Fluorescence of covalently attached pyrene as a general RNA folding probe.

Fluorescence techniques are commonly and powerfully applied to monitor biomolecular folding. In a limited fashion, the fluorescence emission intensity of covalently attached pyrene has been used as a reporter of RNA conformational changes. Here, we pursue two goals: we examine the relationship between tether identity and fluorescence response, and we determine the general utility of pyrene fluorescence to monitor RNA folding. The P4-P6 domain of the Tetrahymena group I intron RNA was systematically modified at multiple nucleotide positions with pyrene derivatives that provide a range of tether lengths and compositions between the RNA and chromophore. Certain tethers typically lead to a superior fluorescence signal upon RNA folding, as demonstrated by equilibrium titrations with Mg2+. In addition, useful fluorescence responses were obtained with pyrene placed at several nucleotide positions dispersed throughout P4-P6. This suggests that monitoring of tertiary folding by fluorescence of covalently attached pyrene will be generally applicable to structured RNA molecules.

General deoxyribozyme-catalyzed synthesis of native 3'-5' RNA linkages.

An elusive goal for nucleic acid enzymology has been deoxyribozymes that ligate RNA rapidly, sequence-generally, with formation of native 3'-5' linkages, and in preparatively useful yield. Using in vitro selection, we have identified Mg2+- and Zn2+-dependent deoxyribozymes that simultaneously fulfill all four of these criteria. The new deoxyribozymes operate under practical incubation conditions and have modest RNA substrate sequence requirements, specifically D downward arrowRA for 9DB1 and A downward arrowR for 7DE5 (D = A, G, or U; R = A or G). These requirements are comparable to those of deoxyribozymes such as 10-23 and 8-17, which are already widely used as biochemical tools for RNA cleavage. We anticipate that the 9DB1 and 7DE5 deoxyribozymes will find immediate practical application for RNA ligation.

Site-specific fluorescent labeling of large RNAs with pyrene.

Pyrene is a useful chromophore for monitoring the tertiary structure and folding of large RNAs. This unit describes the general preparation of a large RNA (>80 nucleotides in length) that has been site-specifically modified with pyrene at the 2'-position of an individual internal nucleotide. A protocol is provided for derivatizing a 2'-amino-RNA oligonucleotide with a suitably activated pyrene reagent. This pyrene-labeled oligonucleotide is then assembled with other RNA(s) either by covalent ligation or by noncovalent hybridization to form a full-length structured RNA, which may then be studied by equilibrium and stopped-flow fluorescence spectroscopy.

Characterization of an anti-tuberculosis resin glycoside from the prairie medicinal plant Ipomoea leptophylla.

The organic soluble extract from the leaves of the native North American prairie plant Ipomoea leptophylla (big root morning glory) showed in vitro activity against M. tuberculosis. Bioassay-guided fractionation of this extract resulted in the identification of two new resin glycosides (6, 7). Base-catalyzed hydrolysis of these glycosides gave operculinic acid (1) as the glycosidic acid component as well as trans-cinnamic acid, propanoic acid, and lauric acid. The complete structure elucidation was accomplished through derivatization, 1D and 2D NMR spectroscopy (TOCSY, ROESY, HSQC, HMBC), and MS/MS experiments on 6 and 7 as well as the permethylated derivative 8.