Immobilized molecules, single molecule

In 1996, partial immobilization of single molecules in an aqueous environment was achieved by using the water-filled pores of poly(acrylamide) gels, a technique that has been demonstrated for organic dye molecules [80] as well... 

Abstract Chemists may find it difficult to admit that their concepts and opportunities have always been strongly influenced by the available methods for characterization and analysis. Physics, has, of course, the lead when it comes to the visualization of single molecules in real space and to the detection of their specific, not ensemble-averaged properties. The challenge for chemistry is to provide molecules as objects of study which really disclose new concepts of structure and function. This chapter presents a chemical approach toward nanosciences which comprises (i) design and synthesis, (ii) immobilization, often using principles of self-assembly, (iii) visualization, e.g. by scanning probe... 

Reduction of analyte occurs at the cathode (on the right-hand side of the cell). Once formed, however, the reduced form of the analyte couple diffuses across the cell - it may also be swept along by the stirred solution - and/or be re-oxidized again at the anode. Clearly, a single molecule of analyte could be oxidized and reduced many times, thus leading to an artificially high charge at the coulometer. For this reason, the two halves of the coulometry cell should be separated if possible, e.g. with a semipermeable membrane or frit, or we should ensure that the product of electron transfer should be a solid, i.e. it is immobilized as soon as it is formed. 

In general, neither the force nor the molecular extension can be controlled in the experiments so definitions in Eqs. (96), (98), and (99) result in approximations to the true mechanical work that satisfy Eqs. (40) and (41). The control parameter in single molecule experiments using optical tweezers is the distance between the center of the trap and the immobilized bead [88]. Both the position of the bead in the trap and the extension of the handles are fluctuating quantities. It has been observed [94—96] that in pulhng experiments the proper work that satisfies the FT includes some corrections to Eqs. (97) and (99) mainly due to the effect of the trapped bead. There are two considerations to take into account when analyzing experimental data. 

Abstract. Various ways of extracting information on the conformational structure, dynamics and correlations between them from single-molecule measurements of florescence resonance energy transfer are surveyed. The information obtained via those various ways is then analyzed in detail in the case of an off-lattice model of a two-stranded coiled-coil polypeptide that follows Langevin dynamics. The analysis includes a consideration of the cases of a freely diffusing and surface-immobilized polypeptide as well as the effect of different types of surface and denaturation conditions. 

Alternatively, the RNA can be immobilized on a shde, in which case single molecules can be studied for many seconds and conformational transitions observed. The time of observation is limited by photochemical effects on the fluorophores, but this can be extended with recently improved oxygen scavenging systems (Aitken et al., 2008 Rasnik et al., 2006). Again there are two choices. A wide-held approach can be used,... 

Kim, H., Nienhaus, G., et al. (2002). Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules. Proc. Natl. Acad. Sci. USA 99(7), 4284-4289. 

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