DNA adsorption at functionalized Si/buffer interfaces studied by x-ray reflectivity

The adsorption of DNA on chemically homogeneous, functionalized, oxide-free single-crystal silicon surfaces is studied by x-ray reflectivity. The adsorption of monodisperse, 294 base-pair double-stranded DNA on a positively charged surface is detected through the deformation of the molecular monolayer of aminated alkyl-chain molecules covalently bonded to the surface. The adsorption of single-stranded DNA does not lead to the same deformation. A detailed quantitative characterization of the density profiles yield surface densities of the covalently grafted, molecular monolayers that are in excellent agreement with infrared spectroscopic measurements. The additional mass density that is measured following the adsorption of DNA corresponds either to the partial embedding of a densely-packed adsorbed layer or to a deeper penetration into the soft surface layer at a lower surface density of the adsorbed double-stranded DNA molecules. The adsorption is found to be irreversible under high added salt concentrations, suggesting a partial dehydration of the double-stranded DNA.     

A velocity map ion imaging study of difluorobenzene-water complexes: binding energies and recoil distributions

The binding energies of the p-, m-, and o-difluorobenzene-H(2)O complexes have been measured by velocity map ion imaging to be 922+/-10, 945+/-10, and 891+/-4 cm(-1), respectively. The lack of variation provides circumstantial evidence for water binding to the three isomers via the same interaction, viz. an in-plane O-H...F hydrogen bond to one of the fluorine atoms on the ring, with a second, weaker interaction of the water O atom with an ortho hydrogen, as determined previously for the p-difluorobenzene-H(2)O complex [Kang et al., J. Phys. Chem. A 109, 767 (2005)]. The ground state binding energies for the difluorobenzene-H(2)O complexes are approximately 5%-11% larger than that for benzene-H(2)O, where binding occurs to the pi electrons out-of-plane. However, in the S(1) state the binding energies of the o- and p-difluorobenzene-H(2)O complexes are smaller than the benzene-H(2)O value, raising an interesting question about whether the geometry at the global energy minimum remains in-plane in the excited electronic states of these two complexes. Recoil energy distributions for dissociation of p-difluorobenzene-H(2)O have been measured from the 3(1), 5(2), and 3(1)5(1) levels of the excited electronic state. These levels are 490, 880, and 1304 cm(-1), respectively, above the dissociation threshold. Within the experimental uncertainty, the recoil energy distributions are the same for dissociation from these three states, with average recoil energies of approximately 100 cm(-1). These recoil energies are 60% larger than was observed for the dissociation of p-difluorobenzene-Ar, which is a substantially smaller increase than the 400% seen in a comparable study of dissociation within the triplet state for pyrazine-Ar, -H(2)O complexes. The majority of the available energy is partitioned into vibration and rotation of the fragments.     

Sensitization of ruthenium nitrosyls to visible light via direct coordination of the dye resorufin: trackable NO donors for light-triggered NO delivery to cellular targets

Three nitrosyl-dye conjugates, namely, [(Me 2bpb)Ru(NO)(Resf)] ( 1-Resf), [(Me 2bQb)Ru(NO)(Resf)] ( 2-Resf), and [((OMe) 2bQb)Ru(NO)(Resf)] ( 3-Resf) have been synthesized via direct replacement of the chloride ligand of the parent {Ru-NO} (6) nitrosyls of the type [(R 2byb)Ru(NO)(L)] with the anionic tricyclic dye resorufin (Resf). The structures of 1-Resf- 3-Resf have been determined by X-ray crystallography. The dye is coordinated to the ruthenium centers of these conjugates via the phenolato-O atom and is trans to NO. Systematic red shift of the d pi(Ru) --> pi*(NO) transition of the parent nitrosyls [(R 2byb)Ru(NO)(L)] due to changes in R and y in the equatorial tetradentate ligand R 2byb (2-) results in its eventual merge with the intense absorption band of the dye around 500 nm in 3-Resf. Unlike the UV-sensitive parent [(R 2byb)Ru(NO)(L)] nitrosyls, these dye-sensitized nitrosyls rapidly release NO when exposed to visible light (lambda >/= 465 nm). Comparison of the photochemical parameters reveals that direct coordination of the light-harvesting chromophore to the ruthenium center in the present nitrosyls results in a significantly greater extent of sensitization to visible light compared to nitrosyls with appended chromophore (linked via alkyl chains). 1-Resf has been employed as a "trackable" NO donor to promote NO-induced apoptosis in MDA-MB-231 human breast cancer cells under the control of light. The results of this work demonstrate that (a) the d pi(Ru) --> pi*(NO) transition (photoband) of {Ru-NO} (6) nitrosyls can be tuned into visible range via careful alteration of the ligand frame(s) and (b) such nitrosyls can be significantly sensitized to visible light by directly ligating a light-harvesting chromophore to the ruthenium center. The potential of these photosensitive nitrosyl-dye conjugates as (i) biological tools to study the effects of NO in cellular environments and (ii) "trackable" NO donors in photodynamic therapy of malignancies (such as skin cancer) has been discussed.     

Designed amino acid ATRP initiators for the synthesis of biohybrid materials

A synthetic strategy to prepare peptide-polymer conjugates with precise sites of attachment is described. Amino acids modified with atom transfer radical polymerization (ATRP) initiators for the polymerization of styrenes and methacrylates were prepared. Fmoc-4-(1-chloroethyl)-phenylalanine (5) was synthesized in four steps from Fmoc-tyrosine. HATU-mediated amidation with glycine-OMe resulted in dipeptide (6). The initiator was effective for Cu(I)/bipyridine mediated bulk polymerization of styrene. Kinetic studies indicated a controlled polymerization, with high conversion (97%), and a polydispersity index (PDI) of 1.25. Fmoc-O-(2-bromoisobutyryl)-serine tert-butyl ester (10) was synthesized from Fmoc-Ser(OTrt)-OH in three steps. This initiator was employed in the ATRP of 2-hydroxyethyl methacrylate (HEMA), and kinetic studies indicated a controlled polymerization. Different monomer to initiator ratios resulted in poly(HEMA) of different molecular weights and narrow PDIs (1.14-1.25). Conversions were between 70 and 99%. HEMA modified with N-acetyl-D-glucosamine (GlcNAc) was also polymerized to 84% conversion and the resulting PDI was 1.19. The t-butyl ester protecting group of 10 was removed, and the resulting amino acid (11) was incorporated into VM(11)VVQTK by standard solid-phase peptide synthesis. Polymerization resulted in the glycopolymer-peptide conjugate in 93% conversion and a PDI of 1.14.     

Structure and absolute stereochemistry of the anticancer agent EBC-23 from the Australian rainforest

EBC-23 (2), a prostate anticancer agent, was isolated from the fruit of Cinnamomum laubatii (family Lauraceae) in the Australian tropical rainforest. Extensive NOE experiments enabled the relative stereochemistry of the proposed EBC-23 (2) structure to be determined. Total synthesis of both enantiopodes over nine linear steps, involving challenging RCM and spiroacetal cyclizations, confirmed the gross structure and relative and absolute stereochemistry.     

A Proximal Bisnitroxide Initiator: Studies in Low-Temperature Nitroxide-Mediated Polymerizations

Nitroxide-mediated "living" radical polymerization with bisalkoxyamine 2,5,5,8,8,11-hexamethyl-4,9-(1-phenylethoxy)-3,10-diphenyl-4,9-diazadodecane produces polymers of controlled length and narrow molecular weight distributions at temperatures ranging from 70 to 110 °C. Polymerizations were run successfully with styrene (St), tert-butyl acrylate (tBA), and dimethylacrylamide (DMA). EPR measurements of the homolysis of this bisalkoxyamine and monoalkoxyamine 2,2,5-trimethyl-3-(1-phenylethoxy)-4-phenyl-3-azahexane at temperatures ranging from 85 to 105 °C give rate constants for the bisalkoxyamine that are approximately twice as large as those for the monoalkoxyamine. (1)H NMR investigations of the decomposition of both alkoxyamines at 125 °C show enhanced decomposition for the bisalkoxyamine. EPR decomposition studies at 120 °C on the corresponding bis- and mononitroxides 2,5,5,8,8,11-hexamethyl-3,10-diphenyl-4,9-diazadodecane-4,9-bisnitroxide and 2,2,5-trimethyl-4-phenyl-3-azahexane-3-nitroxide also show accelerated bisnitroxide decomposition. Low-temperature EPR studies of the bisnitroxide reveal an unusually strong radical-radical interaction, suggesting enhanced stabilization of the intermediate mononitroxide formed during polymerization by interaction with the proximal N-alkoxyamine. The transient mononitroxide is postulated to be stabilized by delocalization of the unpaired electron density over five atoms.     

Steric effects in palladium-catalysed amination of aryl triflates and nonaflates with the primary amines PhCH(R)NH2 (R=H, Me)

A systematic study of the effects of aryl triflate and nonaflate structure on the yield of amination with the primary amines PhCH(R)NH₂ (R=H, Me) under palladium catalysis has been carried out. High throughput screening indicated that a catalyst composed of X-Phos/Pd₂(dba)₃/1,4-dioxane was optimal based on a model reaction of Ar(OR_f) [R_f=Tf (SO₂CF₃), Nf (SO₂(CF₂)₃CF₃)] with PhCH₂NH₂. Comparisons of the reactivity of various ArOTf and ArONf [Ar=4-MePh, 2-naphthyl, 1-naphthyl, 2-PhC₆H₄] indicated that both ortho substitution in the aryl electrophile and at the α-position on the amine are detrimental to the coupling particularly when they occur in combination. Despite being formally a monodentate ligand use of X-Phos leads to only small degrees of racemisation when using (R)-PhCH(Me)NH₂ (typically resulting in a reduction from 97 to 86-94% ee for the amine stereocentre).     

Microfluidic device architecture for electrochemical patterning and detection of multiple DNA sequences

Electrochemical biosensors pose an attractive solution for point-of-care diagnostics because they require minimal instrumentation and they are scalable and readily integrated with microelectronics. The integration of electrochemical biosensors with microscale devices has, however, proven to be challenging due to significant incompatibilities among biomolecular stability, operation conditions of electrochemical sensors, and microfabrication techniques. Toward a solution to this problem, we have demonstrated here an electrochemical array architecture that supports the following processes in situ, within a self-enclosed microfluidic device: (a) electrode cleaning and preparation, (b) electrochemical addressing, patterning, and immobilization of sensing biomolecules at selected sensor pixels, (c) sequence-specific electrochemical detection from multiple pixels, and (d) regeneration of the sensing pixels. The architecture we have developed is general, and it should be applicable to a wide range of biosensing schemes that utilize gold-thiol self-assembled monolayer chemistry. As a proof-of-principle, we demonstrate the detection and differentiation of polymerase chain reaction (PCR) amplicons diagnostic of human (H1N1) and avian (H5N1) influenza.     

Determining the efficacy of liquid sporicides against spores of Bacillus subtilis on a hard nonporous surface using the quantitative three step method: collaborative study

A collaborative study was conducted to validate the quantitative Three Step Method (TSM), a method designed to measure the performance of liquid sporicides on a hard nonporous surface. Ten laboratories agreed to participate in the collaborative study; data from 8 of 10 participating laboratories were used in the final statistical analysis. The TSM uses 5 x 5 x 1 mm glass coupons (carriers) upon which spores have been inoculated and which are introduced into liquid sporicidal agent contained in a microcentrifuge tube. Following exposure to a test chemical and a neutralization agent, spores are removed from carriers in 3 fractions: passive removal (Fraction A), sonication (Fraction B), and gentle agitation (Fraction C). Liquid from each fraction is serially diluted and plated on a recovery medium for spore enumeration. Control counts are compared to the treated counts, and the level of efficacy is determined by calculating the log10 reduction (LR) of spores. The main statistical goals were to evaluate the repeatability and reproducibility of the LR values, to estimate the components of variance for LR, and to assess method responsiveness. AOAC Method 966.04-Method II was used as a reference method. The scope of the validation was limited to testing liquid formulations against spores of Bacillus subtilis, a surrogate for virulent strains of B. anthracis, on a hard nonporous surface (glass). The test chemicals used in the study were sodium hypochlorite, a combination of peracetic acid and hydrogen peroxide, and glutaraldehyde. Each test chemical was evaluated at 3 levels of presumed efficacy: high, medium, and low. Three replications were required. The TSM was validated as it successfully met the statistical parameters for quantitative test methods. Satisfactory validation parameters, such as the repeatability standard deviation (Sr) and reproducibility standard deviation (SR), were obtained for control carrier counts and LR values. Both the TSM and the reference method were responsive to the efficacy levels of the test chemicals. For the 72 total TSM tests conducted, the mean (+/- standard error of the mean) log density of spores per control carrier was 6.86 (+/- 0.08); the Sr and SR were low at 0.15 and 0.27, respectively. Across the range of test chemicals, the Sr and SR estimates associated with LR were also acceptably low. The Sr ranged from 0.17 to 0.72 and the SR ranged from 0.34 to 1.43. Overall, the Sr and SR estimates associated with the efficacy data were within the ranges published for other quantitative methods and meet the performance characteristics necessary for validation.