Biomedical subjects
Boiko Cohen
Publications and source records attributed to Boiko Cohen.
Base stacking controls excited-state dynamics in A.T DNA.
Solar ultraviolet light creates excited electronic states in DNA that can decay to mutagenic photoproducts. This vulnerability is compensated for in all organisms by enzymatic repair of photodamaged DNA. As repair is energetically costly, DNA is intrinsically photostable. Single bases eliminate electronic energy non-radiatively on a subpicosecond timescale, but base stacking and base pairing mediate the decay of excess electronic energy in the double helix in poorly understood ways. In the past, considerable attention has been paid to excited base pairs. Recent reports have suggested that light-triggered motion of a proton in one of the hydrogen bonds of an isolated base pair initiates non-radiative decay to the electronic ground state. Here we show that vertical base stacking, and not base pairing, determines the fate of excited singlet electronic states in single- and double-stranded oligonucleotides composed of adenine (A) and thymine (T) bases. Intrastrand excimer states with lifetimes of 50-150 ps are formed in high yields whenever A is stacked with itself or with T. Excimers limit excitation energy to one strand at a time in the B-form double helix, enabling repair using the undamaged strand as a template.
Singlet excited-state dynamics of 5-fluorocytosine and Cytosine: an experimental and computational study.
The photophysics of singlet excited 5-fluorocytosine (5FC) was studied in steady-state and time-resolved experiments and theoretically by quantum chemical calculations. Femtosecond transient absorption measurements show that replacement of the C5 hydrogen of cytosine by fluorine increases the excited-state lifetime by 2 orders of magnitude from 720 fs to 73 +/- 4 ps. Experimental evidence indicates that emission in both compounds originates from a single tautomeric form. The lifetime of 5FC is the same within experimental uncertainty in the solvents ethanol and dimethyl sulfoxide. The insensitivity of the S(1) lifetime to the protic nature of the solvent suggests that proton transfer is not the principal quenching mechanism for the excited state. Excited-state calculations were carried out for the amino-keto tautomer of 5FC, the dominant species in polar environments, in order to understand its longer excited-state lifetime. CASSCF and CAS-PT2 calculations of the excited states show that the minimum energy path connecting the minimum of the (1)pi,pi state with the conical intersection responsible for internal conversion has essentially the same energetics for cytosine and 5FC, suggesting that both bases decay nonradiatively by the same mechanism. The dramatic difference in lifetimes may be due to subtle changes along the decay coordinate. A possible reason may be differences in the intramolecular vibrational redistribution rate from the Franck-Condon active, in-plane modes to the out-of-plane modes that must be activated to reach the conical intersection region.
Ultrafast excited-state dynamics in nucleic acids.
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Strickler-Berg analysis of excited singlet state dynamics in DNA and RNA nucleosides.
The excited singlet state lifetime of the ribonucleoside uridine was found to be 210+/-30 fs by femtosecond transient absorption spectroscopy. This value is considerably shorter than all previous time-domain measurements. This result and our previous lifetime measurements [see J.-M. L. Pecourt, J. Peon and B. Kohler, J. Am. Chem. Soc., 2001, 123, 10 370] for the other common nucleosides are compared with lifetimes calculated from available photophysical data using the Strickler-Berg (SB) equation. The calculated lifetimes for pyrimidine nucleosides are 10-25% lower than the lifetimes measured in femtosecond transient absorption experiments. For the purine nucleosides, guanosine and adenosine, consideration of just the lowest 1pi --> pi* transition led to predicted lifetimes that are three times greater than experimental ones. On the other hand, inclusion of both of the lowest energy 1pi --> pi* absorption bands in the SB equation resulted in much better agreement with the experimental values. This suggests that both 1pi pi* states of the purine nucleosides contribute to their emission. Decay by the bright 1pi pi* state (or states, in the case of the purines) is believed to be responsible for the experimentally observed lifetimes.
Ultrafast excited-state dynamics of adenine and monomethylated adenines in solution: implications for the nonradiative decay mechanism.
The DNA base adenine and four monomethylated adenines were studied in solution at room temperature by femtosecond pump-probe spectroscopy. Transient absorption at visible probe wavelengths was used to directly observe relaxation of the lowest excited singlet state (S(1) state) populated by a UV pump pulse. In H(2)O, transient absorption signals from adenine decay biexponentially with lifetimes of 0.18 +/- 0.03 ps and 8.8 +/- 1.2 ps. In contrast, signals from monomethylated adenines decay monoexponentially. The S(1) lifetimes of 1-, 3-, and 9-methyladenine are similar to one another and are all below 300 fs, while 7-methyladenine has a significantly longer lifetime (tau = 4.23 +/- 0.13 ps). On this basis, the biexponential signal of adenine is assigned to an equilibrium mixture of the 7H- and 9H-amino tautomers. Excited-state absorption (ESA) by 9-methyladenine is 50% stronger than by 7-methyladenine. Assuming that ESA by the corresponding tautomers of adenine is unchanged, we estimate the population of 7H-adenine in H(2)O at room temperature to be 22 +/- 4% (estimated standard deviation). To understand how the environment affects nonradiative decay, we performed the first solvent-dependent study of nucleobase dynamics on the ultrafast time scale. In acetonitrile, both lowest energy tautomers of adenine are present in roughly similar proportions as in water. The lifetimes of the 9-substituted adenines depend somewhat more sensitively on the solvent than those of the 7-substituted adenines. Transient signals for adenine in H(2)O and D(2)O are identical. These solvent effects strongly suggest that excited-state tautomerization is not an important nonradiative decay pathway. Instead, the data are most consistent with electronic energy relaxation due to state crossings between the optically prepared (1)pipi* state and one or more (1)npi* states and the electronic ground state. The pattern of lifetimes measured for the monomethylated adenines suggests a special role for the (1)npi* state associated with the N7 electron lone pair.
Excited-state proton transfer in chiral environments. 1. Chiral solvents.
Excited-state proton transfer from the "super" photoacid 5,8-dicyano-2-naphthol to 2-butanol is faster in the enantiopure solvent than in its racemic form. The difference observed is discussed in terms of long-range order in homo- and heterodimers of 2-butanol.
Excited state proton transfer in reverse micelles.
The aqueous phase of water/AOT reversed micelles having varying diameters was probed by a single free diffusing proton that was released form a hydrophilic photoacid molecule (2-naphthol-6,8-disulfonate). The fluorescence decay signals were reconstructed through the geminate recombination algorithm, accounting for the reversible nature of the proton-transfer reactions at the surface of the excited molecule and at the water/detergent interface. The radial diffusion of the proton inside the aqueous phase was calculated accounting for both the entropy of dilution and the total electrostatic energy of the ion pair, consisting of the pair-energy and self-energy of the ions. The analysis implied that micellar surface must be modeled with atomic resolution, assuming that the sulfono residue protrudes above the water/hydrocarbon interface by approximately 2 A. The analysis of the fluorescence decay curves implies that the molecule is located in a solvent with physical-chemical properties very similar to bulk water, except for the dielectric constant. For reversed micelles with r(max) > or = 16 A, the dielectric constant of the aqueous phase was approximately 70 and for smaller micelles, where approximately 60% of the water molecule is in contact with the van der Waals surface of the micelle, it is as low as 60. This reduction is a reflection of the increased fraction of water molecule that is in close interaction with the micelle surface.