Persistence Length of Cartilage Aggrecan Macromolecules Measured via Atomic Force Microscopy

Tapping mode atomic force microscopy (TMAFM) was employed to directly calculate the persistence length of individual fetal bovine epiphyseal and mature nasal cartilage aggrecan monomers, as well as their constituent chondroitin sulfate glycosaminoglycan chains.     

Characterization of humic substances: Implications for trihalomethane formation

Humic substances are precursors of carcinogenic trihalomethanes (THMs) formed during disinfection by chlorination in water treatment processes. In an effort to understand the relationship between trihalomethane formation potential (THMFP) and physicochemical properties of humic substances, UV-visible absorbance, fluorescence in emission and synchronous scan modes, and NMR spectra were measured for several aquatic fulvic and humic acids. For comparison, a soil fulvic acid was also examined using these methods. The feasibility of the gradient modified spin-echo (GOSE) NMR experiment to selectively measure singlet resonances arising from isolated protons was examined. In addition, diffusion coefficients were measured for DMSO solutions of the fulvic acids using BPPLED and GOSE-edited pulse sequences. Although none of the methods tested produced results that correlated with THMFP, the GOSE intensities determined for different regions of the NMR spectra did reflect the relative abundance of different types of functional groups produced by lignin oxidation. In addition, the GOSE-edited diffusion results suggest that the isolated protons, those most reactive to chlorination, are more likely contained in the larger molecular weight fractions of fulvic acids.     

Fractal analysis of hydroxyapatite from nitrogen isotherms

Samples of calcium hydroxyapatite, CaHap, were prepared via a wet method and subjected to thermal treatment in air in the temperature range 100-900 degrees C. Nitrogen adsorption-desorption isotherms were obtained on different samples, and their data points were used to analyze the fractal properties of the obtained solids. Both FHH and Neimark's equations were used for such purpose, and the agreement or disagreements between obtained results on using both equations are discussed. Considering the appropriate values of the obtained surface fractal dimensions D, it was concluded that an appreciable defractalization of the prepared hydroxyapatite is only noted upon calcinations at 900 degrees C. Below this temperature the loss in surface area and pore volume result from simultaneous bulk and surface mass transport, which conserve the initial surface roughness and average pore radius. Calcination at 900 degrees C caused sintering to proceed via bulk mass transport, with a consequent pore widening and a decrease in surface roughness.     

Nuclear quadrupole hyperfine structure in the microwave spectrum of HCl-N2O: electric field gradient perturbation of N2O by HCl

The microwave spectra of six isotopomers of HCl-N(2)O have been obtained in the 7-19 GHz region with a pulsed molecular beam, Fourier transform microwave spectrometer. The nuclear quadrupole hyperfine structure due to all quadrupolar nuclei is resolved and the spectra are analyzed using the Watson S-reduced Hamiltonian with the inclusion of nuclear quadrupole coupling interactions. The spectroscopic constants determined include rotational constants, quartic and sextic centrifugal distortion constants, and nuclear quadrupole coupling constants for each quadrupolar nucleus. Due to correlations of the structural parameters, the effective structure of the complex cannot be obtained by fitting to the spectroscopic constants of the six isotopomers. Instead, the parameters for each isotopomer are calculated from the A and C rotational constants and the chlorine nuclear quadrupole coupling constant along the a-axis, chi(aa). There are two possible structures; the one in which hydrogen of HCl interacts with the more electronegative oxygen of N(2)O is taken to represent the complex. The two subunits are approximately slipped parallel. For H (35)Cl-(14)N(2)O, the distance between the central nitrogen and chlorine is 3.5153 A and the N(2)O and HCl subunits form angles of 72.30 degrees and 119.44 degrees with this N-Cl axis, respectively. The chlorine and oxygen atoms occupy the opposite, obtuse vertices of the quadrilateral formed by O, central N, Cl, and H. Nuclear quadrupole coupling constants show that while the electric field gradient of the HCl subunit remains essentially unchanged upon complexation, there is electronic rearrangement about the two nitrogen nuclei in N(2)O.     

Estimating entropies from molecular dynamics simulations

While the determination of free-energy differences by MD simulation has become a standard procedure for which many techniques have been developed, total entropies and entropy differences are still hardly ever computed. An overview of techniques to determine entropy differences is given, and the accuracy and convergence behavior of five methods based on thermodynamic integration and perturbation techniques was evaluated using liquid water as a test system. Reasonably accurate entropy differences are obtained through thermodynamic integration in which many copies of a solute are desolvated. When only one solute molecule is involved, only two methods seem to yield useful results, the calculation of solute-solvent entropy through thermodynamic integration, and the calculation of solvation entropy through the temperature derivative of the corresponding free-energy difference. One-step perturbation methods seem unsuitable to obtain entropy estimates.     

Dendrimer-functionalized self-assembled monolayers as a surface plasmon resonance sensor surface

We report here a multistep route for the immobilization of DNA and proteins on chemically modified gold substrates using fourth-generation NH(2)-terminated poly(amidoamine) dendrimers supported by an underlying amino undecanethiol (AUT) self-assembled monolayer (SAM). Bioactive ultrathin organic films were prepared via layer-by-layer self-assembly methods and characterized by fluorescence microscopy, variable angle spectroscopic ellipsometry, atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and attenuated total internal reflection Fourier transform infrared spectroscopy (ATR-FTIR). The thickness of the AUT SAM base layer on the gold substrates was determined to be 1.3 nm from ellipsometry. Fluorescence microscopy and AFM measurements, in combination with analyses of the XPS/ATR-FTIR spectra, confirmed the presence of the dendrimer/biopolymer molecules on the multilayer sensor surfaces. Model proteins, including streptavidin and rabbit immunoglobulin proteins, were covalently attached to the dendrimer layer using linear cross-linking reagents. Through surface plasmon resonance measurements, we found that sensor surfaces containing a dendrimer layer displayed an increased protein immobilization capacity, compared to AUT SAM sensor surfaces without dendrimer molecules. Other SPR studies also revealed that the dendrimer-based surfaces are useful for the sensitive and specific detection of DNA-DNA interactions. Significantly, the multicomponent films displayed a high level of stability during repeated regeneration and hybridization cycles, and the kinetics of the DNA-DNA hybridization process did not appear to be influenced by surface mass transport limiting effects.     

The effect of octyl glucoside on the lamellar phase of diluted C12E4 and alcohol systems

A systematic study on phase behavior of the mixture of nonionic surfactants with alcohols at 30.0+/-0.1 degrees C was carried out. The total surfactant concentration was kept to 0.1 M varying the mole ratio of n-octyl beta-d-glucopyranoside (OG) and tetraethylene glycol monododecyl ether. Two uniphasic regions were found, the lamellar phase at low OG mole fraction and micelles at high OG mole fraction. The presence of OG favors the lamellae-micelle transition. Alkanols and benzyl alcohol were used as cosurfactants. The more hydrophobic alcohols (octanol and decanol) increase the OG content in the mixed bilayers. On the contrary, benzyl alcohol is not as favorable to the OG incorporation in the lamellar phase as in the mixed micelles. The L(3) phase has only been found as a uniphasic region with hexanol.     

Nucleic acid analysis using an expanded genetic alphabet to quench fluorescence

Organic chemistry has made possible the synthesis of molecules that expand on Nature's genetic alphabet. Using the previously described nonstandard DNA base pair constructed from isoguanine and 5-methylisocytosine, we report a highly specific and sensitive method that allows for the fast and specific quantitation of genetic sequences in a closed tube format. During PCR amplification, enzymatic site-specific incorporation of a quencher covalently linked to isoguanine allows for the simultaneous detection and identification of multiple targets. The specificity of method is then established by analysis of thermal denaturation or melting of the amplicons. The appropriate functions of all reactions are further verified by incorporation of an independent target into the reaction mixture. We report that the method is sensitive down to the single copy level, and specificity is demonstrated by multiplexed end-point genotypic analysis of four targets simultaneously using four separate fluorescent reporters. The method is general enough for quantitative and qualitative analysis of both RNA and DNA using previously developed primer sets. Though the method described employs the commonly used PCR, the enzymatic incorporation of reporter groups into DNA site-specifically should find broad utility throughout molecular biology.     

Role of the spacer in the singlet-singlet energy transfer mechanism (Förster vs Dexter) in cofacial bisporphyrins

The cofacial bisporphyrins H4DPS (DPS = 4,6-bis[5-(2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrinyl)]dibenzothiophene), H4DPO (DPO = 4,6-bis[5-(2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrinyl)]dibenzofuran), H4DPX (DPX = 4,5-bis[5-(2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrinyl)]-9,9-dimethylxanthene), H4DPA (DPA = 1,8-bis[5-(2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrinyl)]anthracene), and H4DPB (DPB = 1,8-bis[5-(2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrinyl)]biphenylene) have been monometalated by Zn(OAc)2.2H2O and by GaCl3 to explore the singlet-singlet energy transfer from the photoexcited metal porphyrin center to the linked free base porphyrin. The spectroscopic (UV-vis and fluorescence) and photophysical properties (fluorescence lifetimes, tauF, and quantum yields, phiF) have been investigated at 298 and 77 K in degassed 2-MeTHF for the donor-acceptor systems, (Zn)H2DPS, (Zn)H2DPO, (Zn)H2DPA, (Zn)H2DPX, and (Zn)H2DPB, as well as for the bis-zinc complexes, (Zn)2DPS, (Zn)2DPO, (Zn)2DPX, and (Zn)2DPB, respectively, and the monoporphyrin derivatives, H2P, (Zn)P, and (Ga-OMe)P (P2- = 5-phenyl-2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrin-dianion). The singlet-singlet energy transfer rate constants (KET) were obtained using KET = (1/tauF -1/tauFo), where tauFo is the fluorescence lifetime of the corresponding bis-zinc(II) systems (or (Zn)P and (Ga-OMe)P) where no energy transfer occurs. The tauF value for three bis-zinc(II) compounds varies from 1.69 to 2.01 ns and is 1.84 (at 298 K) and 3.20 ns (at 77 K) for (Ga-OMe)P. In the donor-acceptor bismacrocycles, depending on the spacer and the temperature, the fluorescence lifetimes decrease down to 50-240 ps. The KET values range from approximately 4 to approximately 21 (ns(-1)) and have been analyzed considering both the F?rster and the Dexter mechanisms. Using the C(meso)-C(meso) distance parameters in the calculations, the F?rster and Dexter mechanisms operate for DPS and DPO, and for DPA, DPX, and DPB spacer systems, respectively. The limit distance where one mechanism dominates over the other is estimated to be around 5-6 A.