Browse
Submit Data
Databases
API
Help

Dataset Information

36 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Rapid RNA strand scission following C2'-hydrogen atom abstraction.

ABSTRACT: C2'-Nucleotide radicals have been proposed as key intermediates in direct strand break formation in RNA exposed to ionizing radiation. Uridin-2'-yl radical (1) was independently generated in single- and double-stranded RNA via photolysis of a ketone precursor. Direct stand breaks result from heterolytic cleavage of the adjacent C3'-carbon-oxygen bond. Trapping of 1 by O2 or ?-mercaptoethanol (1 M) does not compete with strand scission, indicating that phosphate elimination is >10(6) s(-1). Uracil loss also does not compete with strand scission. When considered in conjunction with reports that nucleobase radicals produce 1, this chemistry explains why RNA is significantly more susceptible to strand scission by ionizing radiation (hydroxyl radical) than is DNA.

SUBMITTER: Paul R

PROVIDER: S-EPMC4313564 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Rapid RNA strand scission following C2'-hydrogen atom abstraction.

Paul Rakesh R Greenberg Marc M MM

Journal of the American Chemical Society 20150112 2

C2'-Nucleotide radicals have been proposed as key intermediates in direct strand break formation in RNA exposed to ionizing radiation. Uridin-2'-yl radical (1) was independently generated in single- and double-stranded RNA via photolysis of a ketone precursor. Direct stand breaks result from heterolytic cleavage of the adjacent C3'-carbon-oxygen bond. Trapping of 1 by O2 or β-mercaptoethanol (1 M) does not compete with strand scission, indicating that phosphate elimination is >10(6) s(-1). Uraci ...[more]

PMID: 25580810

Similar Datasets

DNA double strand cleavage via interstrand hydrogen atom abstraction.

Project description:Double strand breaks (DSBs) are the most deleterious form of DNA damage. Natural products that produce them are potent cytotoxic agents. Designing molecules that produce DSBs via a single chemical event is challenging. We determined that formation of a C4'-nucleotide radical in duplex DNA under aerobic conditions gives rise to a DSB. The original radical yields a strand break containing a peroxyl radical, which initiates opposite strand cleavage via C4'-hydrogen atom abstraction. This mechanism provides the impetus to design DNA damaging agents that produce DSBs by abstracting a single hydrogen atom from the biopolymer.

| S-EPMC3852885 | biostudies-literature

Mechanistic Studies on RNA Strand Scission from a C2'-Radical.

Project description:The C2'-carbon-hydrogen bond in ribonucleotides is significantly weaker than other carbohydrate carbon-hydrogen bonds in RNA or DNA. Independent generation of the C2'-uridine radical (1) in RNA oligonucleotides via Norrish type I photocleavage of a ketone-substituted nucleotide yields direct strand breaks via cleavage of the ?-phosphate. The reactivity of 1 in different sequences and under a variety of conditions suggests that the rate constant for strand scission is significantly greater than 106 s-1 at pH 7.2. The initially formed C2'-radical (1) is not trapped under a variety of conditions, consistent with computational studies ( Chem.-Eur. J. 2009 , 15 , 2394 ) that suggest that the barrier to strand scission is very low and that synchronous proton transfer from the 2'-hydroxyl to the departing phosphate group facilitates cleavage. The C2'-radical could be a significant contributor to RNA strand scission by the hydroxyl radical, particularly under anaerobic conditions where 1 can be produced from nucleobase radicals.

| S-EPMC5055465 | biostudies-literature

Beyond the classical thermodynamic contributions to hydrogen atom abstraction reactivity.

Project description:Hydrogen atom abstraction (HAA) reactions are cornerstones of chemistry. Various (metallo)enzymes performing the HAA catalysis evolved in nature and inspired the rational development of multiple synthetic catalysts. Still, the factors determining their catalytic efficiency are not fully understood. Herein, we define the simple thermodynamic factor ? by employing two thermodynamic cycles: one for an oxidant (catalyst), along with its reduced, protonated, and hydrogenated form; and one for the substrate, along with its oxidized, deprotonated, and dehydrogenated form. It is demonstrated that ? reflects the propensity of the substrate and catalyst for (a)synchronicity in concerted H+/e- transfers. As such, it significantly contributes to the activation energies of the HAA reactions, in addition to a classical thermodynamic (Bell-Evans-Polanyi) effect. In an attempt to understand the physicochemical interpretation of ?, we discovered an elegant link between ? and reorganization energy ? from Marcus theory. We discovered computationally that for a homologous set of HAA reactions, ? reaches its maximum for the lowest |?|, which then corresponds to the most synchronous HAA mechanism. This immediately implies that among HAA processes with the same reaction free energy, ?G 0, the highest barrier (??G ?) is expected for the most synchronous proton-coupled electron (i.e., hydrogen) transfer. As proof of concept, redox and acidobasic properties of nonheme FeIVO complexes are correlated with activation free energies for HAA from C-H and O-H bonds. We believe that the reported findings may represent a powerful concept in designing new HAA catalysts.

| S-EPMC6217389 | biostudies-literature

Fast Hydrogen Atom Abstraction by a Hydroxo Iron(III) Porphyrazine.

Project description:A reactive hydroxoferric porphyrazine complex, [(PyPz)FeIII(OH) (OH2)]4+ (1, PyPz = tetramethyl-2,3-pyridino porphyrazine), has been prepared via one-electron oxidation of the corresponding ferrous species [(PyPz)FeII(OH2)2]4+ (2). Electrochemical analysis revealed a pH-dependent and remarkably high FeIII-OH/FeII-OH2 reduction potential of 680 mV vs Ag/AgCl at pH 5.2. Nernstian behavior from pH 2 to pH 8 indicates a one-proton, one-electron interconversion throughout that range. The O-H bond dissociation energy of the FeII-OH2 complex was estimated to be 84 kcal mol-1. Accordingly, 1 reacts rapidly with a panel of substrates via C-H hydrogen atom transfer (HAT), reducing 1 to [(PyPz)FeII(OH2)2]4+ (2). The second-order rate constant for the reaction of [(PyPz)FeIII(OH) (OH2)]4+ with xanthene was 2.22 × 103 M-1 s-1, 5-6 orders of magnitude faster than other reported FeIII-OH complexes and faster than many ferryl complexes.

| S-EPMC6036922 | biostudies-literature

Chemical Kinetics of Hydrogen Atom Abstraction from Propargyl Sites by Hydrogen and Hydroxy Radicals.

Project description:Hydrogen atom abstraction from propargyl C-H sites of alkynes plays a critical role in determining the reactivity of alkyne molecules and understanding the formation of soot precursors. This work reports a systematic theoretical study on the reaction mechanisms and rate constants for hydrogen abstraction reactions by hydrogen and hydroxy radicals from a series of alkyne molecules with different structural propargyl C-H atoms. Geometry optimizations and frequency calculations for all species are performed at M06-2X/cc-pVTZ level of theory and the hindered internal rotations are also treated at this level. The high-level W1BD and CCSD(T)/CBS theoretical calculations are used as a benchmark for a series of DFT calculations toward the selection of accurate DFT functionals for large reaction systems in this work. Based on the quantum chemistry calculations, rate constants are computed using the canonical transition state theory with tunneling correction and the treatment of internal rotations. The effects of the structure and reaction site on the energy barriers and rate constants are examined systematically. To the best of our knowledge, this work provides the first systematic study for one of the key initiation abstraction reactions for compounds containing propargyl hydrogen atoms.

| S-EPMC6650822 | biostudies-other

Mechanisms for Hydrogen-Atom Abstraction by Mononuclear Copper(III) Cores: Hydrogen-Atom Transfer or Concerted Proton-Coupled Electron Transfer?

Project description:In a possibly biomimetic fashion, formally copper(III)-oxygen complexes LCu(III)-OH (1) and LCu(III)-OOCm (2) (L2- = N,N'-bis(2,6-diisopropylphenyl)-2,6-pyridinedicarboxamide, Cm = ?,?-dimethylbenzyl) have been shown to activate X-H bonds (X = C, O). Herein, we demonstrate similar X-H bond activation by a formally Cu(III) complex supported by the same dicarboxamido ligand, LCu(III)-O2CAr1 (3, Ar1 = meta-chlorophenyl), and we compare its reactivity to that of 1 and 2. Kinetic measurements revealed a second order reaction with distinct differences in the rates: 1 reacts the fastest in the presence of O-H or C-H based substrates, followed by 3, which is followed by (unreactive) 2. The difference in reactivity is attributed to both a varying oxidizing ability of the studied complexes and to a variation in X-H bond functionalization mechanisms, which in these cases are characterized as either a hydrogen-atom transfer (HAT) or a concerted proton-coupled electron transfer (cPCET). Select theoretical tools have been employed to distinguish these two cases, both of which generally focus on whether the electron (e-) and proton (H+) travel "together" as a true H atom, (HAT), or whether the H+ and e- are transferred in concert, but travel between different donor/acceptor centers (cPCET). In this work, we reveal that both mechanisms are active for X-H bond activation by 1-3, with interesting variations as a function of substrate and copper functionality.

| S-EPMC7197025 | biostudies-literature

Hydrogen atom abstraction from hydrocarbons by a copper(III)-hydroxide complex.

Project description:With the aim of understanding the basis for the high rate of hydrogen atom abstraction (HAT) from dihydroanthracene (DHA) by the complex LCuOH (1; L = N,N'-bis(2,6-diisopropylphenyl)-2,6-pyridinedicarboxamide), the bond dissociation enthalpy of the reaction product LCu(H2O) (2) was determined through measurement of its pK(a) and E(1/2) in THF solution. In so doing, an equilibrium between 2 and LCu(THF) was characterized by UV-vis and EPR spectroscopy and cyclic voltammetry (CV). A high pK(a) of 18.8 ± 1.8 and a low E(1/2) of -0.074 V vs Fc/Fc(+) in THF combined to yield an O-H BDE for 2 of 90 ± 3 kcal mol(-1) that is large relative to values for most transition metal oxo/hydroxo complexes. By taking advantage of the increased stability of 1 observed in 1,2-difluorobenzene (DFB) solvent, the kinetics of the reactions of 1 with a range of substrates with varying BDE values for their C-H bonds were measured. The oxidizing power of 1 was revealed through the accelerated decay of 1 in the presence of the substrates, including THF (BDE = 92 kcal mol(-1)) and cyclohexane (BDE = 99 kcal mol(-1)). CV experiments in THF solvent showed that 1 reacted with THF via rate-determining attack at the THF C-H(D) bonds with a kinetic isotope effect of 10.2. Analysis of the kinetic and thermodynamic data provides new insights into the basis for the high reactivity of 1 and the possible involvement of species like 1 in oxidation catalysis.

| S-EPMC4311965 | biostudies-literature

Visible Light-Mediated Dearomative Hydrogen Atom Abstraction/ Cyclization Cascade of Indoles.

Project description:The photochemical synthesis of yet unknown 2-oxospiro[azetidine-3,3'-indolines] (17 examples, 80-95 % yield), 2,4-dioxospiro[azetidine-3,3'-indolines] (eight examples, 87-97 % yield), and 1-oxo-1,3-dihydrospiro[indene-2,3'-indolines] (17 examples, 85-97 % yield) is described. Starting from readily accessible 3-substituted indoles, a dearomatization of the indole core was accomplished upon irradiation at λ=420 nm in the presence of thioxanthen-9-one (10 mol%) as the sensitizer. Based on mechanistic evidence (triplet energy determination, deuteration experiments, by-product analysis) it is proposed that the reaction proceeds by energy transfer via a 1,4- or 1,5-diradical intermediate. The latter intermediates are formed by excited state hydrogen atom transfer from suitable alkyl groups within the C3 substituent to the indole C2 carbon atom. Subsequent ring closure proceeds with pronounced diastereoselectivity to generate a 4- or 5-membered spirocyclic dearomatized product with several options for further functionalization.

| S-EPMC9314014 | biostudies-literature

A Thioether-Ligated Cupric Superoxide Model with Hydrogen Atom Abstraction Reactivity.

Project description:The central role of cupric superoxide intermediates proposed in hormone and neurotransmitter biosynthesis by noncoupled binuclear copper monooxygenases like dopamine-β-monooxygenase has drawn significant attention to the unusual methionine ligation of the CuM ("CuB") active site characteristic of this class of enzymes. The copper-sulfur interaction has proven critical for turnover, raising still-unresolved questions concerning Nature's selection of an oxidizable Met residue to facilitate C-H oxygenation. We describe herein a model for CuM, [(TMGN3S)CuI]+ ([1]+), and its O2-bound analog [(TMGN3S)CuII(O2•-)]+ ([1·O2]+). The latter is the first reported cupric superoxide with an experimentally proven Cu-S bond which also possesses demonstrated hydrogen atom abstraction (HAA) reactivity. Introduction of O2 to a precooled solution of the cuprous precursor [1]B(C6F5)4 (-135 °C, 2-methyltetrahydrofuran (2-MeTHF)) reversibly forms [1·O2]B(C6F5)4 (UV/vis spectroscopy: λmax 442, 642, 742 nm). Resonance Raman studies (413 nm) using 16O2 [18O2] corroborated the identity of [1·O2]+ by revealing Cu-O (446 [425] cm-1) and O-O (1105 [1042] cm-1) stretches, and extended X-ray absorption fine structure (EXAFS) spectroscopy showed a Cu-S interatomic distance of 2.55 Å. HAA reactivity between [1·O2]+ and TEMPO-H proceeds rapidly (1.28 × 10-1 M-1 s-1, -135 °C, 2-MeTHF) with a primary kinetic isotope effect of kH/kD = 5.4. Comparisons of the O2-binding behavior and redox activity of [1]+ vs [2]+, the latter a close analog of [1]+ but with all N atom ligation (i.e., N3S vs N4), are presented.

| S-EPMC8023764 | biostudies-literature

Direct strand scission from a nucleobase radical in RNA.

Project description:RNA oxidation is important in the etiology of disease and as a tool for studying the structure and folding kinetics of this biopolymer. Nucleobase radicals are the major family of reactive intermediates produced in RNA exposed to diffusible species such as hydroxyl radical. The nucleobase radicals are believed to produce direct strand breaks by abstracting hydrogen atoms from their own and neighboring ribose rings. By independently generating the formal C5 hydrogen atom addition product of uridine in RNA, we provide the first chemical characterization of the pathway for direct strand scission from an RNA nucleobase radical. The process is more efficient under anaerobic conditions. The preference for strand scission in double-stranded RNA over single-stranded RNA suggests that this chemistry may be useful for analyzing the secondary structure of RNA in hydroxyl radical cleavage experiments if they are carried out under anaerobic conditions.

| S-EPMC2845440 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data