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Project Progress

Chemical information encoded in the nucleobases of DNA and RNA leads to sequence-specific base-pairing and complex three-dimensional structure. Is this type of chemical instruction unique to biomolecules, or can it be designed into synthetic systems of appropriate shape, size, and functionality? The two projects summarized here highlight some of our recent efforts to answer this question using self-complementary molecules. In one example, a fluorescence energy transfer strategy is employed to study molecular capsules based on calixarenes. The technique provides mechanistic and behavioral insight regarding the assembly (dimerization) process, and is the basis for the sensitive detection of small molecules in solution. The second example describes further work on a recently introduced assembly of cavitands. This system is currently being optimized for studies in self-replication.
The nucleobases A, C, G, and T encode the instructions for the sequence-specific base-pairing that ultimately results in the double-helical structure of DNA. Are complex structure/assembly relationships predictable and unique to biomolecules, or can they be exploited in synthetic systems of appropriate shape, size, and functionality? As our own systems become more complex, can we study, understand, and even anticipate their behavior or function? These are a few of the questions that fuel our current research efforts. The two projects highlighted here feature suitably-functionalized, self-complementary molecules that form assemblies held together by weak, non-covalent interactions. In the first case, a fluorescence energy transfer strategy is employed to study molecular capsules based on calixarenes. Not only does the technique provide mechanistic and behavioral insight into the assembly (dimerization) process, but it also provides a basis for the sensitive detection of small molecules in solution. The second example describes further work on a recently introduced “ball-in-socket” assembly of cavitands.
The routine spectroscopic techniques often used to characterize synthetic assemblies (e.g., NMR) become inadequate when the systems get large and are composed of multiple species. We have recently devised a fluorescence protocol to investigate the association and dissociation processes of our calixarene capsules (Figure 1a). When assembly occurs between fluorophore-tagged monomers, fluorescence resonance energy transfer (FRET) occurs upon their assembly. The process can be monitored in real time at two wavelengths (Figure 1b), and both the monomers and assembly can be observed directly. From our studies we have learned that molecules of this type behave much differently at nanomolar concentrations than they do at the millimolar concentrations used in NMR analysis. We have recently published these findings.1
(See figure 1.)
Further studies have shown that the technique is useful in the sensitive detection of small molecules. The assembly process of Figure 1a only occurs in the presence of a suitable guest molecule (which is often just the solvent). If the solvent is a poor guest, then assembly does not take place; addition of a better guest nucleates the dimer and a fluorescence signal results. Representative results are shown in Figure 2. When the two fluorophore-tagged monomers are dissolved in p-xylene no assembly occurs, and there is no emission signal at 450 nm. Addition of 3-methylcyclopentanone, an unlabeled analyte, results in energy transfer with added equivalents of the guest (equiv.). Future assemblies could conceivably be targeted toward specific molecules for detection.
(See figure 2.)

Figure 3 shows an assembly that is constructed from cavitands with “ball-in-socket” complementarity. Here the adamantane “guest” of one molecule fits inside the bowl-shaped portion of another identical molecule, and a stable dimer results. Recent work has shown that there is a huge entropic cost to forming the assembly, but the price is paid by favorable guest-host contacts.2 The dimer is unusual in that it is driven to formation by van der Waals contacts and the filling of space. Our current efforts are directed toward self-replicating systems based on this motif. (See Figure 3.)