Charge Loss in Gas-Phase Multiply Negatively Charged Oligonucleotides

Abstract

In an attempt to shed light on the mechanism by which gaseous samples of negatively charged oligonucleotides undergo extremely slow (i.e., over 1-1000 s) charge loss, we have carried out molecular dynamics simulations on an oligonucleotide anion, T 5 3-, containing five thymine, deoxyribose, and phosphate units in which the first, third, and fifth phosphates are negatively charged. The study is aimed at determining the rate at which an electron is detached from such a trianion by way of an internal Coulomb repulsion induced event. In this process, the intrinsic 5.0-5.1 eV electron binding strength of each phosphate site is reduced by the repulsive Coulomb potentials of the other two negative sites. As geometrical fluctuations cause the distances among the three negative phosphate sites to change, this causes the Coulomb repulsion energies at these sites to fluctuate. Once the Coulomb potential at any phosphate site exceeds ca. 5 eV, the electron on that site is able to undergo autodetachment. Although such an electron must tunnel through a barrier to escape, it is shown that the tunneling rate is not the rate-limiting step in electron loss; instead, it is the rate at which geometrical fluctuations cause the Coulomb potentials to exceed 5 eV that determines the rate of electron loss. Because these rates are extremely slow, special techniques had to be introduced to allow results of dynamics simulations on more flexible models of T 5 3-to be extrapolated to predict the behavior of the actual T 5 3-.

More Than Charged Base Loss — Revisiting the Fragmentation of Highly Charged Oligonucleotides

“…The "terminal effect" has so far not been reported in literature, but the distinct conditions upon which such dissociation pathway is observed suggest that electronic and steric factors are involved. A possible explanation is based on a study of Anusiewicz et al, who performed molecular dynamics simulations on a DNA 5-mer (T 5 3-) with zero and three negative charges on the backbone to investigate the effect of increased Coulombic repulsion on the gas-phase structure [40]. It was shown that a 3-fold negatively charged pentamer is likely to adopt an elongated, stretched configuration, whereas the same ON with a neutral backbone is arranged in a rather compact structure.…”

Base-Dependent Electron Photodetachment from Negatively Charged DNA Strands upon 260-nm Laser Irradiation

“…Thermal electron detachment time constants were in the order of 1-1000 s for dB7 (3- 2-) for various base sequences between 100 and 150 °C. Anusiewicz and co-authors 75 proposed that this electron autodetachment from the ground state could be due to geometrical fluctuations of the oligonucleotide causing fluctuations in the Coulomb potential at a phosphate site of sufficient magnitude (estimated as 5 eV, which is the electron binding energy of H2PO4 -) so that the electron can tunnel through the Coulomb barrier, the rate-limiting step being the rate at which geometrical fluctuations bring the oligonucleotide in a favorable conformation for electron autodetachment. The computed electron autodetachment rate of dT5 3was 0.02-0.5 s -1 at T = 170 °C.…”

Electron Photodetachment from Gas Phase Peptide Dianions. Relation with Optical Absorption Properties

“…Proteins and DNAs can be easily transferred to the gas phase with a high charge state by electrospray , and can be used as prototypes to study detachment mechanisms in highly charged anions and also the influence of the molecular flexibility on detachment. , Gas phase MCAs of DNA have driven many interests , in relation with their redox properties and with photoinduced damages in solution. Recently, we performed energy-resolved spectroscopy experiments on gas phase MCAs of DNAs. , We observed electron detachment and showed that this detachment was strongly base dependent.…”