Singlet-Singlet Energy Transfer Along the Helix of a Double-Stranded Nucleic Acid at Room Temperature

Abstract

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.

Sequence Dependence of Energy Transfer in DNA Oligonucleotides

“…Energy migration within a DNA molecule occurs when the excited state energy of DNA transfers from some specific position to another position along the DNA. Data show that singlet and triplet energy transfers occur at both low temperature (77 K) and room temperature (Gueron et al, 1974;Ballini et al, 1976;Vigny and Ballini, 1977;Georghiou et al, 1990;Ge and Georghiou, 1991a,b;Huang and Georghiou, 1992;Nordlund et al, 1993).…”

“…Nucleic acid bases can act as triplet acceptors from ketones (Lamola, 1969). Georghiou et al studied the dependence of fluorescence anisotropy of polynucleotides on wavelength and concluded there is energy transfer between modified and unmodified DNA bases at room temperature (Georghiou et al, 1990;Ge and Georghiou, 1991a,b;Huang and Georghiou, 1992). By observing that the intensity of the normal-base excitation band in the 260 -270-nm region varies with temperature, while the emission band is identical to that of 2-aminopurine (2AP), we have shown that there is singlet-singlet energy transfer from normal DNA bases to 2AP in the d [CTGA[2AP]TTCAG] 2 B-DNA duplex decamer and that transfer efficiency is temperature dependent (Nordlund et al, 1993).…”

“…To be of significance in explaining the large variation in damage rates at identical sites separated by many tens of bases, such transfer must occur over distances of more than a few adjacent bases. Energy transfer, either of singlet or of triplet excitation, has long been suggested as a possible cause of the preferential formation of photoproducts at specific sites in DNA (Setlow and Setlow, 1961;Gueron et al, 1967;Shafranovskaya et al, 1973;Frank-Kamenetskii and Lazurkin, 1974;Ballini et al, 1976;Suhai, 1984;Rubin and Yegupov, 1987;Georghiou et al, 1990). In this model, excitation energy would tend to accumulate at certain bases because of the variation in base-to-neighboring-base energy transfer rates and directions along the DNA helix.…”

Biphotonic Ionization of DNA: From Model Studies to Cell

“…It is noteworthy that these nonradiative phenomena are strongly sequence‐ and structure‐dependent. Indeed, the occurrence of excited state exciton formation and nonradiative energy migration as well as long‐range hole migration with localization at guanine residues was suggested to explain the heterogeneity of excitation/charge distribution within DNA; however, several aspects still remain matters of debate and controversy. The sequence/secondary structure‐dependent heterogeneity of distribution upon laser biphotonic photolysis of DNA was rationalized on the basis of kinetic equations analysis, bringing into play electronic excitation nonradiative energy transfer‐mediated biphotonic excitation and hole migration toward guanines .…”

Free-Radical Yields in Proton Irradiation of Oriented DNA: Relationship to Energy Transfer Along DNA Chains

“…If the pattern of energy deposition events along a DNA chain in the parallel case is as diffuse as these model calculations suggests, then only long-range modes of intramolecular energy or charge transfer could couple the excitations and ionization in the molecule in ways Georghiou (1990) indicates that singlet excitations of bases in calf thymus DNA at room temperature move only I or 2 base pairs before they are irreversible trapped. Clearly, this type of excitation has a low probability of interacting with other energy deposition events in same DNA chain and should have equivalent effects in both irradiation geometries.…”