Molecular ruler

FRET manifests itself through the quenching of donor fluorescence and a reduction of the fluorescence lifetime, accompanied by an increase in acceptor fluorescence emission. The efficiency of the energy-transfer process varies in proportion to the inverse sixth power of the distance separating the donor and acceptor molecules. Consequently, FRET measurements can be utilised as an effective molecular ruler for determining distances between molecules labelled with an appropriate donor and acceptor fluorophore, provided they are within lOnm of each other. 

Wenzel, T., Eckerskorn, C., Lottspeich, F., and Baumeister, W. Existence of a molecular ruler in proteasomes suggested by analysis of degradation products. FEES Lett. 1994, 349, 205-209. 

Johnson, J. L., Cusack, B., Hughes, T. F., McCullough, E. H., Fauq,A., Romanovskis, P., Spatola, A. F. and Rosenberry, T. L. (2003). Inhibitors tethered near the acetylcholinesterase active site serve as molecular rulers of the peripheral and acylation sites. J. Biol. Chem. 278,38948-38955. 

Like Escherichia coli, clinical isolates of H. pylori produce high-molecular-mass (smooth-form) lipopolysaccharide (LPS) composed of an outermost saccharide moiety, divided into the O-polysaccharide or O-specific chain (O-antigen) and core oligosaccharide (OS) regions, covalently linked to lipid A (Fig. 10.1). H. pylori smooth-form LPS possesses O-polysaccharide chains of relatively constant chain length compared with those of enterobacterial LPS (Moran et al., 1992a Moran, 1999). Their length is determined by an enzymatic molecular ruler mechanism... 

Figure 21. Schematic representation of water structure in aqueous nanochannels 50 A in diameter. By anchoring four Trp probes into lipid bilayers, these molecular rulers measure water motions in different local regions in the channel as shown in positions 1—4- of TBE, TME, melittin, and Trp.

Sonnichsen C, Reinhard BM, Liphardt J, Alivisatos AP. A molecular ruler based on plasmon coupling of single gold and silver nanoparticles. Nat Biotechnol 2005 23 741-5. 

Secondly, the geometric closure of nanoscopic space, either by endo-skeletal or exo-skeletal constructions, creates new surfaces and enclosures upon and where in reactions may be examined. Turro, Barton and Tomalia [40] refer to these domains, whether evolving from micelles, dendrimers or DNA, as nano-reactors". Cram has described such contained space in his carcerands as new phases of matter [41], Miller et al. [42] have used related linear nanostructures as molecular rulers which are observable as single molecular species by transmission electron miecroscope. On the other hand, Amit et al. [16] have shown that important biological events, such as the formation of antigen-antibody complexes involve nanoscopic areas of 600-1000 A2 (6-10 nm2). 

Loo TW, Clarke DM (2001) Determining the dimensions of the drug-binding domain of human P-glycoprotein using thiol cross-linking compounds as molecular rulers. Biol Chem 276 36877-36880... 

The molecular ruler methodology for determining the size of the active site of DNA polymerase was also applied to the investigations of other DNA polymerases, such as T7 DNA polymerase and Dpo4 polymerase [60, 61]. 

Lal, S., Grady, N.K., Goodrich, G.P., and Halas, N.J. (2006) Profiling the near field of a plasmonic nanoparticle with Raman-based molecular rulers. Nano Letters, 6, 2338-2343. 

A. Hatzor, P. S. Weiss, Molecular Rulers for Scaling Down Nanostructures, Science, 291 (2001), 1019-1020. 

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