Fluorometric analysis of the long-wavelength absorption band of N-7 methylated GMP into the constituent bands of the two electronic states

Excited State Dynamics of Methylated Guanosine Derivatives Revealed by Femtosecond Time-resolved Spectroscopy

Methylated DNA/RNA nucleobases are important epigenetic marks in living species and play an important role for targeted therapies. Moreover, they could bring significant changes to the photo-stability of nucleic acid, leading these sites become mutational hotspots for disease such as skin cancer. While a number of studies have demonstrated the relationship between excited state dynamics and the biological function of methylated cytosine in DNA, investigations aimed at unraveling the excited state dynamics of methylated guanosine in RNA have been largely overlooked. In this work, influence of methylation on the excited state dynamics of guanosine is studied by using femtosecond time-resolved spectroscopy. Our results suggest that the effect of methyl substitution on the photophysical properties of guanosine is position sensitive. N1-methylguanosine shows very similar excited state dynamics as that in guanosine, while almost one order of magnitude longer lifetime of the La state is observed in N2, N2-dimethylguanosine. Notably, N7-methylation can lead to a new minimum on the La state, which shows a two orders of magnitude longer excited state lifetime compared with guanosine. These findings not only help understanding excited state dynamics of methylated guanosines, but also lay the foundation for further studying DNA/RNA strands incorporated with these bases.

Solvation of nucleosides in aqueous mixtures of organic solvents: relevance to DNA open basepairs

Toward the goal of understanding how open basepairs in DNA interact with their heterogeneous environment, we have studied the steady-state intrinsic fluorescence properties of the purine and pyrimidine deoxynucleosides in organic solvents in the presence of small amounts of water. The organic solvents used in the present study were: n-butanol, acetonitrile, methanol, n-propanol, isopropanol, and isobutanol. For n-butanol and acetonitrile, which have a high degree of amphiphilicity and weak hydrogen bonding ability, respectively, the fluorescence spectral properties of the purines are found to depend on the sequence of steps in which the aqueous mixtures were formed. By contrast, no such dependence was observed in the mixtures with any of the other solvents used in the present study. Moreover, no such dependence was observed for the pyrimidines. These findings suggest that the final solvation network around the purines is dependent on the nature of the environment to which they were initially exposed. This would tend to present an impediment to the closing of AT or GC basepairs in DNA that become open as a result of structural fluctuations, DNA bending, or protein-DNA interactions.

Fluorescence of matrix isolated guanine and 7-methylguanine

We have prepared argon and nitrogen matrices containing guanine and 7-methylguanine, and measured their absorption, fluorescence excitation and fluorescence emission spectra. The fluorescence excitation spectrum of guanine shows four well-resolved bands in the range from 170 to 290 nm; excitation at the wavelengths of each of these bands results in a fluorescence emission with maximum intensity near 350 nm and a single-exponential decay with a lifetime of about 10 ns. There are significant differences between the fluorescent excitation and emission spectra of guanine and of 7-methylguanine, suggesting that the fluorescence observed from the guanine sample does not arise from a minority tautomer.

Room-temperature steady-state fluorescence properties of poly(dG-dC).poly(dG-dC)

We report the steady-state fluorescence properties of the alternating polynucleotide poly(dG-dC).poly(dG-dC) in low-salt solution at room temperature for excitation at the Hg lines 265, 280 and 297 nm. Its fluorescence spectrum peaks at about 325 nm and, within the experimental error, its shape does not change significantly with the excitation wavelength. The fluorescence anisotropy is found to decrease strongly for short-wavelength excitation, a behavior which is very similar to that exhibited by free guanine. In view of the fact that the anisotropy for free cytosine is virtually constant at the aforementioned three excitation wavelengths, the results suggest that in this polynucleotide the emission stems from guanine. The values of the fluorescence quantum yield for the three excitation wavelengths are found to be very low, 0.8 x 10(-5), 0.8 x 10(-5), and 2.8 x 10(-5), respectively; these are compatible with transfer of energy from the lower-energy electronic state of guanine, before vibronic relaxation is established, to cytosine. Upon denaturation, the fluorescence spectrum becomes very broad and the fluorescence quantum yield increases; these observations support the authenticity of the emission from the nondenatured polynucleotide.

Room-temperature fluorescence properties of the polynucleotide polydA.polydT

The room-temperature fluorescence spectrum of the non-alternating polynucleotide polydA.polydT is found to have its maximum at about 325 nm and, when exciting in the spectral region where both adenine (A) and thymine (T) absorb, to coincide with that obtained for excitation at 293 nm where thymine is selectively excited. The fluorescence anisotropy is found to be equal to 0.18 and independent of the excitation and emission wavelengths. These observations are consistent with: (i) emission stemming from T; and (ii) transfer of electronic energy from A to T being not efficient. These inferences are also supported by the observed dependence of the fluorescence quantum yield on the excitation wavelength.

Excited-state properties of the alternating polynucleotide poly(dA-dT).poly(dA-dT)

Measurements of the steady-state fluorescence spectrum and anisotropy, r, of the alternating polynucleotide poly(dA-dT).poly(dA-dT) were carried out in order to characterize its photophysical properties at room temperature. The shape of the fluorescence spectrum depends on the excitation wavelength, namely, the relative fluorescence intensity of the short-wavelength peak decreases for excitation at short wavelengths. When monitoring the emission at short wavelengths, r is 0.18 and independent of the excitation wavelength. When monitoring the emission at long wavelengths, however, r is very low, about 0.03. These results suggest that: (i) the short-wavelength emission stems from thymine; and (ii) the long-wavelength emission stems from an excited-state complex (excimer), with the same one being formed regardless of whether thymine or adenine is excited. The corresponding fluorescence spectra have been resolved. The occurrence of transfer of electronic energy is discussed.

Singlet-singlet energy transfer along the helix of a double-stranded nucleic acid at room temperature

An irreversible electronic energy trap has been formed in calf thymus DNA by methylating about 75% of its G bases at position N-7. This has allowed us to measure for the first time the efficiency of transfer of energy along the helix of a double-stranded nucleic acid at room temperature. It is found that about one out of every three photons absorbed by the other bases is trapped. We have also simulated the data with a stochastic model that uses the dipole-dipole interaction to calculate the efficiency of transfer. In order to approximate the experimental results, the model requires that: (i) the fluorescence quantum yield of T, C, and G in DNA be about 2 x 10(-3), which is about two orders of magnitude larger than the value of the fluorescence quantum yield reported for DNA; and (ii) the fluorescence quantum yield of A in DNA be negligibly small. Requirement (i) is consistent with energy transfer taking place before a very efficient fluorescence quenching process sets in, which could be formation of excited-state complexes (excimers) that do not fluoresce appreciably. Requirement (ii) implies a very short fluorescence lifetime for A, which is consistent with the reported absence of a significant number of photoproducts formed by A in DNA. The simulations find that, on the average, the excitation energy takes about 1.2 steps to reach the trap; that is to say, bases that are nearest and next nearest neighbors of the trap are, in effect, the only energy donors. Both intra- as well as interstrand energy transfer (the latter only for the C-trap base pair) make significant contributions. The value of the efficiency for pairwise base-base intrastrand transfer is about 60%, whereas those for base-trap intra- and interstand transfer are 90% and 80%, respectively. The corresponding values for the rate constant of transfer are 2 x 10(11), 1 x 10(12), and 4 x 10(11) s-1. Transfer is inefficient when A is the donor or the acceptor. In addition to the dipole-dipole term, the only other significant term in the expansion of the interaction potential is the dipole-quadrupole term which, however, makes only a small contribution to the overall transfer efficiency. The electron exchange interaction appears to be much less efficient than the coulombic interaction.