Multiplexed identification, quantification and genotyping of infectious agents using a semiconductor biochip.

The emergence of pathogens resistant to existing antimicrobial drugs is a growing worldwide health crisis that threatens a return to the pre-antibiotic era. To decrease the overuse of antibiotics, molecular diagnostics systems are needed that can rapidly identify pathogens in a clinical sample and determine the presence of mutations that confer drug resistance at the point of care. We developed a fully integrated, miniaturized semiconductor biochip and closed-tube detection chemistry that performs multiplex nucleic acid amplification and sequence analysis.

Achiral symmetry breaking and positive Gaussian modulus lead to scalloped colloidal membranes.

In the presence of a nonadsorbing polymer, monodisperse rod-like particles assemble into colloidal membranes, which are one-rod-length-thick liquid-like monolayers of aligned rods. Unlike 3D edgeless bilayer vesicles, colloidal monolayer membranes form open structures with an exposed edge, thus presenting an opportunity to study elasticity of fluid sheets. Membranes assembled from single-component chiral rods form flat disks with uniform edge twist.

Colloidal membranes of hard rods: unified theory of free edge structure and twist walls.

Monodisperse suspensions of rod like chiral fd viruses are condensed into a rod-length thick colloidal monolayers of aligned rods by depletion forces. Twist deformations of the molecules are expelled to the monolayer edge as in a chiral smectic A liquid crystal, and a cholesteric band forms at the edge. Coalescence of two such isolated membranes results in a twist wall sandwiched between two regions of aligned rods, dubbed π-walls.

Imprintable membranes from incomplete chiral coalescence.

Coalescence is an essential phenomenon that governs the equilibrium behaviour in a variety of systems from intercellular transport to planetary formation. In this report, we study coalescence pathways of circularly shaped two-dimensional colloidal membranes, which are one rod-length-thick liquid-like monolayers of aligned rods. The chirality of the constituent rods leads to three atypical coalescence pathways that are not found in other simple or complex fluids.

Reconfigurable self-assembly through chiral control of interfacial tension.

From determining the optical properties of simple molecular crystals to establishing the preferred handedness in highly complex vertebrates, molecular chirality profoundly influences the structural, mechanical and optical properties of both synthetic and biological matter on macroscopic length scales. In soft materials such as amphiphilic lipids and liquid crystals, the competition between local chiral interactions and global constraints imposed by the geometry of the self-assembled structures leads to frustration and the assembly of unique materials. An example of particular interest is smectic liquid crystals, where the two-dimensional layered geometry cannot support twist and chirality is consequently expelled to the edges in a manner analogous to the expulsion of a magnetic field from superconductors.

Self-limited self-assembly of chiral filaments.

We discuss dynamical simulations and free energy calculations on patchy spheres with chiral pair interactions that spontaneously assemble into filamentous bundles. The chirality frustrates long-range crystal order by introducing twist between interacting subunits. For some ranges of system parameters this constraint leads to bundles with a finite diameter, and in other cases frustration is relieved by the formation of defects.

Theory of depletion-induced phase transition from chiral smectic- A twisted ribbons to semi-infinite flat membranes.

We consider a theoretical model for the chiral smectic A twisted ribbons observed in assemblies of fd viruses condensed by depletion forces. The depletion interaction is modeled by an edge energy assumed to be proportional to the depletant polymer in solution. Our model is based on the Helfrich energy for surface bending and the de Gennes model of chiral smectic A liquid crystals with twist penetration at the edge.

Direct measurement of the twist penetration length in a single smectic A layer of colloidal virus particles.

In the 1970s, deGennes discussed the fundamental geometry of smectic liquid crystals and established an analogy between the smectic A phase and superconductors. It follows that smectic layers expel twist deformations in the same way that superconductors expel magnetic field. We make a direct observation of the penetration of twist at the edge of a single isolated smectic A layer composed of chiral fd virus particles subjected to a depletion interaction.

Dynamics of the molecular orientation field coupled to ions in two-dimensional ferroelectric liquid crystals.

Molecular orientation fluctuations in ferroelectric smectic liquid crystals produce space charges, due to the divergence of the spontaneous polarization. These space charges interact with mobile ions, so that one must consider the coupled dynamics of the orientation and ionic degrees of freedom. Previous theory and light scattering experiments on thin free-standing films of ferroelectric liquid crystals have not included this coupling, possibly invalidating their quantitative conclusions.

Role of electrostatics in the texture of islands in free-standing ferroelectric liquid crystal films.

Curved textures of ferroelectric smectic-C* liquid crystals produce space charge when they involve divergence of the spontaneous polarization field. Impurity ions can partially screen this space charge, reducing long-range interactions to local ones. Through studies of the textures of islands on very thin free-standing smectic films, we see evidence of this effect, in which materials with a large spontaneous polarization have static structures described by a large effective bend elastic constant.

Unwinding of a strained cholesteric elastomer by disclination loop nucleation.

The application of a sufficiently strong strain perpendicular to the pitch axis of a monodomain cholesteric elastomer unwinds the cholesteric helix. Previous theoretical analyses of this transition ignored the effects of Frank elasticity which we include here. We find that the strain needed to unwind the helix is reduced because of the Frank penalty and the cholesteric state becomes metastable above the transition.

Textural transformations in islands on free standing smectic-C* liquid crystal films.

We report on and analyze the textural transformations in islands, thicker circular domains, floating in very thin free standing chiral Smectic-C* liquid crystal films. As an island is growing, an initial pure bend texture of the director changes into a reversing spiral at a critical size. Another distinct spiral texture is induced by changing the boundary condition at the central point defect in the island.

Buckling instability in liquid crystalline physical gels.

In a nematic gel we observe a low-energy buckling deformation arising from soft and semisoft elastic modes. We prepare the self-assembled gel by dissolving a coil-side-group liquid-crystalline polymer-coil copolymer in a nematic liquid crystal. The gel has long network strands and a precisely tailored structure, making it ideal for studying nematic rubber elasticity.

Isotropic-cholesteric transition in liquid-crystalline gels.

In a nematic gel, the appearance of nematic order is accompanied by a spontaneous elongation of the gel parallel to the nematic director. If such a gel is made chiral, it has a tendency to form a cholesteric helical texture, in which local elongation of the gel parallel to the nematic director is suppressed due to the requirement of elastic compatibility. We show that a conical helix in which the director makes an oblique angle with respect to the helix axis serves as an energy minimizing compromise between the competing tendencies for elongation and twisting.

Electroclinic effect and modulated phases in smectic liquid crystals.

We explore the possibility that the unusually large electroclinic effect observed in the smectic-A phase of a ferroelectric liquid crystal arises from the presence of an ordered array of disclination lines and walls in a smectic-C* phase. If the spacing of these defects is in the subvisible range, this modulated smectic-C* phase would be similar macroscopically to a smectic-A phase. The application of an electric field distorts the array, producing a large polarization, and hence a large electroclinic effect.

Electromechanical Fredericks effects in nematic gels.

The solid nematic equivalent of the Fredericks transition is found to depend on a critical field rather than a critical voltage as in the classical case. This arises because director anchoring is principally to the solid rubbery matrix of the nematic gel rather than to the sample surfaces. Moreover, above the threshold field, we find a competition between quartic (soft) and conventional harmonic elasticity which dictates the director response.

Chiral hedgehog textures in two-dimensional XY-like ordered domains.

The textures associated with a point defect centered in a circular domain of a thin film with XY-like ordering have been analyzed. The family of equilibrium textures, both stable and metastable, can be classified by a new radial topological number in addition to the winding number of the defect. Chiral textures are supported in an achiral system as a result of spontaneously broken chiral symmetry.

Untwisting of a cholesteric elastomer by a mechanical field.

A mechanical strain field applied to a monodomain cholesteric elastomer will unwind the helical director distribution. There are similarities with the classical problem of an electric field applied to a cholesteric liquid crystal but also differences. Frank elasticity is of minor importance unless the gel is very weak.

3'-minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures.

DNA probes with conjugated minor groove binder (MGB) groups form extremely stable duplexes with single-stranded DNA targets, allowing shorter probes to be used for hybridization based assays. In this paper, sequence specificity of 3'-MGB probes was explored. In comparison with unmodified DNA, MGB probes had higher melting temperature (T(m)) and increased specificity, especially when a mismatch was in the MGB region of the duplex.

Targeted mutagenesis of DNA with alkylating RecA assisted oligonucleotides.

Site-specific mutation was demonstrated in a shuttle vector system using nitrogen mustard-conjugated oligodeoxyribonucleotides (ODNs). Plasmid DNA was modified in vitro by ODNs containing all four DNA bases in the presence of Escherichia coli RecA protein. Up to 50% of plasmid molecules were alkylated in the targeted region of the supF gene and mutations resulted upon replication in mammalian cells.

Genetic testing legislation: a review of the past two years.

The American Council of Life Insurance is a national trade association that represents the interests of legal reserve life insurance companies in legislative, regulatory and judicial matters at the federal, state and municipal levels of government and at the National Association of Insurance Commissioners. Its member companies hold more than 90 percent of the life insurance in force in the United States.

Linkers designed to intercalate the double helix greatly facilitate DNA alkylation by triplex-forming oligonucleotides carrying a cyclopropapyrroloindole reactive moiety.

Triplex-forming oligonucleotides (TFOs) bind sequence-specifically in the major groove of double-stranded DNA. Cyclopropapyrroloindole (CPI), the electrophilic moiety that comprises the reactive subunit of the antibiotic CC-1065, gives hybridization-triggered alkylation at the N-3 position of adenines when bound in the minor groove of double-stranded DNA. In order to attain TFO-directed targeting of CPI, we designed and tested linkers to 'thread' DNA from the major groove-bound TFO to the minor groove binding site of CPI.

Triplex targeting of a native gene in permeabilized intact cells: covalent modification of the gene for the chemokine receptor CCR5.

A 12 nucleotide oligodeoxyribopurine tract in the gene for the chemokine receptor CCR5 has been targeted and covalently modified in intact cells by a 12mer triplex forming oligonucleotide (TFO) bearing a reactive group. A nitrogen mustard placed on the 5'-end of the purine motif TFO modified a guanine on the DNA target with high efficiency and selectivity. A new use of a guanine analog in these TFOs significantly enhanced triplex formation and efficiency of modification, as did the use of the triplex-stabilizing intercalator coralyne.

Solution structure of a highly stable DNA duplex conjugated to a minor groove binder.

The tripeptide 1,2-dihydro-(3 H )-pyrrolo[3,2- e ]indole-7-carboxylate (CDPI3) binds to the minor groove of DNA with high affinity. When this minor groove binder is conjugated to the 5'-end of short oligonucleotides the conjugates form unusually stable hybrids with complementary DNA and thus may have useful diagnostic and/or therapeutic applications. In order to gain an understanding of the structural interactions between the CDPI3minor groove binding moiety and the DNA, we have determined and compared the solution structure of a duplex consisting of oligodeoxyribonucleotide 5'-TGATTATCTG-3' conjugated at the 5'-end to CDPI3 and its complementary strand to an unmodified control duplex of the same sequence using nuclear magnetic resonance techniques.