Flying DNA Cation Radicals in the Gas Phase: Generation and Action Spectroscopy of Canonical and Noncanonical Nucleobase Forms

Tureček, František

doi:10.1021/acs.jpcb.1c03674

Cited by 15 publications

(23 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This was reversed in dGC4 + · where the cytosine π-orbital (MO 145α) was 0.05 eV higher than the guanine π-orbital (MO144α) (Figure S4, Supporting Information). We note that spin-unrestricted M06-2X calculations have been found to provide accurate excitation energies for cation radicals of several canonical and noncanonical nucleobases, ,,,, nucleosides, , and nucleotides, − as determined by comparison with both experimental UV–vis action spectra and benchmarking on equation-of-motion coupled cluster calculations.…”

Section: Resultsmentioning

confidence: 94%

“…Ionization of sugar-based C1′-C5′ nucleoside radicals has been addressed by DFT calculations . In addition, recent experimental and computational studies addressed the dynamics of electronic excitation in nucleobase and nucleotide cation radicals at high levels of theory. − Recently, isomeric forms of nucleobase cation radicals have been discovered as stable gas-phase species and characterized by UV–visible photodissociation action spectroscopy . The noncanonical isomer of the thymine cation radical, [4-hydroxy-5-methylene-( 1,3H )pyrimid-2-one] + · , was formed as a major component, along with the canonical isomer, by electron transfer oxidation of thymine in a copper-terpyridine complex .…”

Section: Introductionmentioning

confidence: 99%

“…33−37 Recently, isomeric forms of nucleobase cation radicals have been discovered as stable gas-phase species and characterized by UV−visible photodissociation action spectroscopy. 38 The noncanonical isomer of the thymine cation radical, [4- terpyridine complex. 39 The noncanonical isomer and its enol tautomers have been found by DFT 40 and ab initio coupled cluster CCSD(T) calculations to be thermodynamically more stable than the canonical thymine isomer.…”

Section: ■ Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Noncanonical Isomers of Nucleoside Cation Radicals: An Ab Initio Study of the Dark Matter of DNA Ionization

Shu

Tureček

2022

J. Phys. Chem. A

Self Cite

View full text Add to dashboard Cite

Cation radicals of DNA nucleosides, 2′-deoxyadenosine, 2′-deoxyguanosine, 2′-deoxycytidine, and 2′-deoxythymidine, can exist in standard canonical forms or as noncanonical isomers in which the charge is introduced by protonation of the nucleobase, whereas the radical predominantly resides in the deoxyribose moiety. Density functional theory as well as correlated ab initio calculations with coupled clusters (CCSD(T)) that were extrapolated to the complete basis set limit showed that noncanonical nucleoside ion isomers were thermodynamically more stable than their canonical forms in both the gas phase and as water-solvated ions. This indicated the possibility of exothermic conversion of canonical to noncanonical forms. The noncanonical isomers were calculated to have very low adiabatic ion–electron recombination energies (REad) for the lowest-energy isomers 2′-deoxy-(N-3H)adenos-1′-yl (4.74 eV), 2′-deoxy-(N-7H)guanos-1′-yl (4.66 eV), 2′-deoxy-(N-3H)cytid-1′-yl (5.12 eV), and 2′-deoxy-5-methylene-(O-2H)uridine (5.24 eV). These were substantially lower than the REad value calculated for the canonical 2′-deoxyadenosine, 2′-deoxy guanosine, 2′-deoxy cytidine, and 2′-deoxy thymidine cation radicals, which were 7.82, 7.46, 8.14, and 8.20 eV, respectively, for the lowest-energy ion conformers of each type. Charge and spin distributions in noncovalent cation-radical dA⊂dT and dG⊂dC nucleoside pairs and dAT, dCT, dTC, and dGC dinucleotides were analyzed to elucidate the electronic structure of the cation radicals. Born–Oppenheimer molecular dynamics trajectory calculations of the dinucleotides and nucleoside pairs indicated rapid exothermic proton transfer from noncanonical T+ · to A in both dAT+ · and dA⊂dT+ ·, leading to charge and radical separation. Noncanonical T+ · in dCT+ · and dTC+ · initiated rapid proton transfer to cytosine, whereas the canonical dCT+ · dinucleotide ion retained the cation radical structure without isomerization. No spontaneous proton transfer was found in dGC+ · and dG⊂dC+ · containing canonical neutral and noncanonical ionized deoxycytidine.

show abstract

Section: Resultsmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Noncanonical Isomers of Nucleoside Cation Radicals: An Ab Initio Study of the Dark Matter of DNA Ionization

Shu

Tureček

2022

J. Phys. Chem. A

Self Cite

View full text Add to dashboard Cite

show abstract

“…Finally, therefore, this Feature Article is not an extensive review of all PD spectroscopy strategies. For extended resources the reader is directed to the following reviews on ion-mobility, 4,39–41 the history of ion spectroscopy, 11,13,42 advances and developments in ion spectroscopy, 43 UV-vis photodissociation action spectroscopy, 44 lasers and mass spectrometry for structure determination, 45 conformer resolved photoinduced dynamics for neutral and ionic peptides, 46 action spectroscopy of DNA radical cations, 47 gas-phase dynamics including isomer selective spectroscopy, 48 biological relevant ions with room temperature 49–51 and cryogenic ion spectroscopy. 52,53…”

Section: Introductionmentioning

confidence: 99%

The combination of laser photodissociation, action spectroscopy, and mass spectrometry to identify and separate isomers

Marlton

Trevitt

2022

Chem. Commun.

View full text Add to dashboard Cite

show abstract

“…Despite extensive research of DNA ionization, structure characterization of highly reactive cation-radical intermediates remains challenging . Recent studies have indicated that DNA-related cation radicals, such as nucleobases, nucleosides, and oligonucleotides, can be generated in the gas phase, isolated by mass, and studied by tandem mass spectrometry in combination with action spectroscopy in the infrared or UV–visible regions . This technique relies on wavelength-dependent photodissociation whereby the photofragment ion production is used to reconstruct the absorption profile of the isolated ion .…”

Section: Introductionmentioning

confidence: 99%

Radical Cascade Dissociation Pathways to Unusual Nucleobase Cation Radicals

Zima

Liu

Tureček

2022

J. Am. Soc. Mass Spectrom.

Self Cite

View full text Add to dashboard Cite

We report unusual dissociations of protonated RNA nucleosides tagged with radical initiator groups at ribose 5′-O and furnished with a 2′,3′-O-isopropylidene protecting group. The ions undergo collision-induced radical cascade dissociations starting at the radical initiator that break down the dioxolane ring and trigger the formation of nucleobase cations and cation radicals. The adenine cation radical that was formed by radical cascade dissociations was identified by MS5 UV–vis photodissociation action spectroscopy to be a higher-energy N-3-H tautomer of the canonical ionized nucleobase. The guanine cation radical was formed by radical cascade dissociations as the N-7-H tautomer. In contrast to adenosine and guanosine, radical cascade dissociations of the tagged ribocytidine ion produced protonated cytosine, whereas tagged ribothymidine showed yet different dissociations resulting in predominant thymine loss. Reaction mechanisms were suggested for the cascade dissociations that were based on Born–Oppenheimer molecular dynamics and density functional theory calculations that were used to map the relevant parts of the potential energy surfaces for adenosine, guanosine, and cytidine radical ions. The reported radical cascade dissociations represent a new, nonredox approach to nucleobase and nucleoside cation radicals that has the potential of being expanded to the generation of various oligonucleotide cation radicals.

show abstract

Flying DNA Cation Radicals in the Gas Phase: Generation and Action Spectroscopy of Canonical and Noncanonical Nucleobase Forms

Cited by 15 publications

References 57 publications

Noncanonical Isomers of Nucleoside Cation Radicals: An Ab Initio Study of the Dark Matter of DNA Ionization

Noncanonical Isomers of Nucleoside Cation Radicals: An Ab Initio Study of the Dark Matter of DNA Ionization

The combination of laser photodissociation, action spectroscopy, and mass spectrometry to identify and separate isomers

Radical Cascade Dissociation Pathways to Unusual Nucleobase Cation Radicals

Contact Info

Product

Resources

About