Igor G. Panyutin

Quantitative Detection of 125IdU-Induced DNA Double-Strand Breaks with γ-H2AX Antibody

Abstract Sedelnikova, O. A., Rogakou, E. P., Panyutin, I. G. and Bonner, W. M. Quantitative Detection of 125IdU-Induced DNA Double-Strand Breaks with γ-H2AX Antibody. Radiat. Res. 158, 486–492 (2002). When mammalian cells are exposed to ionizing radiation and other agents that introduce DSBs into DNA, histone H2AX molecules in megabase chromatin regions adjacent to the breaks become phosphorylated within minutes on a specific serine residue. An antibody to this phosphoserine motif of human H2AX (γ-H2AX) demonstrates that γ-H2AX molecules appear in discrete nuclear foci. To establish the quantitative relationship between the number of these foci and the number of DSBs, we took advantage of the ability of 125I, when incorporated into DNA, to generate one DNA DSB per radioactive disintegration. SF-268 and HT-1080 cell cultures were grown in the presence of 125IdU and processed immunocytochemically to determine the number of γ-H2AX foci. The numbers of 125IdU disintegrations per cell were measured by exposing the same immunocytochemically processed samples to a radiation-sensitive screen with known standards. Under appropriate conditions, the data yielded a direct correlation between the number of 125I decays and the number of foci per cell, consistent with the assumptions that each 125I decay yields a DNA DSB and each DNA DSB yields a visible γ-H2AX focus. Based on these findings, we conclude that γ-H2AX antibody may form the basis of a sensitive quantitative method for the detection of DNA DSBs in eukaryotic cells.

Ionizing radiation induces DNA double-strand breaks in bystander primary human fibroblasts.

That irradiated cells affect their unirradiated ‘bystander’ neighbors is evidenced by reports of increased clonogenic mortality, genomic instability, and expression of DNA-repair genes in the bystander cell populations. The mechanisms underlying the bystander effect are obscure, but genomic instability suggests DNA double-strand breaks (DSBs) may be involved. Formation of DSBs induces the phosphorylation of the tumor suppressor protein, histone H2AX and this phosphorylated form, named γ-H2AX, forms foci at DSB sites. Here we report that irradiation of target cells induces γ-H2AX focus formation in bystander cell populations. The effect is manifested by increases in the fraction of cells in a population that contains multiple γ-H2AX foci. After 18 h coculture with cells irradiated with 20 α-particles, the fraction of bystander cells with multiple foci increased 3.7-fold. Similar changes occurred in bystander populations mixed and grown with cells irradiated with γ-rays, and in cultures containing media conditioned on γ-irradiated cells. DNA DSB repair proteins accumulated at γ-H2AX foci, indicating that they are sites of DNA DSB repair. Lindane, which blocks gap-junctions, prevented the bystander effect in mixing but not in media transfer protocols, while c-PTIO and aminoguanidine, which lower nitric oxide levels, prevented the bystander effect in both protocols. Thus, multiple mechanisms may be involved in transmitting bystander effects. These studies show that H2AX phosphorylation is an early step in the bystander effect and that the DNA DSBs underlying γ-H2AX focus formation may be responsible for its downstream manifestations.

Structural polymorphism of intramolecular quadruplex of human telomeric DNA: effect of cations, quadruplex-binding drugs and flanking sequences

G-quadruplex structures formed in the telomeric DNA are thought to play a role in the telomere function. Drugs that stabilize the G-quadruplexes were shown to have anticancer effects. The structures formed by the basic telomeric quadruplex-forming unit G3(TTAG3)3 were the subject of multiple studies. Here, we employ 125I-radioprobing, a method based on analysis of the distribution of DNA breaks after decay of 125I incorporated into one of the nucleotides, to determine the fold of the telomeric DNA in the presence of TMPyP4 and telomestatin, G-quadruplex-binding ligands and putative anticancer drugs. We show that d[G3(TTAG3)3125I-CT] adopts basket conformation in the presence of NaCl and that addition of either of the drugs does not change this conformation of the quadruplex. In KCl, the d[G3(TTAG3)3125I-CT] is most likely present as a mixture of two or more conformations, but addition of the drugs stabilize the basket conformation. We also show that d[G3(TTAG3)3125I-CT] with a 5′-flanking sequence folds into (3+1) type 2 conformation in KCl, while in NaCl it adopts a novel (3+1) basket conformation with a diagonal central loop. The results demonstrate the structural flexibility of the human telomeric DNA; and show how cations, quadruplex-binding drugs and flanking sequences can affect the conformation of the telomeric quadruplex.

SEQUENCE-SPECIFIC DNA BREAKS PRODUCED BY TRIPLEX-DIRECTED DECAY OF IODINE-125

Triplex forming oligonucleotides (TFO) labeled with Auger emitters could be ideal vehicles to deliver radioactive-decay energy to specific DNA sequences, causing DNA breaks and, subsequently, inactivation of these sequences. To demonstrate this approach we labeled with 125I (two 125I per molecule on average) a purine-rich 38-mer which forms a stable triplex with a polypurine x polypyrimidine stretch in the human HPRT gene. Decay of 125I in the bound TFO was shown to cause sequence-specific double strand breaks (DSB) in the target HPRT sequence cloned into plasmid DNA. No sequence-specific breaks were observed if 125I-labeled TFO were not bound to the plasmid DNA. After 60 days of decay accumulation (one 125I half-life) approximately a quarter of all plasmid molecules contained sequence-specific DSB, corresponding to 0.3 site-specific DSB per decay. Sequencing gel analysis shows that the DNA breaks are distributed within a few bases of the maxima at those bases opposite to the positions of 125I in the TFO.

A Structural Transition in d(AT) n ·d(AT) n Inserts within Superhelical DNA

We have constructed plasmids carrying d(AT)n.d(AT)n inserts of different lengths. Two-dimensional gel electrophoresis patterns show that an increase in the negative superhelicity of these DNAs brings about a structural transition within the inserts, resulting in a reduction of the superhelical stress. However, this reduction corresponds to the expected values neither for cruciform nor the Z form. Those DNA topoisomers in which the structural transition had occurred proved to be specifically recognizable by single-strand-specific endonuclease S1, with the cleavage site situated at the centre of the insert. These data, as well as kinetic studies, suggest that the cloned d(AT)n.d(AT)n sequences adopt a cruciform rather than the Z-form structure. We discuss plausible reasons of the discrepancy between the observed superhelical stress release and that expected for the transition of the insert to the cruciform state.

Stabilization of G-quadruplex in the BCL2 promoter region in double-stranded DNA by invading short PNAs.

Numerous regulatory genes have G-rich regions that can potentially form quadruplex structures, possibly playing a role in transcription regulation. We studied a G-rich sequence in the BCL2 gene 176-bp upstream of the P1 promoter for G-quadruplex formation. Using circular dichroism (CD), thermal denaturation and dimethyl sulfate (DMS) footprinting, we found that a single-stranded oligonucleotide with the sequence of the BCL2 G-rich region forms a potassium-stabilized G-quadruplex. To study G-quadruplex formation in double-stranded DNA, the G-rich sequence of the BCL2 gene was inserted into plasmid DNA. We found that a G-quadruplex did not form in the insert at physiological conditions. To induce G-quadruplex formation, we used short peptide nucleic acids (PNAs) that bind to the complementary C-rich strand. We examined both short duplex-forming PNAs, complementary to the central part of the BCL2 gene, and triplex-forming bis-PNAs, complementary to sequences adjacent to the G-rich BCL2 region. Using a DMS protection assay, we demonstrated G-quadruplex formation within the G-rich sequence from the promoter region of the human BCL2 gene in plasmid DNA. Our results show that molecules binding the complementary C-strand facilitate G-quadruplex formation and introduce a new mode of PNA-mediated sequence-specific targeting.

Phosphorylation of Histone H2AX in Radiation-Induced Micronuclei

Abstract Medvedeva, N. G., Panyutin, I. V., Panyutin, I. G. and Neumann, R. D. Phosphorylation of Histone H2AX in Radiation-Induced Micronuclei. Radiat. Res. 168, 493–498 (2007). DNA double-strand breaks are thought to precede the formation of most radiation-induced micronuclei. Phosphorylation of the histone H2AX is an early indicator of DNA double-strand breaks. Here we studied the phosphorylation status of the histone H2AX in micronuclei after exposure of cultured cells to ionizing radiation or treatment with colchicine. In human astrocytoma SF268 cells, after exposure to γ radiation, the proportion of γ-H2AX-positive to γ-H2AX-negative micronuclei increases. The majority of the γ-H2AX-positive micronuclei are centromere-negative. The number of γ-H2AX-positive micronuclei continues to increase even 24 h postirradiation when most γ-H2AX foci in the main nucleus have disappeared. In contrast, in normal human fibroblasts (BJ), the proportion of γ-H2AX-positive to γ-H2AX-negative micronuclei remains constant, and the majority of the centromere-negative cells are γ-H2AX-negative. Treatment of both cell lines with colchicine results in mostly centromere-positive, γ-H2AX-negative micronuclei. Immunostaining revealed co-localization of MDC1 and ATM with γ-H2AX foci in both main nuclei and micronuclei; however, other repair proteins, such as Rad50, 53BP1 and Rad17, that co-localized with γ-H2AX foci in the main nuclei were not found in the micronuclei. Combination of the micronucleus assay with γ-H2AX immunostaining provides new insights into the mechanisms of the formation and fate of micronuclei.

Repair of Sequence-specific 125I-induced Double-strand Breaks by Nonhomologous DNA End Joining in Mammalian Cell-free Extracts

In mammalian cells, nonhomologous DNA end joining (NHEJ) is considered the major pathway of double-strand break (DSB) repair. Rejoining of DSB produced by decay of 125I positioned against a specific target site in plasmid DNA via a triplex-forming oligonucleotide (TFO) was investigated in cell-free extracts from Chinese hamster ovary cells. The efficiency and quality of NHEJ of the “complex” DSB induced by the 125I-TFO was compared with that of “simple” DSB induced by restriction enzymes. We demonstrate that the extracts are indeed able to rejoin 125I-TFO-induced DSB, although at approximately 10-fold decreased efficiency compared with restriction enzyme-induced DSB. The resulting spectrum of junctions is highly heterogeneous exhibiting deletions (1–30 bp), base pair substitutions, and insertions and reflects the heterogeneity of DSB induced by the125I-TFO within its target site. We show that NHEJ of125I-TFO-induced DSB is not a random process that solely depends on the position of the DSB but is driven by the availability of microhomology patches in the target sequence. The similarity of the junctions obtained with the ones found in vivo after125I-TFO-mediated radiodamage indicates that our in vitro system may be a useful tool to elucidate the mechanisms of ionizing radiation-induced mutagenesis and repair.

Expression of pluripotency-associated genes in the surviving fraction of cultured human embryonic stem cells is not significantly affected by ionizing radiation.

Human embryonic stem cells (hESC) are capable to give rise to all cell types in the human body during the normal course of development. Therefore, these cells hold a great promise in regenerative cell replacement based therapeutical approaches. However, some controversy exists in literature concerning the ultimate fate of hESC after exposure to genotoxic agents, in particular, regarding the effect of DNA damaging insults on pluripotency of hESC. To comprehensively address this issue, we performed an analysis of the expression of marker genes, associated with pluripotent state of hESC, such as Oct-4, Nanog, Sox-2, SSEA-4, TERT, TRA-1-60 and TRA-1-81 up to 65h after exposure to ionizing radiation (IR) using flow cytometry, immunocytochemistry and quantitative real-time polymerase chain reaction techniques. We show that irradiation with relatively low doses of gamma-radiation (0.2Gy and 1Gy) does not lead to loss of expression of the pluripotency-associated markers in the surviving hESC. While changes in the levels of expression of some of the pluripotency markers were observed at different time points after IR exposure, these alterations were not persistent, and, in most cases, the expression of the pluripotency-associated markers remained significantly higher than that observed in fully differentiated human fibroblasts, and in hESCs differentiated into definitive endodermal lineage. Our data suggest that exposure of hESC to relatively low doses of IR as a model genotoxic agent does not significantly affect pluripotency of the surviving fraction of hESC.

Strand breaks in whole plasmid DNA produced by the decay of 125I in a triplex-forming oligonucleotide

Abstract Panyutin, I. V., Luu, A. N., Panyutin, I. G. and Neumann, R. D. Strand Breaks in Whole Plasmid DNA Produced by the Decay of 125I in a Triplex-Forming Oligonucleotide. Radiat. Res. 156, 158–166 (2001). DNA strand breaks produced by the decay of 125I 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 125I-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 125I 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 125I 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.