The potential of electrophoretic mobility shift assays for clinical mutation detection

As the understanding of the links between genetic mutations and diseases continues to grow, there is an increasing need for techniques that can rapidly, inexpensively, and sensitively detect DNA sequence alterations. Typically, such analyses are performed on PCR-amplified gene regions. Automated DNA sequencing by capillary array electrophoresis can be used, but is expensive to apply to large numbers of patient samples and/or large genes, and may not always reveal low-abundance mutations in heterozygous samples. Many different types of genetic differences need to be detected, including single-base substitutions and larger sequence alterations such as insertions, deletions, and inversions. Electrophoretic mobility shift assays seem well suited to this purpose and could be used for the efficient screening of patient samples for sequence alterations, effectively reducing the number of samples that must be subjected to full and careful sequencing. While there is much promise, many of the mobility shift assays presently under development have yet to be demonstrated to have the high sensitivity and specificity of mutation detection required for routine clinical application. Hence, further studies and optimization are required, in particular the application of these methods not only to particular genes but also to large numbers of patient samples in blinded studies aimed at the rigorous determination of sensitivity and specificity. This review examines the state-of-the-art of the most commonly used mobility shift assays for mutation detection, including denaturing gradient gel electrophoresis, TGGE, SSCP, heteroduplex analysis, and denaturing HPLC.     

A bio-barcode assay for on-chip attomolar-sensitivity protein detection

Functionalized nanoparticles hold great promise in realizing highly sensitive and selective biodetection. We report a single disposable chip which is capable of carrying out a multi-step process that employs nanoparticles--a bio-barcode assay (BCA) for single protein marker detection. To illustrate the capability of the system, we tested for the presence of prostate specific antigen (PSA) in buffer solution and goat serum. Detection was accomplished at PSA concentrations as low as 500 aM. This corresponds to only 300 copies of protein analytes using 1 microL total sample volume. We established that the on-chip BCA for PSA detection offers four orders of magnitude higher sensitivity compared to commercially available ELISA-based PSA tests.     

Structural change in Li and Na aluminophosphate glasses: evidence of a "structural mixed alkali effect"

The short- and long-range structure of a series of single and mixed aluminophosphate glasses with the general composition [xNa(2)O (46 - x)Li(2)O], [yAl(2)O(3) (54 - y)P(2)O(5)] is analyzed using (31)P and (27)Al magic-angle spinning (MAS) NMR as well as small-angle X-ray scattering. These series of glasses allow analyzing both the effect of alumina incorporation in these glasses, for small alumina content (y = 0, 4, 8), and the structural changes associated with the so-called mixed alkali effect (x = 0, 11.5, 23, 34.5, 46). Our results indicate that aluminum is mainly octahedrally coordinated in these glasses and that there is most likely some segregation of the Al(OP)(6) species. In the pure phosphate glasses, we observe a "classical" continuous variation of the structural properties with the relative alkali content, but in the aluminophosphate, both local and long-range structural results reveal for the first time some nonlinear change as a function of the relative alkali content.     

Peptide-mediated nanoengineering of inorganic particle surfaces: a general route toward surface functionalization via peptide adhesion domains

The peptide-mediated functionalization of inorganic particle surfaces is demonstrated on gadolinium oxide (GdO) particles, revealing specific means to functionalize nano- or microparticles. Phage display screening is exploited to select 12mer peptides, which exhibit sequence-specific adhesion onto surfaces of GdO particles. These peptide adhesion domains are exploited to effectively decorate GdO particles with fluorescently labeled poly(ethylene oxide) (PEO), proving to result in a stable surface modification as shown by significant reduction of protein adsorption by 80%, compared to nonfunctionalized particles. Peptide adhesion and stability of the noncovalent coating are investigated by adsorption/elution experiments and Langmuir isotherms. Fluorescence microscopy, contact angle, and energy dispersive X-ray (EDX) measurements confirmed the sequence specificity of the interactions by comparing adhesion sequences with scrambled peptide sequences. Noncovalent, but specific modification of inorganic particle surfaces represents a generic strategy to modulate functionality and function of nano- or microparticle surfaces.     

A dielectric study of secondary relaxations and the “memory effect” in two compatible polystyrene blends

Dielectric permittivities and loss tangents of 10 and 30% poly(2,6-dimethyl-1,4-phenylene oxide) (PPO)–polystyrene (PS) blends and 10 and 25% poly(vinyl methyl ether) (PVME)–polystyrene blends have been measured from 80 to 360 K at 1 and 10 kHz. The PPO-PS blends have two secondary relaxations below T_g and the PVME-PS blends have three regions. All blends have a β process which appears near 290 K, is independent of PPO or PVME concentration, and is associated with the local modes of motions of PS chains. It is suggested that the β process of PS allows a dipolar reorientation of the PPO or PS chain segments by creating more favorable surroundings for the motions of the latter. The effect of physical aging in the PPO-PS blend is substantial but the “memory effect” is significantly less. This is due to the lower contribution to tanδ from the β process of the blend.     

Acrylamide: update on selected research activities conducted by the European food and drink industry

This paper reviews the progress made by the European food and drink industry (CIAA) on acrylamide with regard to analytical methods, mechanisms of formation, and mitigation research in the major food categories. It is an update on the first CIAA review paper, "A Review of Acrylamide: An Industry Perspective on Research, Analysis, Formation and Control." Initial difficulties with the establishment of reliable analytical methods, in most cases, have now been overcome, but challenges remain in terms of the need to develop simple and rapid test methods and certified reference materials. Many trials have been conducted under laboratory and experimental conditions in a variety of foods, and a number of possible measures have been identified to relatively lower the amounts of acrylamide in food. Promising applications were studied in reconstituted potato models by addition of amino acids or use of asparaginase. In bakery wares, predictive models have been established to determine the role of ammonium carbonate and invert sugar in acrylamide formation. Studies in several commercial foods showed that acrylamide is not stable over time in roasted and ground coffee. Some progress in relatively lowering acrylamide in certain food categories has been achieved, but at this stage can only be considered marginal. Any options that are chosen to reduce acrylamide in commercial products must be technologically feasible and must not adversely affect the quality and safety of the final product.     

New peptidomimetic polymers for antifouling surfaces

Exposure of therapeutic and diagnostic medical devices to biological fluids is often accompanied by interfacial adsorption of proteins, cells, and microorganisms. Biofouling of surfaces can lead to compromised device performance or increased cost and in some cases may be life-threatening to the patient. Although numerous antifouling polymer coatings have enjoyed short-term success in preventing protein and cell adsorption on surfaces, none have proven ideal for conferring long-term biofouling resistance. Here we describe a new biomimetic antifouling N-substituted glycine polymer (peptoid) containing a C-terminal peptide anchor derived from residues found in mussel adhesive proteins for robust attachment of the polymer onto surfaces. The methoxyethyl side chain of the peptoid portion of the polymer was chosen for its chemical resemblance to the repeat unit of the known antifouling polymer poly(ethylene glycol) (PEG), whereas the composition of the 5-mer anchoring peptide was chosen to directly mimic the DOPA- and Lys-rich sequence of a known mussel adhesive protein. Surfaces modified with this biomimetic peptide-peptoid conjugate exhibited dramatic reduction of serum protein adsorption and resistance to mammalian cell attachment for over 5 months in an in vitro assay. These new synthetic peptide based antifouling polymers may provide long-term control of surface biofouling in the physiologic, marine, and industrial environments.     

Effect of polymer matrix and glycerol on rapid single-strand conformation polymorphism analysis by capillary and microchip electrophoresis for detection of mutations in K-ras gene

We present the rapid single-strand conformation polymorphism (SSCP) analysis by capillary and microchip electrophoresis to detect the mutations in K-ras gene. Parameters that might affect the analysis of mutation in K-ras gene, such as the polymer and the additive in the sieving matrix, have been studied systematically. Under the optimal conditions, the analysis of seven mutants of K-ras gene could be finished within 10 min by capillary electrophoresis (CE). Furthermore, with the wild-type gene as the inner standard, the analysis accuracy of mutations could be improved. In addition, by studying the properties of polymer solutions, the matrix suitable for microchip electrophoresis was found, and the detection of mutations in K-ras gene could be further shortened to 1 min.     

C-glycosyl derivatives. XIV. Synthesis of 5-glycosyl-delta2-isoxazolines

Treatment of terminal-unsaturated sugars with stable aromatic nitrile oxides led to the expected Δ₂-isoxazolines, obtained as a mixture of two diastereoisomers epimeric at the new asymmetric carbon. One isomer (and in some cases both) has been isolated in a pure state. These compounds are potentially useful in the drug-design of therapeutically active molecules.     

Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains

Substantial progress has been made in the synthesis and characterization of various oligomeric molecules capable of autonomous folding to well-defined, repetitive secondary structures. It is now possible to investigate sequence-structure relationships and the driving forces for folding in these systems. Here, we present detailed analysis by X-ray crystallography, NMR, and circular dichroism (CD) of the helical structures formed by N-substituted glycine (or "peptoid") oligomers with alpha-chiral, aliphatic side chains. The X-ray crystal structure of a N-(1-cyclohexylethyl)glycine pentamer, the first reported for any peptoid, shows a helix with cis-amide bonds, approximately 3 residues per turn, and a pitch of approximately 6.7 A. The backbone dihedral angles of this pentamer are similar to those of a polyproline type I peptide helix, in agreement with prior modeling predictions. This crystal structure likely represents the major solution conformers, since the CD spectra of analogous peptoid hexamers, dodecamers, and pentadecamers, composed entirely of either (S)-N-(1-cyclohexylethyl)glycine or (S)-N-(sec-butyl)glycine monomers, also have features similar to those of the polyproline type I helix. Furthermore, this crystal structure is similar to a solution NMR structure previously described for a peptoid pentamer comprised of chiral, aromatic side chains, which suggests that peptoids containing either aromatic or aliphatic alpha-chiral side chains adopt fundamentally similar helical structures in solution, despite distinct CD spectra. The elucidation of detailed structural information for peptoid helices with alpha-chiral aliphatic side chains will facilitate the mimicry of biomolecules, such as transmembrane protein domains, in a distinctly stable form.