Styrene Oxide Adducts in an Oligodeoxynucleotide Containing the Human N-ras Codon 12 Sequence:  Structural Refinement of the Minor Groove R(12,2)- and S(12,2)-α-(N2-Guanyl) Stereoisomers from 1H NMR

Zegar, Irene S.; Setayesh, Feloora R.; DeCorte, Bart L.; Harris, Constance M.; Harris, Thomas M.; Stone, Michael P.

doi:10.1021/bi952086s

Cited by 23 publications

(33 citation statements)

References 68 publications

(82 reference statements)

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“…Montay-Gruel et al 4 recently reported an interesting observation associated with UHDR FLASH radiation therapy. In measuring H 2 O 2 , they detected lower levels at UHDR than at CDR; they further found that the difference between H 2 O 2 levels at UHDR and CDR was considerably greater at higher doses compared with lower doses (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). This group also reported that doubling the oxygen concentration in the brain (by carbogen breathing during irradiation) reversed the neurocognitive benefits of FLASH radiation therapy.…”

Section: Discussionmentioning

confidence: 94%

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Oxygen depletion in FLASH ultra‐high‐dose‐rate radiotherapy: A molecular dynamics simulation

2020

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Purpose We present a first‐principles molecular dynamics (MD) simulation and expound upon a mechanism of oxygen depletion hypothesis to explain the mitigation of normal tissue injury observed in ultra‐high‐dose‐rate (UHDR) FLASH radiotherapy. Methods We simulated damage to a segment of DNA (also representing other biomolecules such as RNA and proteins) in a simulation box filled with H2O and O2 molecules. Attoseconds physical interactions (ionizations, electronic, and vibrational excitations) were simulated by using the Monte Carlo track structure code Geant4‐DNA. Immediately after ionization, ab initio Car–Parrinello molecular dynamics (CPMD) simulation was used to identify which H2O and O2 molecules surrounding the DNA molecule were converted into reactive oxygen species (ROS). Subsequently, the femto‐ to nanosecond reactions of ROS were simulated by using MD with reactive force field (ReaxFF), to illustrate ROS merging into new types of non‐reactive oxygen species (NROS) due to strong coupling among ROS. A coarse‐grained model was constructed to describe the relevant collective phenomenon at the macroscopic level on ROS aggregation and formation of NROS agglomerates consistent with the underlying microscopic pathways obtained from MD simulations. Results Time‐dependent molecular simulations revealed the formation of metastable and transient spaghetti‐like complexes among ROS generated at UHDR. At the higher ROS densities produced under UHDR, stranded chains (i.e., NROS) are produced, mediated through attractive electric polarity forces, hydrogen bonds, and magnetic dipole–dipole interactions among hydroxyl (.OH) radicals. NROS tend to be less mobile than cellular biomolecules as opposed to the isolated and sparsely dense ROS generated at conventional dose rates (CDR). We attribute this effect to the suppression of biomolecular damage induced per particle track. At a given oxygen level, as the dose rate increases, the size and number of NROS chains increase, and correspondingly the population of toxic ROS components decreases. Similarly, at a given high dose rate, as the oxygen level increases, so do the size and number of NROS chains until an optimum level of oxygen is reached. Beyond that level, the amount of oxygen present may be sufficient to saturate the production of NROS chains, thereby reversing the sparing effects of UHDRs. Conclusions We showed that oxygen depletion, hypothesized to lead to lower normal‐tissue toxicity at FLASH dose rates, takes place within femto‐ to nanoseconds after irradiation. The mechanism is governed by the slow dynamics of chains of ROS complexes (NROS). Under physoxic (≈ 4–5% oxygen) conditions (i.e., in normal tissues), NROS are more abundant than in hypoxic conditions (e.g., <0.3% in parts of tumors), suggesting that biomolecular damage would be reduced in an environment with physoxic oxygen levels. Hence irradiation at UHDRs would be more effective for sparing physoxic normal tissues but not tumors containing regions of hypoxia. At much higher levels of oxygen (e.g., >10–1...

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Section: Discussionmentioning

confidence: 94%

“…The structure of DNA, extracted from a protein database (pdb) 20 and used for our molecular simulations, is shown in Fig. 1(a); the same DNA structure surrounded by water and oxygen molecules is shown in Fig.…”

Section: Methodsmentioning

confidence: 99%

Oxygen depletion in FLASH ultra‐high‐dose‐rate radiotherapy: A molecular dynamics simulation

2020

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“…The NMR solution structures have been previously solved for both of the 11-mer SO-containing oligonucleotides in these reactions (3). The relative orientations of the R and S SO enantiomers on the template DNA were shown to be 3Ј and 5Ј, respectively (3).…”

Section: Discussionmentioning

confidence: 99%

“…To further test whether DNA adducts can give insight into the structure and functioning of HIV-1 RT, we have carried out a study in which monocyclic, minor groove adducts known to cause no significant perturbation to the local DNA structure (3) were used to probe DNA-protein contacts. This study was designed to accomplish the following: 1) determine the effects that these minor groove DNA lesions might have on HIV-1 RT replication, 2) monitor the movement of DNA at a distance from the catalytic site as it traverses through the polymerase, and 3) identify key amino acid residues important for adduct bypass when the adducts are positioned in the template-primer duplex.…”

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confidence: 99%

Probing Structure/Function Relationships of HIV-1 Reverse Transcriptase with Styrene Oxide N2-Guanine Adducts

Forgács

Latham

Beard

et al. 1997

Journal of Biological Chemistry

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Details of the interactions between the human immunodeficiency virus (HIV-1) reverse transcriptase and substrate DNA were probed both by introducing sitespecific and stereospecific modifications into DNA and by altering the structure of potential critical residues in the polymerase. Unadducted 11-mer DNAs and 11-mer DNAs containing R and S enantiomers of styrene oxide at N 2 -guanine were ligated with two additional oligonucleotides to create 63-mers that served as templates for HIV-1 reverse transcriptase replication. Oligonucleotides that primed synthesis 5 bases 3 to the adducts could be extended up to 1 base 3 and opposite the lesion. However, when the positions of the 3-OH of the priming oligonucleotides were placed 1, 2, 3, 4, 5, and 6 bases downstream of the styrene oxide guanine adducts, replication was initiated, only to be blocked after incorporating 4, 5, 6, and 7 bases beyond the lesion. The sites of this adduct-induced termination corresponded to the position of the DNA where ␣-helix H makes contact with the DNA minor groove, 3-5 bases upstream of the growing 3 end. In addition, mutants of the polymerase in ␣-helix H (W266A and G262A) alter the termination probabilities caused by these DNA adducts, suggesting that ␣-helix H is a sensitive monitor of modifications in the minor groove of newly synthesized template-primer DNA several bases distal to the 3-OH.During the last 10 years, the use of site-specifically and stereospecifically modified oligonucleotides has played a major role not only in defining which DNA adducts are mutagenic but also in instructing us how different DNA polymerases interact at those sites. We have expanded these studies to use DNA lesions as a probe of polymerase structure and function. The decision to use HIV-1 1 RT as the polymerase of choice is warranted not only because the cocrystal structure is known for an intact enzyme/DNA complex (1) but also because of the tremendous biological significance of RT. Previously using this strategy, we demonstrated that the major groove DNA adducts, N 6 -adenine SO lesions, were readily bypassed by wild type RT, only to experience termination/pause sites 3-5 bases beyond the site of the lesion (2). These sites of enhanced termination probabilities corresponded to the adduct being positioned in the template-primer duplex near the thumb subdomain of the polymerase, where the DNA is in close contact with an ␣-helix and is making the transition from A to B form DNA. Our results could be rationalized because in this bend, the minor groove is widened with a compensatory narrowing of the major groove. The presence of an adduct in the major groove at this position was hypothesized to be the likely source of the enhanced termination through alteration of the minor groove ␣-helix H contacts, 3-5 bases upstream of the 3Ј-OH.To further test whether DNA adducts can give insight into the structure and functioning of HIV-1 RT, we have carried out a study in which monocyclic, minor groove adducts known to cause no significant perturbation to the local ...

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“…The structure of DNA, extracted from a protein database (pdb) [20] and used for our molecular simulations, is shown in Figure 1a; the same DNA structure surrounded by water and oxygen molecules is shown in Figure 1b. We filled the DNA environment with water and oxygen molecules corresponding to a water density equal to 1 g/cm 3 by using the computational tools available in the Groningen Machine for Chemical Simulations molecular-dynamics package (GROMACS), which is another MD package to simulate proteins, lipids, and nucleic acids [21].…”

Section: Methodsmentioning

confidence: 99%

Oxygen depletion in FLASH ultra-high-dose-rate radiotherapy: A molecular dynamics simulation

Abolfath,

Grosshans,

Mohan

2020

Preprint

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Purpose: We present a first-principles molecular dynamics (MD) simulation and expound upon a mechanism of oxygen depletion hypothesis to explain the mitigation of normal tissue injury observed in ultra-high-dose-rate (UHDR) FLASH radiotherapy.Methods: We simulated damage to a segment of DNA (also representing other bio-molecules such as RNA and proteins) in a simulation box filled with H2O and O2 molecules. Attoseconds physical interactions (ionizations, electronic and vibrational excitations) were simulated by using the Monte Carlo track structure code Geant4-DNA. Immediately after ionization, ab initio Car-Parrinello molecular dynamics (CPMD) simulation was used to identify which H2O and O2 molecules surrounding the DNA-molecule were converted into reactive oxygen species (ROS). Subsequently, the femto-to nano-second reactions of ROS were simulated by using MD with Reactive Force Field (ReaxFF), to illustrate ROS merging into new types of non-reactive oxygen species (NROS) due to strong coupling among ROS. A coarse-grained model was constructed to describe the relevant collective phenomenon at the macroscopic level on ROS aggregation and formation of NROS agglomerates consistent with the underlying microscopic pathways obtained from MD simulations.Results: Time-dependent molecular simulations revealed the formation of metastable and transient spaghetti-like complexes among ROS generated at UHDR. At the higher ROS densities produced under UHDR, stranded chains (i.e., NROS) are produced, mediated through attractive electric polarity forces, hydrogen bonds, and magnetic dipole-dipole interactions among hydroxyl ( • OH) radicals. NROS tend to be less mobile than cellular biomolecules as opposed to the isolated and sparsely dense ROS generated at conventional dose rates (CDR). We attribute this effect to the suppression of bio-molecular damage induced per particle track. At a given oxygen level, as the dose rate increases, the size and number of NROS chains increase, and correspondingly the population of toxic ROS components decreases. Similarly, at a given high dose rate, as the oxygen level increases, so do the size and number of NROS chains until an optimum level of oxygen is reached. Beyond that level, the amount of oxygen present may be sufficient to saturate the production of NROS chains, thereby reversing the sparing effects of UHDRs.Conclusions: We showed that oxygen depletion, hypothesized to lead to lower normal-tissue toxicity at FLASH dose rates, takes place within femto-to nano-seconds after irradiation. The mechanism is governed by the slow dynamics of chains of ROS complexes (NROS). Under physoxic (≈ 4-5% oxygen) conditions (i.e., in normal tissues), NROS are more abundant than in hypoxic conditions (e.g., < 0.3% in parts of tumors), suggesting that bio-molecular damage would be reduced in an environment with physoxic oxygen levels. Hence irradiation at UHDRs would be more effective for sparing physoxic normal tissues but not tumors containing regions of hypoxia. At much higher levels of oxygen (e.g.,...

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Styrene Oxide Adducts in an Oligodeoxynucleotide Containing the Human N-ras Codon 12 Sequence: Structural Refinement of the Minor Groove R(12,2)- and S(12,2)-α-(N²-Guanyl) Stereoisomers from ¹H NMR

Cited by 23 publications

References 68 publications

Oxygen depletion in FLASH ultra‐high‐dose‐rate radiotherapy: A molecular dynamics simulation

Oxygen depletion in FLASH ultra‐high‐dose‐rate radiotherapy: A molecular dynamics simulation

Probing Structure/Function Relationships of HIV-1 Reverse Transcriptase with Styrene Oxide N2-Guanine Adducts

Oxygen depletion in FLASH ultra-high-dose-rate radiotherapy: A molecular dynamics simulation

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