Isomer-Selected Photoelectron Spectroscopy of Isolated DNA Oligonucleotides: Phosphate and Nucleobase Deprotonation at High Negative Charge States (original) (raw)
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Photoelectron spectroscopy of homogeneous nucleic acid base dimer anions
Physical chemistry chemical physics : PCCP, 2010
We report the photoelectron spectra of homogeneous dimer anions of the nucleobases: uracil, thymine, cytosine, adenine, and guanine, i.e., U(2)(-), T(2)(-), C(2)(-), A(2)(-), and G(2)(-) along with DFT calculations on U(2)(-) and T(2)(-). Based on these calculations the photoelectron spectrum of T(2)(-) was assigned as being due to both a proton transferred and a non-proton transferred isomer, while the photoelectron spectrum of U(2)(-) was assigned in terms of a single dominant barrier-free proton transferred isomer. Photoelectron spectra were also measured with a different source and on a different type of photoelectron spectrometer for U(2)(-), T(2)(-), A(2)(-), (1-MeT)(2)(-) and (1,3-Me(2)U)(2)(-).
Electronic Structure of Genomic DNA: A Photoemission and X-ray Absorption Study
The Journal of Physical Chemistry B, 2010
The electronic structure of genomic DNA has been comprehensively characterized by synchrotron-based X-ray absorption and X-ray photoelectron spectroscopy. Both unoccupied and occupied states close to the Fermi level have been unveiled and attributed to particular sites within the DNA structure. A semiconductor-like electronic structure with a band gap of ∼2.6 eV has been found at which the π and π* orbitals of the nucleobase stack make major contributions to the highest occupied and lowest unoccupied molecular orbitals, respectively, in agreement with previous theoretical predictions.
Journal of the American Chemical Society, 2007
DNA multiply charged anions stored in a quadrupole ion trap undergo one-photon electron ejection (oxidation) when subjected to laser irradiation at 260 nm (4.77 eV). Electron photodetachment is likely a fast process, given that photodetachment is able to compete with internal conversion or radiative relaxation to the ground state. The DNA [6-mer] 3ions studied here show a marked sequence dependence of electron photodetachment yield. Remarkably, the photodetachment yield (dG6 > dA6 > dC6 > dT6) is inversely correlated with the base ionization potentials (G < A < C < T). Sequences with guanine runs show increased photodetachment yield as the number of guanine increases, in line with the fact that positive holes are the most stable in guanine runs. This correlation between photodetachment yield and the stability of the base radical may be explained by tunneling of the electron through the repulsive Coulomb barrier. Theoretical calculations on dinucleotide monophosphates show that the HOMO and HOMO-1 orbitals are localized on the bases. The wavelength dependence of electron detachment yield was studied for dG 6 3-. Maximum electron photodetachment is observed in the wavelength range corresponding to base absorption (260-270 nm). This demonstrates the feasibility of gas-phase UV spectroscopy on large DNA anions. The calculations and the wavelength dependence suggest that the electron photodetachment is initiated at the bases and not at the phosphates. This also indicates that, although direct photodetachment could also occur, autodetachment from excited states, presumably corresponding to base excitation, is the dominant process at 260 nm. Excited-state dynamics of large DNA strands still remains largely unexplored, and photo-oxidation studies on trapped DNA multiply charged anions can help in bridging the gap between gas-phase studies on isolated bases or base pairs and solution-phase studies on full DNA strands.
Electronic Spectroscopy of Isolated DNA Polyanions
In solution, UV-vis spectroscopy is often used to investigate structural changes in biomolecules (i.e., nucleic acids), owing to changes in the environment of their chromophores (i.e., the nucleobases). Here we address whether action spectroscopy could achieve the same for gas-phase ions, while taking the advantage of additional mass spectrometry and ion mobility separation of complex mixtures. We therefore systematically studied the action spectroscopy of homo-base 6-mer DNA strands (dG6, dA6, dC6, dT6), and discuss the results in light of gas-phase structures validated by ion mobility spectrometry and infrared ion spectroscopy, and in light of electron binding energies measured by photoelectron spectroscopy, and calculated electronic photo-absorption spectra. When UV photons interact with oligonucleotide polyanions, two main actions may take place: (1) fragmentation and (2) electron detachment. The action spectra reconstructed from fragmentation follow the absorption spectra well,...
Electron spectra of DNA model compounds, adenosine-thymidine and guanosine-cytidine nucleoside base pairs, as well as the relevant homogeneous stacked base pair steps in A-DNA and B-DNA conformations, were investigated using ZINDO semiempir-ical quantum-chemical method. This work confirms that, in DNA with intact Watson– Crick hydrogen bonding and base stacking, the highest occupied molecular orbitals (HOMO) are residing on purine base residues, whereas the lowest unoccupied molecular orbitals (LUMO) — on pyrimidine base residues. In general, the present results are satisfactorily comparable with the available experimental data. The role of charge transfer excitations in the polymer DNA 260 nm spectral band is discussed.
Electron Binding to Nucleic Acid Bases. Experimental and Theoretical Studies. A Review
Collection of Czechoslovak Chemical Communications, 2004
Published as: Svozil D., Jungwirth P., Havlas Z., Electron binding to nucleic acid bases. Experimental and theoretical studies. A review., Collection Of Czechoslovak Chemical Communications 69 (7): Abstract An in-depth knowledge of an excess electron binding mechanism to DNA and RNA nucleobases is important for our understanding of radiation damage influence on the biological functions of nucleic acids, as well as for the possible use of DNA molecules as wires in molecular electronic circuits. The nature of anions created by electron attachment to individual nucleic acid bases is discussed in detail. The principles of the experimental and theoretical approaches to the description of these anions are outlined, and the available results concerning valence-and dipole-bound anions of nucleic acid bases are reviewed. Keywords: DNA; RNA; nucleobase; anion; dipole-bound; valence-bound; ab initio; photoelectron spectroscopy; Rydberg electron transfer; vertical detachment energy; adiabatic electron affinity; vertical electron affinity 1 Biochemists perceive double-helical DNA primarily as a target for molecular recognition. To understand in detail the remarkable variety of reactions involving the double helix in the cell, such as repair of DNA damage or coordination of the transcription of different genes, it becomes important to explore and consider also the rich physical chemistry of DNA. One of the most intriguing and fascinating issues is the charge transfer process in DNA. DNA-mediated charge transfer processes can be categorised either as oxidative hole transfer or as reductive electron transfer. Major efforts have focused on the investigation of oxidative hole transfer, 1-4 resulting in detailed insights on the mechanism. 5,6 On the other hand, the details of the electron transfer are still unclear. The biological implications of charge transfer in DNA are considerable. This is because the most important harmful effect of UV radiation on the living cell is the damage to the DNA component of the chromosome. 7 Radiation triggers 8,9 a release of free electrons and, consequently, single-electron oxidation or reduction initiates a cascade of reactions, the outcomes of which are far-reaching. 10,11 Ionising radiation can be absorbed directly by DNA, leading to the ionization of bases 12,13 (the direct effect), or react indirectly with the surrounding water molecules, 14,15 creating highly reactive radicals (the indirect effect). Radiation damage to DNA can be classified as (a) structural damage leading to a breakage of phosphodiester bonds and subsequent single-strand or double-strand breaks and, (b) change in information caused by the chemical modification of individual DNA bases. 16-18 Both types of damage can be lethal, and both may lead to mutagenic changes causing aging and disease. 7
Israel Journal of Chemistry, 2007
Many of the mutagenic or lethal effects of ionization radiation can be attributed to damage caused to the DNA by low-energy electrons. In order to gain insight on the parameters affecting this process, we measured the low-energy electron (<2 eV) transmission yield through self-assembled monolayers of short DNAoligomers. The electrons that are not transmitted are captured by the layer. Hence, the transmission reflects the capturing efficiency of the electrons by the layer. The dependence of the capturing probability on the base sequence was studied as well as the state of the captured electrons. In addition, two-photon photoelectron (TPPE) spectroscopy studies were performed that established the binding energy of electrons on the DNA.
Chemical Physics, 2008
Using the ab initio Hartree-Fock crystal orbital method in its linear combination of atomic orbital form, the energy band structure of the four homo-DNA-base stacks and those of poly(adenilic acid), polythymidine, and polycytidine were calculated both in the absence and presence of their surrounding water molecules. For these computations Clementi's double ζ basis set was applied. To facilitate the interpretation of the results, the calculations were supplemented by the calculations of the six narrow bands above the conduction band of poly(guanilic acid) with water. Further, the sugar-phosphate chain as well as the water structures around poly(adenilic acid) and polythymidine, respectively, were computed. Three important features have emerged from these calculations. (1) The nonbase-type or water-type bands in the fundamental gap are all close to the corresponding conduction bands. (2) The very broad conduction band (1.70 eV) of the guanine stack is split off to seven narrow bands in the case of poly(guanilic acid) (both without and with water) showing that in the energy range of the originally guanine-stack-type conduction band, states belonging to the sugar, to PO4-, to Na+, and to water mix with the guanine-type states. (3) It is apparent that at the homopolynucleotides with water in three cases the valence bands are very similar (polycytidine, because it has a very narrow valence band, does not fall into this category). We have supplemented these calculations by the computation of correlation effects on the band structures of the base stacks by solving the inverse Dyson equation in its diagonal approximation taken for the self-energy the MP2 many body perturbation theory expression. In all cases the too large fundamental gap decreased by 2-3 eV. In most cases the widths of the valence and conduction bands, respectively, decreased (but not in all cases). This unusual behavior is most probably due to the rather large complexity of the systems. From all this emerges the following picture for the charge transport in DNA: There is a possibility in short segments of the DNA helix of a Bloch-type conduction of holes through the nucleotide base stacks of DNA combined with hopping (and in a lesser degree with tunneling). The motivation of this large scale computation was that recently in Zürich (ETH) they have performed high resolution x-ray diffraction experiments on the structure of the nucleosomes. The 8 nucleohistones in them are wrapped around by a DNA superhelix of 147 base pairs in the DNA B form. The most recent investigations have shown that between the DNA superhelix (mostly from its PO4- groups) there is a charge transfer to the positively charged side chains (first of all arginines and lysines) of the histones at 120 sites of the superhelix. This would cause a hole conduction in DNA and an electronic one in the proteins.
Electronic energy delocalization and dissipation in single- and double-stranded DNA
Proceedings of The National Academy of Sciences, 2007
The mechanism that nature applies to dissipate excess energy from solar UV light absorption in DNA is fundamental, because its efficiency determines the vulnerability of all genetic material to photodamage and subsequent mutations. Using femtosecond time-resolved broadband spectroscopy, we have traced the electronic excitation in both time and space along the base stack in a series of single-stranded and double-stranded DNA oligonucleotides. The obtained results demonstrate not only the presence of delocalized electronic domains (excitons) as a result of UV light absorption, but also reveal the spatial extent of the excitons.