Container-shaped molecules provide structured environments that impart geometric bounds on the motions and conformations of smaller molecular occupants. Moreover, they provide ''solvation'' that is constrained in time and space. When inwardly directed functional groups are present, they can interact chemically with the occupants. Additionally, the potential for reactivity and catalysis is greatly enhanced. Deep cavitands, derived from resorcinarenes, nearly surround smaller molecules and have been one of the most successful platforms for elaboration with functional groups. Derivatives bearing organic and metal-binding functional groups have been shown to affect recognition properties and selectively accelerate diverse reactions. In this review, we examine recent examples of these systems with an emphasis on how and why ordered nanoenvironments impart changes in the properties and reactivity of their occupants.nanoenvironments ͉ supramolecular M olecular recognition became a popular theme in physical organic chemistry during the late 1980s, and many of those studies evaluated intermolecular forces as models for biochemical phenomena. Synthetic receptors of increasing sophistication such as clefts (1), armatures (2), tweezers (3), bowls (4), and other vehicles (5, 6) were devised for the study of reversible interactions, both in aqueous and nonaqueous media. The emergence of site-directed mutagenesis replaced much of this activity. The strength of a hydrogen bond inside, say, an enzyme can be determined in situ through substitution of an unnatural amino acid (7) with the appropriate functional groups. In addition, enzymes, aptamers, ribozymes, and catalytic antibodies can fold more or less completely around a target molecule. This creates a structured environment for the functional group interactions in question, a feature missing in the various concave structures invented by synthetic chemists. A receptor that completely and reversibly encapsulated sizable molecules was prepared in 1995 (8), but it lacked any appropriately positioned functionality. It took us another 5 years to synthesize a receptor that could, more or less, surround a target molecule and present it with a reactive functional group. This led to changes in reactivity of the sort encountered in the macromolecular complexes of biology. We do not intend here to promote these as model systems. Instead, this review is concerned with effects of physical restraints on a molecule surrounded by another; the physical organic chemistry of structured environments. More specifically, the structures are specially modified cavitands, macrocyclic compounds featuring a cavity that is sealed at one end and functionalized at the other. Cavitands have a long history in studies of molecular recognition, and several reviews are available that cover the literature up to 2002 (9-13). With rare exceptions, these cavitands offer only spaces to be filled by smaller molecules. Our departure was their functionalization with groups that are directed at the molecules held tempo...

We studied the incorporation of the fluorescent cytidine analogues 1, 3-diaza-2-oxo-phenothiazine (tC) and 1, 3-diaza-2-oxo-phenoxazine (tCo) by human DNA polymerase α and Klenow fragment of DNA polymerase I (E. coli). These tricyclic nucleobases possess the regular hydrogen bonding interface of cytosine but are significantly size expanded toward the major groove. Despite the size alteration both DNA polymerases insert dtCTP and dtCoTP with remarkable catalytic efficiency. Polymerization opposite guanine is comparable to the insertion of dCTP, while the insertion opposite adenine is only ∼4-11 times less efficient than the formation of a T-A base pair. Both enzymes readily extend the formed tC(o)-G and tC(o)-A base pairs, and can incorporate at least 4 consecutive nucleotide analogues. Consistent with these results, both DNA polymerases efficiently polymerize dGTP and dATP when tC and tCo are in the template strand. KF inserts dGTP with a 4-to 9-fold higher probability than dATP, while pol α favors dGTP over dATP by a factor of 30-65. Overall, the properties of tC(o) as templating base and as incoming nucleotide are surprisingly symmetrical and may be universal for A and B family DNA polymerases. This finding suggests that the aptitude for ambivalent base pairing is a consequence of the electronic properties of tC(o).

Most fluorescent nucleoside analogues are quenched when base stacked and some maintain their brightness, but there has been little progress toward developing nucleoside analogues that markedly increase their fluorescence upon duplex formation. Here, we report on the design and synthesis of a new tricyclic cytidine analogue, 8-diethylamino-tC (8-DEA-tC), that responds to DNA duplex formation with up to a 20-fold increase in fluorescent quantum yield as compared with the free nucleoside, depending on neighboring bases. This turn-on response to duplex formation is the greatest of any reported nucleoside analogue that can participate in Watson–Crick base pairing. Measurements of the quantum yield of 8-DEA-tC mispaired with adenosine and, separately, opposite an abasic site show that there is almost no fluorescence increase without the formation of correct Watson–Crick hydrogen bonds. Kinetic isotope effects from the use of deuterated buffer show that the duplex protects 8-DEA-tC against quenching by excited state proton transfer. These results, supported by DFT calculations, suggest a rationale for the observed photophysical properties that is dependent on duplex integrity and the electronic structure of the analogue.

We report a host molecule with an inwardly directed methyl ester and its reaction with a series of tertiary amines. The reaction product is a complex of the host carboxylate with a guest quaternary ammonium salt. The rate of the reaction is highly dependent on the suitability of the amine to occupy the host cavity and the intrinsic reactivity of the resulting complex. A kinetic study of the reaction of 2-(dimethylamino)ethanol to produce choline gives the activation parameters DeltaH = 25.1 +/- 0.5 kcal mol-1 and DeltaS = 12 +/- 2 cal mol-1 K-1. The complex, once formed, is poised to reach the transition state; a rate acceleration of greater than 2 x 104 fold is estimated when compared with similar reactions having no supramolecular effects.

Fluorescent RNA is an important analytical tool in medical diagnostics, RNA cytochemistry and RNA aptamer development. We have synthesized the fluorescent ribonucleotide analogue 1,3-diaza-2-oxophenothiazine-ribose-5′-triphosphate (tCTP) and tested it as substrate for T7 RNA polymerase in transcription reactions, a convenient route for generating RNA in vitro. When transcribing a guanine, T7 RNA polymerase incorporates tCTP with 2-fold higher catalytic efficiency than CTP and efficiently polymerizes additional NTPs onto the tC. Remarkably, T7 RNA polymerase does not incorporate tCTP with the same ambivalence opposite guanine and adenine with which DNA polymerases incorporate the analogous dtCTP. While several DNA polymerases discriminated against a d(tC-A) base pair only by factors < 10, T7 RNA polymerase discriminates against tC-A base pair formation by factors of 40 and 300 when operating in the elongation and initiation mode, respectively. These catalytic properties make T7 RNA polymerase an ideal tool for synthesizing large fluorescent RNA, as we demonstrated by generating a ~800 nucleotide RNA, in which every cytosine was replaced with tC.