Immobilized molecules, single molecule studies

A very elegant demonstration of the functional detail that can be obtained from single molecule studies of immobilized molecules was given by Ha et al. [10]. Their system of interest involves a helicase—a protein which binds to double-stranded DNA and unwinds the helical structure. Helicases are protein motors that are driven by the binding and hydrolysis of ATP. Some helicases function as hexameric rings but the fundamental form of other helicases is a subject of debate, which is addressed in this paper. Previously, bulk studies had been able to... 

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... 

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. 

To achieve single-molecule fluorescence detection, there are three common experimental practices. First, experiments are done at low concentrations (10 9-l() 12 mol I ) to spatially separate molecules, so each of them can be studied without interference from surrounding molecules. Second, fluorescence signal detection is confined to a small volume (<10-151) to minimize background noises for single-molecule sensitivity. Third, biomolecules are often immobilized, so a single molecule can be studied over time. 

The host cavity of a resorcin[4]arene bearing two anthracene moieties at the wider rim can be switched by the known photodimerization of the two anthracene substituents resulting in a closed cavity. The process can be reversed by heating of the solution. Whereas the cavity of the open state is well suited to bind ammonium ions such as 2-mer-captoethylamine hydrochloride, the closed form does not bind ammonium ions. The affinity modulation has also been studied by single-molecule force spectroscopy (Figure 12.7). For this purpose, the host has been modified with four didecylsulfide linkers in order to immobilize the host on gold surfaces. ... 

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