Exonuclease I aided enzyme-linked aptamer assay for small-molecule detection.

A novel enzyme-linked aptamer assay (ELAA) with the aid of Exonuclease I (Exo I) for colorimetric detection of small molecules was developed. The fluorescein isothiocyanate (FITC)-labeled aptamer was integrated into a double-stranded DNA (dsDNA). In the presence of target, the binding of aptamer with target protected the aptamer from Exo I degradation, which resulted in the FITC tag remaining on the aptamer. Then, the anti-FITC-HRP conjugate was used to produce an optically observable signal. By monitoring the color change, we were able to detect two model molecules, ATP and L-argininamide, with high selectivity and high sensitivity even in the serum matrix. It is expected to be a simple and general ELAA method with wide applicability.

Communication: crystallite nucleation in supercooled glycerol near the glass transition.

Heterogeneity and solid-like structures found near the glass transition provide a key to a better understanding of supercooled liquids and of the glass transition. However, the formation of solid-like structures and its effect on spatial heterogeneity in supercooled liquids is neither well documented nor well understood. In this work, we reveal the crystalline nature of the solid-like structures in supercooled glycerol by means of neutron scattering. The results indicate that inhomogeneous nucleation happens at temperatures near T(g). Nevertheless, the thermal history of the sample is essential for crystallization. This implies such structures in supercooled liquids strongly depend on thermal history. Our work suggests that different thermal histories may lead to different structures and therefore to different length and time scales of heterogeneity near the glass transition.

Temperature-cycle single-molecule FRET microscopy on polyprolines.

Accessing the microsecond dynamics of a single fluorescent molecule in real time is difficult because molecular fluorescence rates usually limit the time resolution to milliseconds. We propose to apply single-molecule temperature-cycle microscopy to probe molecular dynamics at microsecond timescales. Here, we follow donor and acceptor signals of single FRET-labeled polyprolines in glycerol to investigate their conformational dynamics. We observe a steady-state FRET efficiency distribution which differs from theoretical distributions for isotropically orientated fluorescent labels. This may indicate that the orientation of fluorescent labels in glycerol is not isotropic and may reflect the influence of the dye linkers. With proper temperature-cycle parameters, we observed large FRET changes in long series of cycles of the same molecule. We attribute the main conformational changes to reorientations of the fluorescent labels with respect to the oligopeptide chain, which take place in less than a few microseconds at the highest temperature of the cycle (250 K). We were able to follow the FRET efficiency of a particular construct for more than 2000 cycles. This trajectory displays switching between two conformations, which give rise to maxima in the FRET efficiency histogram. Our experiments open the possibility to study biomolecular dynamics at a time scale of a few microseconds at the single-molecule level.

Single molecules as optical nanoprobes for soft and complex matter.

The optical signals of single molecules provide information about structure and dynamics of their nanoscale environment, free from space and time averaging. These new data are particularly useful whenever complex structures or dynamics are present, as in polymers or in porous oxides, but also in many other classes of materials, where heterogeneity is less obvious. We review the main uses of single molecules in studies of condensed matter at nanometer scales, especially in the fields of soft matter and materials science. We discuss several examples, including the orientation distribution of molecules in crystals, rotational diffusion in glass-forming molecular liquids, polymer studies with probes and labeled chains, porous and heterogeneous oxide materials, blinking of single molecules and nanocrystals, and the potential of surface-enhanced Raman scattering for local chemical analysis. All these examples show that static and dynamic heterogeneities and the spread of molecular parameters are much larger than previously imagined.

Micron-sized structure in a thin glycerol film revealed by fluorescent probes.

We report on micrometer-sized structures in supercooled glycerol observed by imaging fluorescent probes at the temperatures close to, but above, the glass transition temperature (190 K). Two distinct heterogeneous patterns of the fluorescence intensity were detected, depending on how fast the sample was cooled down. In a slowly cooled sample, we observed a Swiss cheese-like pattern in which many micrometer-sized dark spots were nucleated in a bright background. A quickly cooled sample resulted in a spinodal decomposition pattern where many bright island-like features on micrometer scale were dispersed in a dark matrix. Similar patterns were seen earlier in triphenyl phosphite, another molecular liquid, which shows solid-like behavior at temperatures above its glass transition. Once the heterogeneous patterns are formed in the glycerol, they can persist for days, unless the samples are heated above 260 K for more than 10 h. Such heterogeneous patterns are ascribed to differential dye distributions in the glycerol film, pointing to long-lived and micrometer-scale density fluctuations in supercooled glycerol. The observation of such heterogeneity may provide additional understanding on how supercooled glycerol behaves before it turns into a glass.

Soft glassy rheology of supercooled molecular liquids.

We probe the mechanical response of two supercooled liquids, glycerol and ortho-terphenyl, by conducting rheological experiments at very weak stresses. We find a complex fluid behavior suggesting the gradual emergence of an extended, delicate solid-like network in both materials in the supercooled state-i.e., above the glass transition. This network stiffens as it ages, and very early in this process it already extends over macroscopic distances, conferring all well known features of soft glassy rheology (yield-stress, shear thinning, aging) to the supercooled liquids. Such viscoelastic behavior of supercooled molecular glass formers is difficult to observe because the large stresses in conventional rheology can easily shear-melt the solid-like structure. The work presented here, combined with evidence for long-lived heterogeneity from previous single-molecule studies [Zondervan R, Kulzer F, Berkhout GCG, Orrit M (2007) Local viscosity of supercooled glycerol near T(g) probed by rotational diffusion of ensembles and single dye molecules. Proc Natl Acad Sci USA 104:12628-12633], has a profound impact on the understanding of the glass transition because it casts doubt on the widely accepted assumption of the preservation of ergodicity in the supercooled state.