We have found strong supporting evidence for the helical structures of single-stranded nucleic acids by stretching individual molecules of polyadenylic acid [poly(A)] and polycytidylic acid [poly(C)]. Analyzing the force versus extension data using a two-state elastic model in which random-coil domains alternate with rigid helical domains allows one to extract the thermodynamic and structural properties. In addition, it also yields moderate to low cooperativity of the helix-coil transition for poly(A) and poly(C), respectively.

Competitive hybridization, at the surface and in the bulk, lowers the sensitivity of DNA chips. Competitive surface hybridization occurs when different targets can hybridize with the same probe. Competitive bulk hybridization takes place when the targets can hybridize with free complementary chains in the solution. The effects of competitive hybridization on the thermodynamically attainable performance of DNA chips are quantified in terms of the hybridization isotherms of the spots. These relate the equilibrium degree of the hybridization to the bulk composition. The hybridization isotherm emerges as a Langmuir isotherm modified for electrostatic interactions within the probe layer. The sensitivity of the assay in equilibrium is directly related to the slope of the isotherm. A simpler description is possible, in terms of c(50) values specifying the bulk composition corresponding to 50% hybridization at the surface. The effects of competitive hybridization are important for the quantitative analysis of DNA chip results, especially when used to study point mutations.

The design of DNA chip experiments utilizes hybridization isotherms relating the equilibrium hybridization at the surface to the composition of the solution. Within this family, the Langmuir isotherm is the simplest and the most frequently used. This tutorial review summarizes the domain of validity of the Langmuir isotherm and discusses the modifications necessary to allow for competitive hybridization in the bulk and at the surface, probe polydispersity and interactions between the probe sites. The equilibrium constant of hybridization at an impenetrable surface is described, as well as the relative merits of the melting temperature and c 50 as design parameters. The relevance to various experimental situations, including two-colour experiments, study of point mutations for cancer diagnostics, genotyping of pooled samples and aspects of Latin square experiments, is discussed.

In biology experiments, oligonucleotide microarrays are contacted with a solution of long nucleic acid targets. The hybridized probes thus carry long tails. When the surface density of the oligonucleotide probes is high enough, the progress of hybridization gives rise to a polyelectrolyte brush due to mutual crowding of the nucleic acid tails. The free-energy penalty associated with the brush modifies both the hybridization isotherms and the rate equations: the attainable hybridization is lowered significantly as is the hybridization rate. When the equilibrium hybridization fraction, x(eq), is low, the hybridization follows a Langmuir type isotherm, x(eq)/(1 - x(eq)) = c(t)K where c(t) is the target concentration and K is the equilibrium constant. K is smaller than its bulk value by a factor (n/N)(2/5) due to wall effects where n and N denote the number of bases in the probe and the target. At higher x(eq), when the brush is formed, the leading correction is x(eq)/(1 - x(eq)) = c(t)K exp - const'x(eq)(2/3) - x(B)(2/3) where x(B) corresponds to the onset of the brush regime. The denaturation rate constant in the two regimes is identical. However, the hybridization rate constant in the brush regime is lower, the leading correction being exp -const' x(2/3) - x(B)(2/3).

We present an analysis of hybridization experiments on a DNA chip studied by surface plasmon resonance imaging. The reaction constants at various temperatures and for different probe lengths are obtained from Langmuir isotherms and hybridization kinetics. The melting curves from temperature scans are also obtained without any labeling of the targets. The effects of the probe length on the hybridization thermodynamics, deduced from the temperature dependence of the reaction constants as well as from the melting curves, suggest dispersion in the length of the hybridization segments of the probes accessible to the targets. Those are, however, sufficient to suggest efficient point mutation detection from temperature scans.

We study the out-of-equilibrium fluctuation-dissipation (FD) relations in the low temperature, finite time, physical aging regime of two simple models with strong glass behaviour, the FredricksonAndersen model and the square-plaquette interaction model. We explicitly show the existence of unique, waiting-time independent dynamical FD relations. While in the Fredrickson-Andersen model the FD theorem is obeyed at all times, the plaquette model displays piecewise linear FD relations, similar to what is found in disordered mean-field models and in simulations of supercooled liquids, and despite the fact that its static properties are trivial. We discuss the wider implications of these results.PACS numbers: 64.70. Pf, 75.10.Hk, 05.70.Ln The common feature to all glassy systems, like supercooled liquids, spin glasses, and, to a certain degree, even soft materials like gently driven powders, is an extremely slow relaxational dynamics at low temperatures or high densities (for reviews see [1][2][3]). Often, glassy systems display a dynamical behaviour known as aging, which corresponds to the asymptotic regime in which one-time quantities, like energy or magnetization, are stationary, but two-time quantities, like response and autocorrelation functions, still depend on the time elapsed since the system was prepared, rather than just on time differences, as in equilibrium. While in this situation response and autocorrelations do not obey the fluctuationdissipation theorem (FDT) [4], exact results for meanfield models [5,2] have suggested that FD relations are generalized in a well defined way, that the breakdown of FDT can be understood in terms of 'effective' temperatures [6], and that there may be a close connection between out-of-equilibrium FD relations and equilibrium properties [7]. Nontrivial asymptotic FD relations have also been found in other (non-glassy) out-of-equilibrium situations, like ferromagnetic domain growth [8] and systems at criticality [9], and FD plots similar to the ones of discontinuous mean-field models have been observed in simulations of supercooled liquids [10,11] and of frustrated [12] and constrained [13] lattice gases.However, both in experiments and simulations, a relevant regime is that of long but finite times where onetime quantities are not stationary, but are slowly relaxing towards their equilibrium values, a situation known as 'physical' aging [14]. A second issue is that near the glass transition activated processes, which are explicitly excluded in mean-field, play an essential role. With respect to this, simulations of simple models with activated dynamics [15,16] have shown nonmonotonic response functions, which, superficially, lead to meaningless FD relations (something analogous occurs in models of vibrated granular matter [17]). And finally, there is evidence, at least for molecular glasses, for the absence of any thermodynamic phase transition underlying the dynamical arrest [18], so that if nontrivial FD relations exist for these systems they cannot be interpreted in te...

The extension elasticity of rod-coil mutliblock copolymers is analyzed for two experimentally accessible situations. In the quenched case, when the architecture is fixed by the synthesis, the force law is distinguished by a sharp change in the slope. In the annealed case, where interconversion between rod and coil states is possible, the resulting force law is sigmoid with a pronounced plateau. This last case is realized, for example, when homopolypeptides capable of undergoing a helix-coil transition are extended from a coil state. Both scenarios are relevant to the analysis and design of experiments involving single molecule mechanical measurements of biopolymers and synthetic macromolecules.PACS numbers: 61.25. Hq, 61.41.+e, 87.15.He With the advent of single molecule mechanical measurements it became possible to study the force laws characterizing the extension of individual macromolecules [1]. In turn, these provide a probe of internal degrees of freedom associated with intrachain self assembly or with monomers that can assume different conformational states. A molecular interpretation of the force laws thus obtained requires appropriate theoretical models allowing for the distinctive "internal states" of each system. The formulation of such models is a challenging task in view of the complexity and diversity of the systems investigated. These include DNA [2], the muscle protein titin [3] and the extracellular matrix protein tenascin [4], the polyscharides dextran [5] and xanthan [6] as well as the synthetic polymer poly(ethelene-glycol) [7].In this letter we consider two unexplored yet accessible systems where a detailed confrontation between theory and experiment is possible. In particular, we present a theory for the extension force law of multiblock copolymers consisting of alternating rod and coil blocks. Two scenarios are considered, both focusing on the equilibrium force law of long chains undergoing quasistatic extension. In one, the architecture is "quenched" that is, the block structure is set by the chemistry and no interconversion is possible. Such is the case, for example, for segmented polyurethans [8]. In the second scenario the monomers can interconvert between coil and rod states. The "annealed" architecture is realized, for instance, in homopolypeptides capable of undergoing a cooperative helix-coil transition [9][10][11]. In this system, the highly rigid helical domains play the part of the rod blocks. As we shall see, the two scenarios lead to distinctive force laws (Figure). The force law of the quenched case is characterized by an abrupt change of slope. This arises because the rod blocks are more susceptible to orientation by the applied tension. In the annealed scenario, the extension of a chain that is initially in a coil state leads to a sigmoid force profile exhibiting a pronounced plateau. The plateau is traceable to a one dimensional coexistence of helical and coil domains where the chain extension favors the helical state because of its low configurational entropy. These res...

Monitoring volatile organic compounds (VOCs) is an important issue, but difficult to achieve on a large scale and on the field using conventional analytical methods. Electronic noses (eNs), as promising alternatives, are still compromised by their performances due to the fact that most of them rely on a very limited number of sensors and use databases devoid of kinetic information. To narrow the performance gap between human and electronic noses, we developed a novel optoelectronic nose, which features a large sensor microarray that enables multiplexed monitoring of binding events in real-time with a temporal response. For the first time, surface plasmon resonance imaging is demonstrated as a promising novel analytical tool for VOC detection in the gas phase. By combining it with cross-reactive sensor microarrays, the obtained optoelectronic nose shows a remarkably high selectivity, capable of discriminating between homologous VOCs differing by only a single carbon atom. In addition, the optoelectronic nose has good repeatability and stability. Finally, the preliminary assays using VOC binary and ternary mixtures show that it is also very efficient for the analysis of more complex samples, opening up the exciting perspective of applying it to "real-world" samples in diverse domains.