Microenvironmental control of photochemical reactions: II. Fluorescence quenching of naphthalene and 1,3-di-(α-naphthyl)propane by RNA and bases in aqueous methanol

The fluorescence quenching of naphthalene ( 2 ) and 1,3-di(α-naphythyl)propane ( 1 ) by RNA and bases in methanol-water (v:v = 1:1) binary solvents in the presence or absence of cyclodextrin (CD) has been investigated. The results show that both the monomer and excimer fluorescence of 1 can be quenched by these quenchers. The quenching and rates depend on the quencher and temperature. It is shown that there is a critical temperature (Tc) for each quencher. Below Tc, the excimer fluorescence spectra show vibrational structures and the Stern-Volmer plots are straight lines (for uracil and cytosine); while above the Tc, the vibrational structures disappear and the Stern-Volmer plots deviate from linearity and curve upward. The former is a static process; while the latter is a mixture of both static and dynamic processes. The addition of α-CD has no effect on the fine structure; whereas β-CD prevents the appearance of this structure efficiently. The quenching rates both for the monomer and excimer of 1 by bases except cytosine in the presence of β-CD at ambient temperature are not changed; the quenching of fluorescence of 1 by RNA in the presence of β-CD, however, is hindered. Time-resolved fluorescence study shows that the excimer fine structures appear from the zero time. The intensity of fine structures depend on the fraction of water (π) in binary solvents, and it is independent of the pH value of the solvents. It is suggested that bases and RNA induced aggregates (perhaps microcrystal) are formed, in which the motion of molecules 1 is limited.