No abstract

The RNA genomes of a number of pathogenic RNA viruses, such as HIV-1, have extensive folded conformations with imperfect A-form duplexes that are essential for virus function and could serve as targets for structure-specific antiviral drugs. As an initial step in the discovery of such drugs, the interactions with RNA of a wide variety of compounds, which are known to bind to DNA in the minor groove, by classical or by threading intercalation, have been evaluated by thermal melting and viscometric analyses. The corresponding sequence RNA and DNA polymers, poly(A).poly(U) and poly(dA).poly(dT), were used as test systems for analysis of RNA binding strength and selectivity. Compounds that bind exclusively in the minor groove in AT sequences of DNA (e.g., netropsin, distamycin, and a zinc porphyrin derivative) do not have significant interactions with RNA. Compounds that bind in the minor grove in AT sequences of DNA but have other favorable interactions in GC sequences of DNA (e.q., Hoechst 33258, DAPI, and other aromatic diamidines) can have very strong RNA interactions. A group of classical intercalators and a group of intercalators with unfused aromatic ring systems contain compounds that intercalate and have strong interactions with RNA. At this time, no clear pattern of molecular structure that favors RNA over DNA interactions for intercalators has emerged. Compounds that bind to DNA by threading intercalation generally bind to RNA by the same mode, but none of the threading intercalators tested to date have shown selective interactions with RNA.

This paper reports both continuous and time-resolved spectroscopic studies of the emission properties of photoexcited pyrene labels covalently attached to uridine nucleosides and oligonucleotides. For all nucleic acid systems, uridine is substituted with pyrene at the 2'-oxygen position, 2'-0-[hexyl-/V-(l-pyrenepropylcarbonyl)amino]uridine, U(12)*. Three types of nucleic acid systems are investigated: the 5'-OH (1) and the S'-ODMT (2) substituted U(12)*-nucleosides; four pentameric oligonucleotides, X2U(12)*X2, where X is 2'-deoxyadenosine (A), 2'-deoxyguanosine (G), 2'-deoxythymidine (T), or 2'-deoxycytidine (C); and four duplexes with 18 base pairs each containing one strand with a central U(12)* label. The central U(12)* label in the duplexes has the following flanking base-sequences, 5'-• • •AX2U( 12)* 2 • • '-3', where X is A, G, T, or C. The 400-nm region emission kinetics for the four U(12)*-labeled pentamers establish the following order of pyrene*-quenching reactivities by flanking DNA bases: A < G < T < C. This ordering of reactivities is generally consistent with expected reactivites based on estimates of the free energies of pyrene* quenching by electron transfer, AG°(ET), to or from flanking DNA bases. Emission spectra and lifetimes in the 495nm region for both U(12)*-labeled pentamers and duplexes provide direct evidence for the formation and decay of the pyrene*+/U(12)'_ charge-transfer (CT) product. In general ca. 20% of the amplitude of the CT emission decays in the 1-7 ns time range and 70-80% of its amplitude decays in <0.2 ns. The C2U(12)*C2 pentamer has uniquely short , * emission decay with its longest emission-lifetime component lasting only 5.6 ns and its average emission lifetime <0.6 ns. (In contrast the longest , * emission components for pyrene butanoic acid (PBA) and U(12)*OH (1) in methanol last, respectively, 231 and 37 ns.) Finally, the longest , * emission lifetimes of U(12)*-labeled DNA duplexes exceed those of the corresponding pentamers.A measure of duplex-induced restricted access of pyrene* to base-paired nucleosides in double-strand (ds) versus single-strand (ss) DNA can be obtained by noting that the average , * emission lifetimes (for greater than 1 ns components) lengthen 3-fold on going from the T2U(12)*T2 pentamer to the corresponding •••AT2U(12)*T2A••• duplex and 9-fold on going from the C2U(12)*C2 pentamer to the •"AC2U(12)*C2A••• duplex.

No abstract

An alternative "signal on" immunosensor for ultrasensitive detection of apurinic/apyrimidinic endonuclease 1 (APE-1) was designed utilizing the self-enhanced electrochemiluminescence (ECL) of a novel Ru(II) complex functionalized coil-like nanocomposite as signal labels. The desirable self-enhanced ECL luminophore was achieved by combining the coreactant of poly(ethylenimine) (PEI) and the luminophor of bis(2,2'-bipyridine)-5-amino-1,10-phenanthroline ruthenium(II) [Ru(bpy)2(5-NH2-1,10-phen)(2+)] to form one novel Ru(II) complex, which exhibited significantly enhanced ECL efficiency and stability. Moreover, the carbon nanotubes (CNTs) were employed as nanocarriers for self-enhanced Ru(II) complex loading via π-π stacking to obtain the coil-like nanocomposite to act as signal probe. Compared with traditional ECL immunoassay, our proposed strategy is simple and sensitive, avoiding the adding of any coreactant into testing solution for signal amplification, and shows a detection limit down to subfemtogram per milliliter level under the optimized experimental condition.