Molecular beacon DNA probes, containing 1−4 pyrene monomers on the 5‘ end and the quencher DABCYL on the 3‘ end, were engineered and employed for real-time probing of DNA sequences. In the absence of a target sequence, the multiple-pyrene labeled molecular beacons (MBs) assumed a stem-closed conformation resulting in quenching of the pyrene excimer fluorescence. In the presence of target, the beacons switched to a stem-open conformation, which separated the pyrene label from the quencher molecule and generated an excimer emission signal proportional to the target concentration. Steady-state fluorescence assays resulted in a subnanomolar limit of detection in buffer, whereas time-resolved signaling enabled low-nanomolar target detection in cell-growth media. It was found that the excimer emission intensity could be scaled by increasing the number of pyrene monomers conjugated to the 5‘ terminal. Each additional pyrene monomer resulted in substantial increases in the excimer emission intensities, quantum yields, and excited-state lifetimes of the hybridized MBs. The long fluorescence lifetime (∼40 ns), large Stokes shift (130 nm), and tunable intensity of the excimer make this multiple-pyrene moiety a useful alternative to traditional fluorophore labeling in nucleic acid probes.

RNase H is a ribonuclease that degrades the RNA strand in a RNA-DNA hybrid to produce 3'-hydroxyl-and 5'-phosphateterminated products. It is a nonspecific endonuclease that catalyzes the cleavage of RNA through an endonucleolytic mechanism, [1] aided by an enzyme-bound divalent metal ion; however, DNA strands or unhybridized RNA strands are not degraded. The enzyme is involved in several important cellular processes including DNA replication, DNA repair, and transcription. [2] Members of the RNase H family can be found in nearly all organisms, from archaea and prokaryota to eukaryota. RNase H also has wide applications in molecular biology and biotechnology in terms of its unique cleaving property. Retroviral RNase H, a part of viral reverse transcriptase, is an important pharmaceutical target, as it is absolutely necessary for the proliferation of retroviruses, such as HIV. Inhibitors of this enzyme could therefore provide new drugs against diseases like AIDS. E. coli RNase H usually requires at least six base pairs of RNA-DNA hybrids as substrates to bind and cleave effectively in solution, while the hybrid length required in living cells might be somewhat greater.[3] The complete digestion of poly(rA):poly(dT) by E. coli RNase H yields oligoribonucleotides with varying chain lengths, ranging from monomers to hexamers.[4] In order to understand more about these functions and processes, and more importantly, to screen new drugs against retroviruses, it is necessary to develop a fast, real-time, sensitive, and isotope-label-free system to assay the cleavage activity of RNase H. A number of traditional methods have been used to assay the enzyme activities and evaluate the kinetic parameters, such as the acid-soluble release of RNA fragment, [5] gel electrophoresis, [4] and HPLC.[6] The acid-soluble and gel-electrophoresis techniques require radioisotope-labeled substrates, and the HPLC method needs micromolar concentrations of substrate. All of these methods are indirect, discontinuous, and time-consuming. Recently, an RNA-DNA duplex was incorporated into a fluorescent probe to study RNase H in real time; however, only very short substrate sequences could be analyzed. Moreover, the complexity in the RNA-DNA oligonucleotide synthesis can also result in a low yield and restrict its general utility in enzyme-activity studies. [7] Here we describe a real-time fluorescence method in which the signal transduction is achieved by taking advantage of the light-switching excimer mechanism inherent to molecular beacons (MBs). A molecular beacon is a single-stranded DNA that can form an intramolecular hairpin structure with a fluorophore and quencher at either end.[8] DNA MB assays have been described for a few enzyme studies, such as single-stranded specific DNases, endonuclease BamHI, and small nonenzyme DNA cleavage agents.[9-11] Enzyme activity was detected and characterized by taking advantage of the signal-transduction mechanism built into the MBs. The change in fluorescence signal reflects the conformational change of...

In the search for a selective adenosine A1 receptor antagonist with greater aqueous solubility than the compounds currently in clinical trials as diuretics, a series of 1,4-substituted 8-cyclohexyl and 8-bicyclo[2.2.2]octylxanthines were investigated. The binding affinities of a variety of cyclohexyl and bicyclo[2.2.2]octylxanthines for the rat and human adenosine A1, A2A, A2B, and A3 receptors are presented. Bicyclo[2.2.2]octylxanthine 16 exhibited good pharmaceutical properties and in vivo activity in a rat diuresis model (ED50=0.3 mg/kg po). Optimization of the bridgehead substituent led to propionic acid 29 (BG9928), which retained high potency (hA1, Ki=7 nM) and selectivity for the adenosine A1 receptor (915-fold versus adenosine A2A receptor; 12-fold versus adenosine A2B receptor) with improved oral efficacy in the rat diuresis model (ED50=0.01 mg/kg) as well as high oral bioavailability in rat, dog, and cynomolgus monkey.