Radioprobing of DNA: distribution of DNA breaks produced by decay of 125I incorporated into a triplex-forming oligonucleotide correlates with geometry of the triplex.

The distribution of breaks produced in both strands of a DNA duplex by the decay of 125I carried by a triplex-forming DNA oligonucleotide was studied at single nucleotide resolution. The 125I atom was located in the C5 position of a single cytosine residue of an oligonucleotide designed to form a triple helix with the target sequence duplex. The majority of the breaks (90%) are located within 10 bp around the decay site. The addition of the free radical scavenger DMSO produces an insignificant effect on the yield and distribution of the breaks. These results suggest that the majority of these breaks are produced by the direct action of radiation and are not mediated by diffusible free radicals. The frequency of breaks in the purine strand was two times higher that in the pyrimidine strand. This asymmetry in the yield of breaks correlates with the geometry of this type of triplex; the C5 of the cytosine in the third strand is closer to the sugar-phosphate backbone of the purine strand. Moreover, study of molecular models shows that the yield of breaks at individual bases correlates with distance from the 125I decay site. We suggest the possible use of 125I decay as a probe for the structure of nucleic acids and nucleoprotein complexes.     

Biological damage from the Auger effect,possible benefits

Summary Decay of radioactive isotopes by K-capture leads to the Auger effect and results in the loss of several orbital electrons and the emission of X-rays. Whereas radiation effects are produced from the emitted electrons, the consequences of the Auger effect are strictly localized to the site of the decaying nuclide.The paper reviews the biological consequences of the decay of¹²⁵I which produces the Auger effect. Nearly all data were obtained from DNA labeled with¹²⁵I-5-iodo-2-deoxyuridine (IUdR) in bacteria and mammalian cells. Parameters of effects were cell death, DNA strand breaks, and mutation induction. In order to recognize in a cell the contribution from the Auger effect and that of absorbed radiation, experimental data are analysed in terms of the specific energy for the nuclear volume which contains the isotope.The data indicate that decay of¹²⁵I is far more toxic than is expected on the basis of absorbed dose to the labeled nucleus. Moreover, it is emphasized that the toxicity of the¹²⁵I decay is largely determined by events immediately localized to the site of decay.Because the consequences of the Auger effect are strictly localized to the molecular site of the decay,¹²⁵I and perhaps other nuclides decaying by K-capture promise to be interesting tools in cell biology and molecular biology. First data on the Auger effect as a tool are summarized.It appears that recognizable biological damage is only observed when the Auger effect takes place in vitally important molecules, an example of which is DNA.Dedicated to Prof. Dr. H. Muth on the occasion of his 60th birthday.     

Simulation of <Superscript>125</Superscript>I decay in a synthetic oligodeoxynucleotide with normal and distorted geometry and the role of radiation and non-radiation actions

Within the track structure code PARTRAC, DNA strand break induction by direct and indirect radiation action was calculated for the E. coli catabolite gene activator protein (CAP) DNA complex with ¹²⁵I located at the position of the H₅ atom of the cytosine near the center. The shape of the resulting DNA fragment size distributions was found to be in reasonable agreement with corresponding experimental results. However, the calculated yield was considerably lower than the measured one. To study possible reasons for this, recently published experimental data on DNA strand breaks in a 41-mer synthetic oligodeoxynucleotide (oligoDNA) with incorporated ¹²⁵I were analyzed aiming at an evaluation of the non-radiation-related component due to the neutralization of the initially highly charged ^125mTe daughter ion. This was done by assuming that the differences between simulated radiation-induced distribution and the measured total fragment size distributions were due to the neutralization process. The neutralization effect defined in this way was found to dominate the strand breakage frequency within a range of 5–7 base pairs around the ¹²⁵I decay site on both strands. After implementing this neutralization effect derived from the oligoDNA analysis into the PARTRAC simulation for the CAP-DNA complex, the agreement of the calculated DNA fragment distributions with the corresponding experimental data was considerably improved. The results indicate that DNA conformation may be explored by incorporation of ¹²⁵I into the DNA, measurement of fragment size distributions, and comparison with simulation calculation for various hypothetical DNA models.     

Repairable and unrepairable DNA strand breaks induced by decay of3H and125I incorporated into DNA of mammalian cells

Summary Chinese hamster cells (Cl : 1) were labelled with³H-thymidine or¹²⁵Iododeoxyuridine for 18 h and after 3 h in non-radioactive medium they were stored at 0° C up to 6 h. The number of DNA strand breaks observed after the labelling period (37° C) or after treatment at 0° C was determined using the DNA-unwinding technique.¹²⁵I-decays in DNA were significantly more efficient than³H-decays in introducing unrepairable DNA strand breaks during the labelling period. 32% of¹²⁵I-induced and 3% of³H-induced DNA strand breaks were unrepaired after 21 h at 37° C. Comparison between the effects of¹²⁵I- or 3H-disintegrations in DNA in three different ways shows 7–12 times more pronounced effects for¹²⁵I-decays. For¹²⁵I-labelled cells 3–4 DNA strand breaks were found per decay and the corresponding value for³H- labelled cells was 2.     

Detecting the DNA kinks in a DNA-CRP complex in solution with iodine-125 radioprobing.

Auger-electron-emitting radioisotopes such as 125I produce DNA strand breaks within nanometer range of the decay site. Here we analyze these breaks in order to study changes in DNA conformation upon binding with cyclic AMP receptor protein (CRP) in solution. The clear difference we found in break frequency in the CRP-DNA complex, as compared to the naked DNA duplex, correlates with the increased distances between the deoxyriboses and the radioiodine atom caused by the CRP-induced kink observed in the cocrystal. Thus, we demonstrate that 125I radioprobing can be used to study fine conformational changes of DNA within DNA-protein complexes.     

125Iodine decay in DNA: A discussion of its effectiveness for the breaking of DNA strands

Summary ¹²⁵I incorporated in DNA is known to be exceptionally toxic. Values of D₀ range from about 40 to about 90 decays for survival of mammalian cells. The effectiveness of¹²⁵I in DNA with respect to the induction of breaks of the DNA strands, however, appears to be comparatively low. The numbers of strand breaks per energy deposited in subnuclear cellular structures such as DNA is smaller for a disintegration of¹²⁵I than for-rays. The difference in effectiveness diminishes with increasing mass of the considered sensitive volume. The apparent inefficiency of¹²⁵I-decay may, on one hand, result from a waste of local energy deposition. On the other hand, it may be caused by a multitude of local strand breaks (clusters) induced by¹²⁵I-decay which are measured as one break only by the conventionally applied techniques of strand break measurement. The apparent inefficiency of¹²⁵I may be evidence furthermore for the importance of considering not only the DNA as the sensitive target but with equal pertinence the gross sensitive volume, i.e. the whole cell nucleus [12]. Further, for drawing meaningful comparisons, it may be necessary to take into consideration the microdosimetric event size distributions for the critical targets [1].Dedicated to Prof. L.E. Feinendegen on the occasion of his 60th birthday     

RNA facilitates RecA-mediated DNA pairing and strand transfer between molecules bearing limited regions of homology

The RecA protein ofEscherichia coli catalyzes homologous pairing and strand exchange between a wide range of molecules showing nucleotide sequence complementarity, including a linear duplex and a single-stranded DNA molecule. We demonstrate that RecA can promote formation of joint molecules when the duplex contains an RNA/DNA hairpin and a single-stranded circle serves as the pairing partner. A chimeric RNA/DNA hairpin can be used to form stable joint molecules with as little as 15 bases of shared homology as long as the RNA stretch contains complementarity to the circle. The joint molecule bears some resemblance to a triple helical structure composed of RNA residues surrounded by two DNA strands which are in a parallel orientation. Evidence is presented that supports the notion that short stretches of RNA can be used in homologous pairing reactions at lengths below that required for DNA-DNA heteroduplex formation.     

Iodine-125 decay in a synthetic oligodeoxynucleotide. II. The role of auger electron irradiation compared to charge neutralization in DNA breakage

Lobachevsky, P. N. and Martin, R. F. Iodine-125 Decay in a Synthetic Oligodeoxynucleotide. II. The Role of Auger Electron Irradiation Compared to Charge Neutralization in DNA Breakage. The dramatic chemical and biological effects of the decay of DNA-incorporated (125)I stem from two consequences of the Auger electron cascades associated with the decay of the isotope: high local deposition of radiation energy from short-range Auger electrons, and neutralization of the multiply charged tellurium atom. We have analyzed the extensive data reported in the companion paper (Radiat. Res. 153, 000-000, 2000), in which DNA breakage was measured after (125)I decay in a 41-bp oligoDNA. The experimental data collected under scavenging conditions (2 M dimethylsulfoxide) were deconvoluted into two components denoted as radiation and nonradiation, the former being attributed to energy deposition by Auger electrons. The contribution of the components was estimated by adopting various assumptions, the principal one being that DNA breakage due to the radiation mechanism is dependent on the distance between the decaying (125)I atom and the cleaved deoxyribosyl unit, while the nonradiation mechanism, associated with neutralization of the multiply charged tellurium atom, contributes equally at corresponding nucleotides starting from the (125)I-incorporating nucleotide. Comparison of the experimental data sets collected under scavenging and nonscavenging (without dimethylsulfoxide) conditions was used to estimate the radiation-scavengeable component. Our analysis showed that the nonradiation component plays the major role in causing breakage within 4-5 nucleotides from the site of (125)I incorporation and produces about 50% of all single-stranded breaks. This overall result is consistent with the relative amounts of energy associated with Auger electrons and the charged tellurium atom. However, the nonradiation component accounts for almost four times more breaks in the top strand, to which the (125)I is bound covalently, than in the bottom strand, thus suggesting an important role of covalent bonds in the energy transfer from the charged tellurium atom. The radiation component dominates at the distances beyond 8-9 nucleotides, and 36% of the radiation-induced breaks are scavengeable.     

Auger electron-induced double-strand breaks depend on DNA topology

From a structural perspective, the factors controlling and the mechanisms underlying the toxic effects of ionizing radiation remain elusive. We have studied the consequences of superhelical/torsional stress on the magnitude and mechanism of DSBs induced by low-energy, short-range, high-LET Auger electrons emitted by (125)I, targeted to plasmid DNA by m-[(125)I]iodo-p-ethoxyHoechst 33342 ((125)IEH). DSB yields per (125)I decay for torsionally relaxed nicked (relaxed circular) and linear DNA (1.74+/-0.11 and 1.62+/-0.07, respectively) are approximately threefold higher than that for torsionally strained supercoiled DNA (0.52+/-0.02), despite the same affinity of all forms for (125)IEH. In the presence of DMSO, the DSB yield for the supercoiled form remains unchanged, whereas that for nicked and linear forms decreases to 1.05+/-0.07 and 0.76+/-0.03 per (125)I decay, respectively. DSBs in supercoiled DNA therefore result exclusively from direct mechanisms, and those in nicked and linear DNA, additionally, from hydroxyl radical-mediated indirect effects. Iodine-125 decays produce hydroxyl radicals along the tracks of Auger electrons in small isolated pockets around the decay site. We propose that relaxation of superhelical stress after radical attack could move a single-strand break lesion away from these pockets, thereby preventing further breaks in the complementary strand that could lead to DSBs.     

Evidence that lipid peroxidation in microsomal membranes of epidermis is associated with generation of hydrogen peroxide and singlet oxygen

¹²⁵I-labelled triiodothyronine which binds to specific nuclear receptors induce DNA strand breaks in Chinese hamster cells. A large fraction of these breaks is left unrepaired and seems to be double strand breaks. The efficiency of inducing such breaks is as high as after incorporation into DNA of [¹²⁵I-]iododeoxyuridine which is known to be very radiotoxic.     

A functional hybrid ribosome binding site in tryptophan operon messenger RNA of Escherichia coli

We present evidence that repair of DNA damage induced by decay of incorporated ¹²⁵I after replication of the labeled duplex of Escherichia coli requires the recA⁺ gene function. Furthermore, only about half of the cells survive after label segregation even when that repair function is present. Our results support the possibility that repair of ¹²⁵I decay-induced lesions is asymmetric, being limited to damage initiated in only one of the two strands of the DNA duplex.     

125I-induced DNA double strand breaks: use in calibration of the neutral filter elution technique and comparison with X-ray induced breaks

The neutral filter elution assay, for measurement of DNA double strand breakage, has been calibrated using mouse L cells and Chinese hamster V79 cells labelled with [125I]dUrd and then held at liquid nitrogen temperature to accumulate decays. The basis of the calibration is the observation that each 125I decay, occurring in DNA, produces a DNA double strand break. Linear relationships between 125I decays per cell and lethal lesions per cell (minus natural logarithm survival) and the level of elution, were found. Using the calibration data, it was calculated that the yield of DNA double strand breaks after X-irradiation of both cell types was from 6 to 9 X 10(-12) DNA double strand breaks per Gy per dalton of DNA, for doses greater than 6 Gy. Neutral filter elution and survival data for X-irradiated and 125I-labelled cells suggested that the relationships between lethal lesions and DNA double strand breakage were significantly different for both cell types. An attempt was made to study the repair kinetics for 125I-induced DNA double strand breaks, but was frustrated by the rapid DNA degradation which occurs in cells that have been killed by the freezing-thawing process.     

Iodine-125 decay in a synthetic oligodeoxynucleotide. I. Fragment size distribution and evaluation of breakage probability

Lobachevsky, P. N. and Martin, R. F. Iodine-125 Decay in a Synthetic Oligodeoxynucleotide. I. Fragment Size Distribution and Evaluation of Breakage Probability. Incorporation of (125)I-dC into a defined location of a double-stranded oligodeoxynucleotide was used to investigate DNA breaks arising from decay of the Auger electron-emitting isotope. Samples of the oligodeoxynucleotide were also labeled with (32)P at either the 5' or 3' end of either the (125)I-dC-containing (so-called top) or opposite (bottom) strand and incubated in 20 mM phosphate buffer or the same buffer plus 2 M dimethylsulfoxide at 4 degrees C during 18-20 days. The (32)P-end-labeled fragments produced by (125)I decays were separated on denaturing polyacrylamide gels, and the (32)P activity in each fragment was determined by scintillation counting after elution of fragments from the gel. The relative fragment size distributions were then normalized on a per decay basis and converted to a distribution of single-strand break probabilities as a function of distance from the (125)I-dC. The results of three to five experiments for each of eight possible combinations of labels and incubation conditions are presented as a table showing the relative numbers of (32)P counts in different fragments as well as graphs of normalized fragment size distributions and probabilities of breakage. The average numbers of single-strand breaks per (125)I decay are 3. 3 and 3.7 in the top strand and 1.3 and 1.5 in the bottom strand with and without dimethylsulfoxide, respectively. Every (125)I decay event produces a break in the top strand, and breakage of the bottom strand occurs in 75-80% of the events. Thus a double-strand break is produced by (125)I decay with a probability of approximately 0.8.     

Strand breaks in plasmid DNA after positional changes of Auger electron-emitting iodine-125: direct compared to indirect effects.

To elucidate the nature and kinetics of DNA strand breaks caused by low-energy Auger electron emitters, we compared the yields of DNA breaks in supercoiled pUC19 DNA in the presence of the (.)OH scavenger dimethyl sulfoxide (DMSO) after the decay of (125)I (1) in proximity to DNA after minor-groove binding ((125)I-iodoHoechst 33342, (125)IH) and (2) at a distance from DNA ((125)I-iodoantipyrine, (125)IAP). DMSO is efficient at protecting supercoiled plasmid DNA from the decay of (125)I free in solution (dose modification factor, DMF = 59 +/- 4) and less effective when the (125)I decays occur close to DNA (DMF = 3.8 +/- 0.3). This difference is due mainly to the inability of DMSO to protect DNA from the double-strand breaks produced by groove-bound (125)I (DMF = 1.0 +/- 0.2). Additionally, the fragmentation of plasmid DNA beyond the production of single-strand and double-strand breaks that is seen after the decay of (125)IH and not (125)IAP (Kassis et al., Radiat. Res. 151, 167-176, 1999) cannot be modified by DMSO. These results demonstrate that the mechanisms underlying double-strand breaks caused by the decay of (125)IH differ in nature from those caused by the decay of (125)IAP.     

A measurement of the fraction of chloroplast DNA transcribed in Euglena

The fraction of the chloroplast DNA transcribed in the single celled alga $\text{Euglena}$ has been determined by RNA-DNA hybridization. A vast excess of total cell RNA from cells which were rapidly dividing in the light was hybridized in liquid to [¹²⁵I] — chloroplast DNA, and the resulting duplexes separated on hydroxyapatite columns. The contribution of DNA-DNA duplex formation was determined separately and was used to calculate that portion of the duplex which was actually a RNA-DNA hybrid. Sixteen percent of the single stranded chloroplast DNA forms a duplex with this RNA suggesting that 32 percent of the double stranded DNA molecule is being transcribed into RNA under these conditions of cell growth.     

Strand breaks in whole plasmid dna produced by the decay of (125)I in a triplex-forming oligonucleotide.

DNA strand breaks produced by the decay of (125)I positioned against a specific site in plasmid DNA via a triplex-forming oligonucleotide were studied both in the immediate vicinity of the site of the decay with a single nucleotide resolution and in the whole plasmid by measuring the percentages of supercoiled, open-circular and linear forms. The localized breaks are distributed within 10 bp in each direction from the decay site with maxima in both strands just opposite the (125)I-dC residue in the triplex-forming oligonucleotide. The distributions of breaks in the two DNA strands are almost symmetrical, in agreement with the geometry of the pyrimidine motif triplex. We found that about 25% of the double-strand breaks were located outside the 90-bp fragment containing the triplex-forming oligonucleotide binding sequence. The ratio of single- to double-strand breaks in the whole plasmid was 11 for bound triplex-forming oligonucleotide compared to 26 when the triplex-forming oligonucleotide was free in solution. The number of double-strand breaks per decay of (125)I was 0.46 for bound triplex-forming oligonucleotide and 0.17 for free triplex-forming oligonucleotide. Comparing the data on the localized damage and those for the whole plasmid, we concluded that, in addition to DNA breaks that are confined to a helical turn around the (125)I atom, the decay can produce breaks hundreds of base pairs away in the plasmid molecule. This linear plasmid molecule containing radiation-induced damage at a specific DNA site should be useful in studies of the molecular mechanisms of DNA repair.     

The structure of replicating adenovirus 2 DNA molecules

Adenovirus 2 (Ad2)-infected KB cells were exposed to a 2.5 min pulse of ³H-thymidine at 19 hr after infection. The labeled DNA molecules were separated from cell DNA and mature Ad2 DNA by sucrose gradient sedimentation and CsCI equilibrium centrifugation under conditions designed to minimize branch migration and hybridization of single strands. Electron microscopy-of fractions containing radioactivity revealed two basic types of putative replicating molecules: Ad2 length duplex DNA molecules with one or more single-stranded branches (type I) and Ad2 length linear DNA molecules with a single-stranded region extending a variable distance from one end (type II). Length measurements, partial denaturation studies and 3′ terminal labeling experiments were consistent with the following model for Ad2 DNA replication. Initiation of DNA synthesis occurs at or near an end of the Ad2 duplex. Following initiation, a daughter strand is synthesized in the 5′ to 3′ direction, displacing the parental strand with the same polarity. This results in the formation of a branched replicating molecule (type I). Initiations at the right and left molecular ends are approximately equal in frequency, and multiple initiations on the same replicating molecule are common. At any given displacement fork in a type I molecule, only one of the two parental strands is replicated. Two nonexclusive mechanisms are proposed to account for the replication of the other parental strand. In some cases, before completion of a round of displacement synthesis initiated at one end of the Ad2 duplex, a second initiation will occur at the opposite end. In these doubly initiated molecules, both parental strands serve as templates for displacement synthesis. Two type II molecules are generated when the oppositely moving displacement forks meet. Alternatively, displacement synthesis may proceed to the end of the Ad2 duplex, resulting in the formation of a daughter duplex and a parental single strand. Replication of the displaced parental strand is then initiated at or near its 3′ terminus, producing a type II molecule. Daughter strand synthesis proceeds in the 5′ to 3′ direction in type II molecules generated by either mechanism, and completion of synthesis results in the formation of a daughter duplex.     

A new calculation on spectrum of direct DNA damage induced by low-energy electrons

In this work, direct DNA damage induced by low-energy electrons (<5 keV) is simulated using Monte Carlo methods, and the resulting yield of various strand breaks and base damages in cellular environment is presented. The simulation is based on a new inelastic cross section for the production of electron track structure in liquid water, and on ionization cross sections of DNA bases to generate base radical. Especially, a systematic approach of simulating detailed base damage is suggested. This approach includes improvement of a volume model of DNA, generation of the DNA base sequence, conversion of ionization events in liquid water at hit site to the ionization interaction of electrons with DNA bases and development of an algorithm to convert a base radical to a damage. The results obtained in terms of strand breaks are compared with those of experiments and other theoretical calculations, and good agreement was obtained. The yield of detailed base damages and clustered DNA damages caused by the combination of various strand breaks and base damages is presented, and the corresponding distribution characteristics are analyzed. The influence of the relative content of base pairs A-T and G-C in a DNA segment on the yield of both strand breaks and base damages is also explored. The present work provides fundamental information on DNA damage and represents the first effort toward the goal of obtaining the spectrum of clustered DNA damage including detailed base damages, for the mechanistic interpretation and prediction of radiation effects.     

Induction of Thioguanine- and Ouabain-Resistant Mutants and Single-Strand Breaks in the DNA of Chinese Hamster Ovary Cells by 3H-Thymidine

Cultured Chinese hamster cells were labeled with 6-³H-thymidine or 5-methyl-³H-thymidine and allowed to accumulate damage from ³H decays for various periods of time while frozen. The frequencies of cells resistant to 6-thioguanine or ouabain and the amount of DNA damage (i.e., number of single-strand breaks) were determined and compared with the mutation frequencies resulting from X and ultraviolet light irradiation. Whereas ³H decays and X rays made only 6-thioguanine-resistant mutants, ultraviolet light made both 6-thioguanine- and ouabain-resistant mutants. ³H decays originating at the 6 position were two to three times as effective as decays at the 5-methyl position in making drug-resistant mutants, but decays at both sites were equally effective in making single-strand breaks. Mutants and strand breaks produced by beta irradiation of the nucleus probably are the same irrespective of the site of the decay in thymine; these results indicate that the local transmutation effects of ³H decay produce more mutations when they occur at the 6 position than at the 5-methyl position.     

The extracellular nuclease of Serratia marcescens: studies on the activity in vitro and effect on transforming DNA in a groundwater aquifer microcosm

A quantitative endonuclease assay, which relies on the introduction of single and double strand breaks into supercoiled plasmid DNA, was used to study the activity of the extracellular nuclease of Serratia marcescens SM6 in buffer and in groundwater. The parallel enzyme concentration-dependent production of relaxed and linear plasmid molecules suggests that the nuclease produces single and double strand breaks in duplex DNA. Bovine serum albumin stimulated the nuclease activity towards DNA and RNA and increased the stability of the enzyme against thermal inactivation. The DNase activity at 4 °C and 50 °C was almost half of that at the optimum temperature (37 °C). The nuclease was active in groundwater, although the specific activity was lower than in buffer. In a groundwater aquifer microcosm, mineral-adsorbed transforming DNA was substantially less accessible to the nuclease than was dissolved DNA. The data suggest that the extracellular nuclease of Serratia marcescens may contribute to DNA turnover in the environment and that adsorption of DNA to minerals provides protection against the nuclease.Abbreviations GW groundwater GWA groundwater aquifer