Yasuo Fujisaki

FLUORESCENCE QUENCHING OF 10-METHYLACRJDINIUM CHLORIDE BY NUCLEOTIDES

Abstract— All nucleotides examined (AMP, GMP, TMP and CMP) quench the fluorescence or 10–methylacridinium chloride (10–MEAC). The fluorescence spectrum of 10–MEAC‐nucleotide system is identical with that of 10–MEAC itself, and the fluorescence decay kinetics follow a single‐exponential decay law. The dependence of fluorescence quantum yields and fluorescence lifetimes upon the concentration of nucleotides indicates that the fluorescence of 10–MEAC is greatly quenched in both dynamic and static processes by nucleotides. The quenching constants increase in the order: AMP ≳ GMP > TMP ≳ CMP. The results of 10–MEAC are compared with those of other acridine dyes (proflavine, 9–aminoacridine and acridine orange).

Flow dichroism, flow polarized fluorescence and viscosity of the DNA acridine complexes.

The strong binding of various acridine dyes to DNA has been studied by the measurements of flow dichroism, flow polarized fluorescence and viscosity. Negative flow dichroism and percentage change in polarized fluorescence intensity show that intercalated dye molecules are oriented rather perpendicularly to the main axis of the DNA helix, like base pairs. On the other hand, viscosity measurements show that the increase of the contour length of DNA depends on the dye structure, being much smaller in the case of dyes with bulky substituents compared to that of the other dyes. This may be attributed to the formation of the outside bound complex. Further, the introduction of bulk substituents to the acridine ring leads to a little smaller values of the reduced dichroism and intensity change of polarized fluorescence. The results may be qualitatively understood if we assume that the outside bound dye lies in the groove of the DNA helix and the plane of the dye tilts from the perpendicular direction relative to the main axis of the helix.

Fluorescence decay studies of the DNA-3,6-diaminoacridine complexes

The interaction of several 3,6-diaminoacridines with DNAs of various base composition has been studied by steady-state and transient fluorescence measurements. The acridine dyes employed are of the following two classes: class I - proflavine, acriflavine and 10-benzyl proflavine; class II - acridine yellow, 10-methyl acridine yellow and benzoflavine. It is found that the fluorescence decay kinetics follows a single-exponential decay law for free dye and the poly[d(A-T)]-dye complex, while that of the dye bound to DNA obeys a two-exponential decay law. The long lifetime (tau 1) for each complex is almost the same as the lifetime for the poly[d(A-T)]-dye complex, and the amplitude alpha 1 decreases with increasing GC content of DNA. The fluorescence quantum yields (phi F) of dye upon binding to DNA decrease with increasing GC content; the phi F values for class I are nearly zero when bound to poly(dG) X poly(dC), but those for class II are not zero. This is in harmony with the finding that GMP almost completely quenches the fluorescence for class I, whereas a weak fluorescence arises from the GMP-dye complex for class II. The fluorescence spectra of the DNA-dye complexes gradually shift toward longer wavelengths with increasing GC content. In this connection, the fluorescence decay parameters show a dependence on the emission wavelength; alpha 1 decreases with an increase in the emission wavelength. In view of these results, it is proposed that the decay behavior of the DNA-dye complexes has its origin in the heterogeneity of the emitting sites; the long lifetime tau 1 results from the dye bound to AT-AT sites, while the short lifetime tau 2 is attributable to the dye bound in the vicinity of GC pairs. Since GC pairs almost completely quench the fluorescence for class I, partly intercalated or externally bound dye molecules may play an important role in the component tau 2.

Interaction of 9-aminoacridine with 7-methylguanosine and 1,N6-ethenoadenosine monophosphate.

Abstract—Fluorescence properties of 9‐aminoacridine in aqueous solutions of 7‐methylguanosine (7MeG) and 1,N6‐ethenoadenosine monophosphate (εAMP) have been examined. It was found that fluorescence of the dye was quenched by 7MeG and εAMP as well as by unmodified nucleotides such as GMP and AMP. Quantitative analysis of the results shows that both dynamic and static quenching processes are responsible for the quenching of fluorescence.

Fluorescence decay studies of modified dinucleoside monophosphates containing 1-N6-ethenoadenosine

Five dinucleoside monophosphates containing 1-N6-ethenoadenosine (epsilon A) have been studied using fluorescence measurements. The fluorescence spectra of these dinucleoside monophosphates are almost the same as the fluorescence spectrum of epsilon AMP. Fluorescence quantum yields of these dimers are greatly reduced compared to that of epsilon AMP. Intramolecular base-base interactions may be responsible for fluorescence quenching. It is found that the fluorescence decay kinetics does not obey a simple decay law but that the decay data can be well described as a sum of three exponentials. This implies that these dimers cannot be characterized as a two-state system, but can be described as systems consisting of three or more conformational states. Sequence effects upon the fluorescence behavior are observed. The fluorescence quenching and decay parameters of Gp epsilon A and Up epsilon A indicate a higher degree of base-base interaction than in their epsilon ApG and epsilon ApU counterparts.

Fluorescence decay studies of poly(riboadenylic acid) containing 1-N6-ethenoadenosine

The fluorescence properties of the 1-N6-etheno derivatives of poly(riboadenylic acid) (poly(rA, epsilon rA)) have been examined. The fluorescence quantum yield of poly(rA, epsilon rA) decreases with an increase in the degree of the epsilon A substitution and is much smaller than that for epsilon AMP even for low degrees of epsilon A substitution. The nearest-neighbor interactions such as epsilon-adenine-adenine and epsilon-adenine-epsilon-adenine may be responsible for this behavior. It is found that the fluorescence decay kinetics obeys a three-exponential decay law for poly(rA, epsilon rA), suggesting that there exist at least three different stacked conformational states.