Boronated Condensed DNA as a Heterochromatic Radiation Target Model.

The compound 4-dihydroxyboryl-l-phenylalanine (BPA) has found use in clinical trials of boron neutron capture therapy (BNCT). Here, we have examined the interaction with DNA of an amide-blocked BPA derivative of hexa-l-arginine (Ac-BPA-Arg6-NH2). Physical and spectroscopic assays show that this peptide binds to and condenses DNA. The resulting condensates are highly resistant to the effects of nuclease incubation (68-fold) and gamma (38-fold) irradiation. Radioprotection was modeled by Monte Carlo track structure simulations of DNA single strand breaks (SSBs) with TOPAS-nBio. The differences between experimental and simulated SSB yields for uncondensed and condensed DNAs were ca. 2 and 18%, respectively. These observations indicate that the combination of a plasmid DNA target, the BPA-containing peptide, and track structure simulation provides a powerful approach to characterize DNA damage by the high-LET radiation associated with neutron capture on boron.

DNA Condensation with a Boron-Containing Cationic Peptide for Modeling Boron Neutron Capture Therapy.

The amino acid derivative 4-borono-L-phenylalanine (BPA) has been used in the radiation medicine technique boron neutron capture therapy (BNCT). Here we have characterized its interaction with DNA when incorporated into a positively charged hexa-L-arginine peptide. This ligand binds strongly to DNA and induces its condensation, an effect which is attenuated at higher ionic strengths. The use of an additional tetra-L-arginine ligand enables the preparation of a DNA condensate in the presence of a negligible concentration of unbound boron. Under these conditions, Monte Carlo simulation indicates that >85% of energy deposition events resulting from thermal neutron irradiation derive from boron fission. The combination of experimental model systems and simulations that we describe here provides a valuable tool for accurate track structure modeling of the DNA damage produced by the high LET particles involved in BNCT.

Yields of damage to C4' deoxyribose and to pyrimidines in pUC18 by the direct effect of ionizing radiation.

Our mechanistic understanding of damage formation in DNA by the direct effect relies heavily on what is known of free radical intermediates studied by EPR spectroscopy. Bridging this information to stable product formation requires methods with comparable sensitivities, a criterion met by the (32)P-post-labeling assay developed by Weinfeld and Soderlind, [Weinfeld,M. and Soderlind,K.-J.M. (1991) (32)P-Postlabeling detection of radiation-induced DNA damage: identification and estimation of thymine glycols and phosphoglycolate termini. Biochemistry, 30, 1091-1097] which when applied to the indirect effect, detected phosphoglycolate (pg) and thymine glycol (Tg). Here we applied this assay to the direct effect, measuring product yields in pUC18 films with hydration levels (Γ) of 2.5, 16 or 23 waters per nucleotide and X-irradiated at either 4 K or room temperature (RT). The yields of pg [G(pg)] for Γ ≈ 2.5 were 2.8 ± 0.2 nmol/J (RT) and 0.2 ± 0.3 nmol/J (4 K), which is evidence that the C4' radical contributes little to the total deoxyribose damage via the direct effect. The yield of detectable base damage [G(B*)] at Γ ≈ 2.5 was found to be 30.2 ± 1.0 nmol/J (RT) and 12.9 ± 0.7 nmol/J (4 K). While the base damage called B*, could be due to either oxidation or reduction, we argue that two reduction products, 5,6-dihydrouracil and 5,6-dihydrothymine, are the most likely candidates.

Mechanistic investigation of seeded growth in triblock copolymer stabilized gold nanoparticles.

We report the seeded synthesis of gold nanoparticles (GNPs) via the reduction of HAuCl4 by (L31 and F68) triblock copolymer (TBP) mixtures. In the present study, we focused on [TBP]/[Au(III)] ratios of 1-5 (≈1 mM HAuCl4) and seed sizes ~20 nm. Under these conditions, the GNP growth rate is dominated by both the TBP and seed concentrations. With seeding, the final GNP size distributions are bimodal. Increasing the seed concentration (up to ~0.1 nM) decreases the mean particle sizes 10-fold, from ~1000 to 100 nm. The particles in the bimodal distribution are formed by the competitive direct growth in solution and the aggregative growth on the seeds. By monitoring kinetics of GNP growth, we propose that (1) the surface of the GNP seeds embedded in the TBP cavities form catalytic centers for GNP growth and (2) large GNPs are formed by the aggregation of GNP seeds in an autocatalytic growth process.

The value of Clinical signs in the diagnosis of Degenerative Cervical Myelopathy - A Systematic review and Meta-analysis.

STUDY DESIGN: Delayed diagnosis of degenerative cervical myelopathy (DCM) is likely due to a combination of its subtle symptoms, incomplete neurological assessments by clinicians and a lack of public and professional awareness. Diagnostic criteria for DCM will likely facilitate earlier referral for definitive management. OBJECTIVES: This systematic review aims to determine (i) the diagnostic accuracy of various clinical signs and (ii) the association between clinical signs and disease severity in DCM? METHODS: A search was performed to identify studies on adult patients that evaluated the diagnostic accuracy of a clinical sign used for diagnosing DCM. Studies were also included if they assessed the association between the presence of a clinical sign and disease severity. The QUADAS-2 tool was used to evaluate the risk of bias of individual studies. RESULTS: This review identified eleven studies that used a control group to evaluate the diagnostic accuracy of various signs. An additional 61 articles reported on the frequency of clinical signs in a cohort of DCM patients. The most sensitive clinical tests for diagnosing DCM were the Tromner and hyperreflexia, whereas the most specific tests were the Babinski, Tromner, clonus and inverted supinator sign. Five studies evaluated the association between the presence of various clinical signs and disease severity. There was no definite association between Hoffmann sign, Babinski sign or hyperreflexia and disease severity. CONCLUSION: The presence of clinical signs suggesting spinal cord compression should encourage health care professionals to pursue further investigation, such as neuroimaging to either confirm or refute a diagnosis of DCM.

The Frequency of Symptoms in Patients With a Diagnosis of Degenerative Cervical Myelopathy: Results of a Scoping Review.

STUDY DESIGN: Delayed diagnosis of degenerative cervical myelopathy (DCM) is associated with reduced quality of life and greater disability. Developing diagnostic criteria for DCM has been identified as a top research priority. OBJECTIVES: This scoping review aims to address the following questions: What is the diagnostic accuracy and frequency of clinical symptoms in patients with DCM? METHODS: A scoping review was conducted using a database of all primary DCM studies published between 2005 and 2020. Studies were included if they (i) assessed the diagnostic accuracy of a symptom using an appropriate control group or (ii) reported the frequency of a symptom in a cohort of DCM patients. RESULTS: This review identified three studies that discussed the diagnostic accuracy of various symptoms and included a control group. An additional 58 reported on the frequency of symptoms in a cohort of patients with DCM. The most frequent and sensitive symptoms in DCM include unspecified paresthesias (86%), hand numbness (82%) and hand paresthesias (79%). Neck and/or shoulder pain was present in 51% of patients with DCM, whereas a minority had back (19%) or lower extremity pain (10%). Bladder dysfunction was uncommon (38%) although more frequent than bowel (23%) and sexual impairment (4%). Gait impairment is also commonly seen in patients with DCM (72%). CONCLUSION: Patients with DCM present with many different symptoms, most commonly sensorimotor impairment of the upper extremities, pain, bladder dysfunction and gait disturbance. If patients present with a combination of these symptoms, further neuroimaging is indicated to confirm the diagnosis of DCM.

Radioprotective effects produced by the condensation of plasmid DNA with avidin and biotinylated gold nanoparticles.

The treatment of aqueous solutions of plasmid DNA with the protein avidin results in significant changes in physical, chemical, and biochemical properties. These effects include increased light scattering, formation of micron-sized particles containing both DNA and protein, and plasmid protection against thermal denaturation, radical attack, and nuclease digestion. All of these changes are consistent with condensation of the plasmid by avidin. Avidin can be displaced from the plasmid at higher ionic strengths. Avidin is not displaced from the plasmid by an excess of a tetra-arginine ligand, nor by the presence of biotin. Therefore, this system offers the opportunity to reversibly bind biotin-labeled species to a condensed DNA-protein complex. An example application is the use of biotinylated gold nanoparticles. This system offers the ability to examine in better detail the chemical mechanisms involved in important radiobiological effects. Examples include protein modulation of radiation damage to DNA, and radiosensitization by gold nanoparticles.

Damage clusters after gamma irradiation of a nanoparticulate plasmid DNA peptide condensate.

We have gamma-irradiated plasmid DNA in aqueous solution in the presence of submillimolar concentrations of the ligand tetra-arginine. Depending upon the ionic strength, under these conditions, the plasmid can adopt a highly compacted and aggregated form which attenuates by some two orders of magnitude the yield of damage produced by the indirect effect. The yields of DNA single- and double-strand breaks (SSB and DSB) which result are closely comparable with those produced in living cells. The radical lifetimes, diffusion distances, and track structure are expected to be similarly well reproduced. After irradiation, the aggregation was reversed by adjusting the ionic conditions. The approximate spatial distribution of the resulting DNA damage was then assayed by comparing the increases in the SSB and DSB yields produced by a subsequent incubation with limiting concentrations of the eukaryotic base excision repair enzymes formamidopyrimidine-DNA N-glycosylase (the FPG protein) and endonuclease III. Smaller increases in DSB yields were observed in the plasmid target that was irradiated in the condensed form. By modeling the spatial distribution of DNA damage, this result can be interpreted in terms of a greater extent of damage clustering.

DNA Binding Hydroxyl Radical Probes.

The hydroxyl radical is the primary mediator of DNA damage by the indirect effect of ionizing radiation. It is a powerful oxidizing agent produced by the radiolysis of water and is responsible for a significant fraction of the DNA damage associated with ionizing radiation. There is therefore an interest in the development of sensitive assays for its detection. The hydroxylation of aromatic groups to produce fluorescent products has been used for this purpose. We have examined four different chromophores which produce fluorescent products when hydroxylated. Of these, the coumarin system suffers from the fewest disadvantages. We have therefore examined its behavior when linked to a cationic peptide ligand designed to bind strongly to DNA.

MoveStrong at home: a feasibility study of a model for remote delivery of functional strength and balance training combined with nutrition education for older pre-frail and frail adults.

Exercise and nutrition interventions are often recommended for frailty; however, effective strategies are required for real-world implementation. Our primary aim was to assess the feasibility and acceptability of telephone and virtual delivery of MoveStrong, an 8-week exercise and nutrition program with a 4-week follow-up for older pre-frail and frail adults. A priori criteria for success included: recruitment (≥25/12 weeks), retention at follow-up (≥80%), and adherence to exercise and nutrition sessions (≥70%). We recruited community-dwelling Ontario residents; ≥60 years, ≥1 chronic condition, ≥1 FRAIL scale score. Participants received mailed materials, a personalized exercise program, 11 remote one-on-one training sessions with an exercise physiologist and 3 online dietitian-led nutrition education sessions. We completed exploratory analyses of secondary outcomes including physical function and dietary protein intake. Semi-structured interviews supported program evaluation. In total, 30 participants were enrolled. 28 (93%) participants completed program and follow-up assessments. Adherence to exercise and nutrition sessions (CI) was 84% (77%-91%) and 82% (70%-93%) respectively. At program end and follow-up [mean change (CI)], significant improvements were measured in 30-second chair stand test [3.50 (1.12-5.86), 4.54 (1.94-7.13) chair stands] and dietary protein intake [12.9 (5.7-20.0), 9.2 (0.4-18.1) g]. Overall, participants were satisfied with program delivery. Trial registration number: NCT04663685.

Encouraging older adults with pre-frailty and frailty to "MoveStrong": an analysis of secondary outcomes for a pilot randomized controlled trial. / Encourager les personnes âgées souffrant de préfragilité et de fragilité à participer au programme d'exercice et de nutrition « MoveStrong ¼ : analyse des résultats secondaires d'un essai pilote comparatif randomisé.

BACKGROUND: This 8-week pilot stepped-wedge randomized controlled trial evaluated the MoveStrong program for teaching adults who have frailty/pre-frailty about balance and functional strength training and sufficient protein intake to prevent falls and improve mobility. METHODS: We recruited individuals aged 60 years and over, with a FRAIL scale score of 1 or higher and at least one chronic condition, who were not currently strength training. The program included 16 exercise physiologist-led hour-long group sessions and two dietitian-led hour-long nutrition sessions. We analyzed secondary outcomes-weight, gait speed, grip strength, physical capacity (fatigue levels), sit-to-stand functioning, dynamic balance, health-related quality of life (HRQoL), physical activity levels and protein intake-using a paired t test and a generalized estimating equation (GEE). RESULTS: Of 44 participants (mean [SD] age 79 [9.82] years), 35 were pre-frail and 9 were frail. At follow-up, participants had significantly improved grip strength (1.63 kg, 95% CI: 0.62 to 2.63); sit-to-stand functioning (2 sit-to-stands, 95% CI: 1 to 3); and dynamic balance (1.68 s, 95% CI: 0.47 to 2.89). There were no significant improvements in gait speed, HRQoL index scores, self-rated health, physical activity levels (aerobic activity and strength training) or protein intake. GEE analysis revealed an interaction between exposure to MoveStrong and gait speed, sit-to-stand functioning, dynamic balance and HRQoL index scores. The total cost to administer the program and purchase equipment was CAD 14 700, equivalent to CAD 377 per participant. CONCLUSION: Exploratory analyses suggest MoveStrong exercises may improve gait speed, sit-to-stand functioning, dynamic balance and HRQoL index scores in older individuals who are frail and pre-frail.

Establishing the Socio-Economic Impact of Degenerative Cervical Myelopathy Is Fundamental to Improving Outcomes [AO Spine RECODE-DCM Research Priority Number 8].

STUDY DESIGN: Literature Review (Narrative). OBJECTIVE: To contextualize AO Spine RECODE-DCM research priority number 5: What is the socio-economic impact of DCM? (The financial impact of living with DCM to the individual, their supporters, and society as a whole). METHODS: In this review, we introduce the methodology of health-economic investigation, including potential techniques and approaches. We summarize the current health-economic evidence within DCM, so far focused on surgical treatment. We also cover the first national estimate, in partnership with Myelopathy.org from the United Kingdom, of the cost of DCM to society. We then demonstrate the significance of this question to advancing care and outcomes in the field. RESULTS: DCM is a common and often disabling condition, with a significant lack of recognition. While evidence demonstrates the cost-effectives of surgery, even among higher income countries, health inequalities exist. Further the prevalent residual disability in myelopathy, despite treatment affects both the individual and society as a whole. A report from the United Kingdom provides the first cost-estimate to their society; an annual cost of ∼£681.6 million per year, but this is likely a significant underestimate. CONCLUSION: A clear quantification of the impact of DCM is needed to raise the profile of a common and disabling condition. Current evidence suggests this is likely to be globally substantial.

Improving Awareness Could Transform Outcomes in Degenerative Cervical Myelopathy [AO Spine RECODE-DCM Research Priority Number 1].

STUDY DESIGN: Literature Review (Narrative). OBJECTIVE: To introduce the number one research priority for Degenerative Cervical Myelopathy (DCM): Raising Awareness. METHODS: Raising awareness has been recognized by AO Spine RECODE-DCM as the number one research priority. This article reviews the evidence that awareness is low, the potential drivers, and why this must be addressed. Case studies of success from other diseases are also reviewed, drawing potential parallels and opportunities for DCM. RESULTS: DCM may affect as many as 1 in 50 adults, yet few will receive a diagnosis and those that do will wait many years for it. This leads to poorer outcomes from surgery and greater disability. DCM is rarely featured in healthcare professional training programs and has received relatively little research funding (<2% of Amyotrophic Lateral Sclerosis or Multiple Sclerosis over the last 25 years). The transformation of stroke and acute coronary syndrome services, from a position of best supportive care with occasional surgery over 50 years ago, to avoidable disability today, represents transferable examples of success and potential opportunities for DCM. Central to this is raising awareness. CONCLUSION: Despite the devastating burden on the patient, recognition across research, clinical practice, and healthcare policy are limited. DCM represents a significant unmet need that must become an international public health priority.

Characterization of a lipophilic plasmid DNA condensate formed with a cationic peptide fatty acid conjugate.

In the presence of cationic ligands, DNA molecules can become aggregated into larger particles in a process known as condensation. DNA condensates are of interest as models for the dense packing found in naturally occurring structures such as phage heads and chromatin. They have found extensive application in DNA transfection and also provide convenient models with which to study DNA damage by the direct effect of ionizing radiation. Further, conjugates of cationic peptides with fatty acids may represent a class of attractive ligands for these areas because of their simple synthesis. When plasmid pUC18 is used as the DNA target and N-caproyl-penta-arginine amide (Cap-R(5)-NH(2)) is used as the ligand, the physical properties of the resulting mixtures were characterized using static and dynamic light scattering, sedimentation, dye exclusion, circular dichroism, nanoparticle tracking, and atomic force microscopy. Their chemical properties were assayed using solvent extraction and protection against hydroxyl radical attack and nuclease digestion. Titration of the plasmid with the Cap-R(5)-NH(2) ligand produced sharply defined changes in both chemical and physical properties, which was associated with the formation of condensed DNA particles in the 100-2000 nm size range. The caproyl group at the ligand's N-terminus produced a large increase in the partitioning of the resulting condensate from water into chloroform and in its binding to the neutral detergent Pluronic F-127. Both the physical and chemical data were all consistent with condensation of the plasmid by the ligand where the presence in the ligand of the caproyl group conferred an extensive lipophilic character upon the condensate.

The MoveStrong program for promoting balance and functional strength training and adequate protein intake in pre-frail older adults: A pilot randomized controlled trial.

BACKGROUND: Balance and functional strength training can improve muscle strength and physical functioning outcomes and decrease the risk of falls in older adults. To maximize the benefits of strength training, adequate protein intake is also important. However, the number of older individuals that consume enough protein or routinely engage in strength training remains low at less than 5% and even lower for activities that challenge balance. Our primary aim was to assess the feasibility of implementing a model (MoveStrong) of service delivery to teach older adults about balance and functional strength training and methods to increase protein intake. METHODS: This study was a closed cohort stepped wedge randomized controlled trial. We recruited individuals ≥60 years considered pre-frail or frail with at least one chronic condition who were not currently engaging in regular strength training from Northern (rural) and Southern (urban) Ontario sites in Canada. The primary outcome was feasibility of implementation, defined by recruitment, retention, and adherence, and safety (defined by monitoring adverse events). We also reported participants' and providers' experience with MoveStrong, adaptations to the model based on participant's and provider's experience, and program fidelity. RESULTS: We recruited 44 participants to the study and the average adherence rate was 72% with a retention of 71%. The program had a high-fidelity score. One person experienced a fall-related injury during exercise, while two other participants reported pain during certain activities. Five individuals experienced injuries or health problems that were not related to the program. Suggestions for future trials include modifying some exercises, exploring volunteer assistance, increasing the diversity of participants enrolled, and considering a different study design. CONCLUSIONS: Our pilot trial demonstrates the feasibility of recruitment and adherence for a larger multisite RCT of balance and functional strength training with attention to protein intake in pre-frail and frail older adults.

Fall prevention interventions for older community-dwelling adults: systematic reviews on benefits, harms, and patient values and preferences.

BACKGROUND: An estimated 20-30% of community-dwelling Canadian adults aged 65 years or older experience one or more falls each year. Fall-related injuries are a leading cause of hospitalization and can lead to functional independence. Many fall prevention interventions, often based on modifiable risk factors, have been studied. Apart from the magnitude of the benefits and harms from different interventions, the preferences of older adults for different interventions as well as the relative importance they place on the different potential outcomes may influence recommendations by guideline panels. These reviews on benefits and harms of interventions, and on patient values and preferences, will inform the Canadian Task Force on Preventive Health Care to develop recommendations on fall prevention for primary care providers. METHODS: To review the benefits and harms of fall prevention interventions, we will update a previous systematic review of randomized controlled trials with adaptations to modify the classification of interventions and narrow the scope to community-dwelling older adults and primary-care relevant interventions. Four databases (MEDLINE, Embase, Cochrane Central Register of Controlled Trials, Ageline), reference lists, trial registries, and relevant websites will be searched, using limits for randomized trials and date (2016 onwards). We will classify interventions according to the Prevention of Falls Network Europe (ProFANE) Group's taxonomy. Outcomes include fallers, falls, injurious falls, fractures, hip fractures, institutionalization, health-related quality of life, functional status, and intervention-related adverse effects. For studies not included in the previous review, screening, study selection, data extraction on outcomes, and risk of bias assessments will be independently undertaken by two reviewers with consensus used for final decisions. Where quantitative analysis is suitable, network or pairwise meta-analysis will be conducted using a frequentist approach in Stata. Assessment of the transitivity and coherence of the network meta-analyses will be undertaken. For the reviews on patient preferences and outcome valuation (relative importance of outcomes), we will perform de novo reviews with searches in three databases (MEDLINE, PsycInfo, and CINAHL) and reference lists for cross-sectional, longitudinal quantitative, or qualitative studies published from 2000. Selection, data extraction, and risk of bias assessments suitable for each study design will be performed in duplicate. The analysis will be guided by a narrative synthesis approach, which may include meta-analysis for health-state utilities. We will use the CINeMa approach to a rate the certainty of the evidence for outcomes on intervention effects analyzed using network meta-analysis and the GRADE approach for all other outcomes. DISCUSSION: We will describe the flow of literature and characteristics of all studies and present results of all analyses and summary of finding tables. We will compare our findings to others and discuss the limitations of the reviews and the available literature. SYSTEMATIC REVIEW REGISTRATION: This protocol has not been registered.

Reduction of electron deficient guanine radical species in plasmid DNA by tyrosine derivatives.

Guanine bases are the most easily oxidized sites in DNA and therefore electron deficient guanine radical species are major intermediates in the direct effect of ionizing radiation (ionization of the DNA itself) on DNA as a consequence of hole migration to guanine. As a model for this process we have used gamma-irradiation in the presence of thiocyanate ions to generate single electron oxidized guanine radicals in a plasmid target in aqueous solution. The stable species formed from these radicals can be detected and quantified by the formation of strand breaks in the plasmid after a post-irradiation incubation using a suitable enzyme. If a tyrosine derivative is also present during irradiation, the production of guanine oxidation products is decreased by electron transfer from tyrosine to the intermediate guanyl radical species. By using cationic tyrosine containing ligands we are able to observe this process when the tyrosine is electrostatically bound to the plasmid. The driving force dependence of this reaction was determined by comparing the reactivity of tyrosine with its 3-nitro analog. The results imply that the electron transfer reaction is coupled to a proton transfer. The experimental conditions used in this model system provide a reasonable approximation to those involved in the radioprotection of DNA by tightly bound proteins in chromatin.

Structure reactivity relationship in the reaction of DNA guanyl radicals with hydroxybenzoates.

In DNA, guanine bases are the sites from which electrons are most easily removed. As a result of hole migration to this stable location on guanine, guanyl radicals are major intermediates in DNA damage produced by the direct effect of ionizing radiation (ionization of the DNA itself and not through the intermediacy of water radicals). We have modeled this process by employing gamma irradiation in the presence of thiocyanate ions, a method which also produces single electron oxidized guanyl radicals in plasmid DNA in aqueous solution. The stable products formed in DNA from these radicals are detected as strand breaks after incubation with the FPG protein. When a phenolic compound is present in solution during gamma irradiation, the formation of guanyl radical species is decreased by electron donation from the phenol to the guanyl radical. We have quantified the rate of this reaction for four different phenolic compounds bearing carboxylate substituents as proton acceptors. A comparison of the rates of these reactions with the redox strengths of the phenolic compounds reveals that salicylate reacts ca. 10-fold faster than its structural analogs. This observation is consistent with a reaction mechanism involving a proton coupled electron transfer, because intra-molecular transfer of a proton from the phenolic hydroxyl group to the carboxylate group is possible only in salicylate, and is favored by the strong 6-membered ring intra-molecular hydrogen bond in this compound.

Multiplicity of DNA single-strand breaks produced in pUC18 exposed to the direct effects of ionizing radiation.

The transition of plasmid DNA from a supercoiled to an open circle conformation, as detected by gel electrophoresis, affords an extraordinarily sensitive method for detecting single-strand breaks (SSBs), one measure of deoxyribose damage. To determine the yield of SSBs, G(ssb), by this method, it is commonly assumed that Poisson statistics apply such that, on average, one SSB occurs per supercoiled plasmid lost. For the direct effect, at a large enough plasmid size, this assumption may be invalid. In this report, the assumption that one SSB occurs per pUC18 plasmid (2686 bp) is tested by measuring free base release (fbr), which is also a measure of deoxyribose damage in films prepared under controlled relative humidity so as to produce known levels of DNA hydration. The level of DNA hydration, Gamma, is expressed in mol water/mol nucleotide. The yield of free base release, G(fbr), was measured by HPLC after exposure of the films to 70 kV X rays and subsequent dissolution in water. It is well known that damage in deoxyribose leads to SSBs and free base release. Based on known mechanisms, there exists a close correspondence between free base release and SSBs, i.e., G(fbr) congruent with G(ssb). Following this assumption, the SSB multiplicity, m(ssb), was determined, where m(ssb) was defined as the mean number of SSBs per supercoiled plasmid lost. The yield of lost supercoil was determined previously (S. Purkayastha et al., J. Phys. Chem. B 110, 26286-26291, 2006). We found that m(ssb) = 1.4 +/- 0.2 at Gamma = 2.5 and m(ssb) = 2.8 +/- 0.5 to 3.1 +/- 0.5 at Gamma = 22.5, indicating that the assumption of one SSB per lost supercoil is not likely to hold for a 2686-bp plasmid exposed to the direct effect. In addition, an increase in G(fbr), upon stepping from Gamma = 2.5 to Gamma = 22.5, was paralleled by an increase in the yield of trapped deoxyribose radicals, G(dRib)(fr), also measured previously. As a consequence, the shortfall between SSBs and trapped radicals, G(diff) = G(ssb) - G(dRib)(fr), remained relatively constant at 90-110 nmol/J. The lack of change between the two extremes of hydration is in keeping with the suggestion that non-radical species, such as doubly oxidized deoxyribose, are responsible for the shortfall.

On the chemical yield of base lesions, strand breaks, and clustered damage generated in plasmid DNA by the direct effect of X rays.

The purpose of this study was to determine the yield of DNA base damages, deoxyribose damage, and clustered lesions due to the direct effects of ionizing radiation and to compare these with the yield of DNA trapped radicals measured previously in the same pUC18 plasmid. The plasmids were prepared as films hydrated in the range 2.5 < Gamma < 22.5 mol water/mol nucleotide. Single-strand breaks (SSBs) and double-strand breaks (DSBs) were detected by agarose gel electrophoresis. Specific types of base lesions were converted into SSBs and DSBs using the base-excision repair enzymes endonuclease III (Nth) and formamidopyrimidine-DNA glycosylase (Fpg). The yield of base damage detected by this method displayed a strikingly different dependence on the level of hydration (Gamma) compared with that for the yield of DNA trapped radicals; the former decreased by 3.2 times as Gamma was varied from 2.5 to 22.5 and the later increased by 2.4 times over the same range. To explain this divergence, we propose that SSB yields produced in plasmid DNA by the direct effect cannot be analyzed properly with a Poisson process that assumes an average of one strand break per plasmid and neglects the possibility of a single track producing multiple SSBs within a plasmid. The yields of DSBs, on the other hand, are consistent with changes in free radical trapping as a function of hydration. Consequently, the composition of these clusters could be quantified. Deoxyribose damage on each of the two opposing strands occurs with a yield of 3.5 +/- 0.5 nmol/J for fully hydrated pUC18, comparable to the yield of 4.1 +/- 0.9 nmol/J for DSBs derived from opposed damages in which at least one of the sites is a damaged base.