensity of the high-temperature TL peaks, form the most suitable traps for intense and long-lasting persistent luminescence, too. The location of the 4f and 5d ground levels of the R3+ and R2+ ions were deduced in relation to the band structure of CaAl2O4. No clear correlation was found between the trap depths and the R3+ or R2+ level locations. The traps may thus involve more complex mechanisms than the simple charge transfer to (or from) the R3+ ions. A new persistent luminescence mechanism presented is based on the photoionization of the electrons from Eu2+ to the conduction band followed by the electron trapping to an oxygen vacancy, which is aggregated with a calcium vacancy and a R3+ ion. The migration of the electron from one trap to another and also to the aggregated R3+ ion forming R2+ (or R3+-e-) is then occurring. The reverse process of a release of the electron from traps to Eu2+ will produce the persistent luminescence. The ability of the R3+ ions to trap electrons is probably based on the different reduction potentials and size of the R3+ ions. Hole trapping to a calcium vacancy and/or the R3+ ion may also occur. The mechanism presented can also explain why Na+, Sm3+, and Yb3+ suppress the persistent luminescence.     

Polymer physics inspired approaches for the study of the mechanical properties of amyloid fibrils

Amyloid structures constitute a class of highly ordered nanomaterials formed by insoluble protein aggregates. These aggregates are characterized by a cross‐β structural motif in which β‐sheets are oriented perpendicular to the fibril axis and bound together by a dense hydrogen bonding network. Although they have been associated with several neurodegenerative disorders, such as Alzheimer's and Parkinson's diseases, amyloid fibrils have also been found in many physiologically beneficial roles, for instance in adhesives and hormone storage. Inspired by this natural occurrence of functional amyloid, the hierarchal self‐assembly of these structures has recently been used to develop artificial biomaterials for applications in medicine and nanotechnology. In order to realize the full potential of amyloids as functional materials, it is important to understand their fundamental mechanical properties. This review explores a range of experimental strategies to determine the mechanical properties of amyloid fibrils and discusses the results in the context of polymer physics concepts. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014 , 52, 281–292     

Kato's square root problem in Banach spaces

Let L be an elliptic differential operator with bounded measurable coefficients, acting in Bochner spaces Lp(Rn;X) of X -valued functions on Rn. We characterize Kato's square root estimates and the H^∞-functional calculus of L in terms of R-boundedness properties of the resolvent of L, when X is a Banach function lattice with the UMD property, or a noncommutative Lp space. To do so, we develop various vector-valued analogues of classical objects in Harmonic Analysis, including a maximal function for Bochner spaces. In the special case X=C, we get a new approach to the Lp theory of square roots of elliptic operators, as well as an Lp version of Carleson's inequality.     

Bisphosphonate derivatives of nucleoside antimetabolites: hydrolytic stability and hydroxyapatite adsorption of 5'-beta,gamma-methylene and 5'-beta,gamma-(1-hydroxyethylidene) triphosphates of 5-fluorouridine and ara-cytidine

Kinetics of the hydrolytic reactions of four bisphosphonate derivatives of nucleoside antimetabolites, viz., 5-fluorouridine 5'-beta,gamma-(1-hydroxyethylidene) triphosphate ( 4), 5-fluorouridine 5'-beta,gamma-methylene triphosphate ( 5), ara-cytidine 5'-beta,gamma-(1-hydroxyethylidene) triphosphate ( 6), and ara-cytidine 5'-beta,gamma-methylene triphosphate ( 7), have been studied over a wide pH range (pH 1.0-8.5) at 90 degrees C. With each compound, the disappearance of the starting material was accompanied by formation of the corresponding nucleoside 5'-monophosphate, the reaction being up to 2 orders of magnitude faster with the beta,gamma-(1-hydroxyethylidene) derivatives ( 4, 6) than with their beta,gamma-methylene counterparts ( 5, 7). With compound 7, deamination of the cytosine base competed with the phosphate hydrolysis at pH 3-6. The measurements at 37 degrees C (pH 7.4) in the absence and presence of divalent alkaline earth metal ions (Mg (2+) and Ca (2+)) showed no sign of metal ion catalysis. Under these conditions, the initial product, nucleoside 5'-monophosphate, underwent rapid dephosphorylation to the corresponding nucleoside. Hydrolysis of the beta,gamma-methylene derivatives ( 5, 7) to the corresponding nucleoside 5'-monophosphates was markedly faster in mouse serum than in aqueous buffer (pH 7.4), the rate-acceleration being 5600- and 3150-fold with 5 and 7, respectively. In human serum, the accelerations were 800- and 450-fold compared to buffer. In striking contrast, the beta,gamma-(1-hydroxyethylidene) derivatives did not experience a similar decrease in hydrolytic stability. The stability in human serum was comparable to that in aqueous buffer (tau 1/2 = 17 and 33 h with 4 and 6, respectively), and on going to mouse serum, a 2- to 4-fold acceleration was observed. To elucidate the mineral-binding properties of 4- 7, their retention on a hydroxyapatite column was studied and compared to that of zoledronate ( 1a) and nucleoside mono-, di-, and triphosphates.