The stability of DNA triplexes inside cells as studied by iodine-125 radioprinting.

We studied the stability of a DNA triplex resulting from the binding of a 38 nt long purine motif triplex-forming oligonucleotide (TFO) to a covalently closed plasmid containing a target sequence from the human HPRT gene. Our in vitro experiments showed that the triplex formed at plasmid and TFO concentrations as low as 10(-9)M. Once formed, the triplex was remarkably stable and could withstand 10 min incubation at 65 degrees C. We next delivered these TFO-plasmid complexes into cultured human cells. To monitor the TFO-plasmid complexes inside cells we applied a new technique that we call 'radioprinting'. Because the TFO was(125)I labeled, we could quantitatively monitor the triplexes by measuring(125)I-induced DNA strand breaks in the target plasmid sequence. We found that the triplexes remain stable inside the cells for at least 48 h. Based on these findings we propose using TFO for indirect labeling of intact plasmid DNA. As a demonstration, we show that the intracellular distribution of a fluorescein-labeled TFO was different when it was liposome-delivered into cultured human cells alone or in a complex with the plasmid. In the latter case, the fluorescence was detected in nearly all the cells while detection of the plasmid by use of a marker gene (beta-galactosidase) revealed expression of the gene in only half of the cells.     

Chemical and biological consequences of the radioactive decay of iodine-125 in plasmid DNA

Doubly labeled [U-14C, 5-125I]iododeoxycytidine (IdC) triphosphate was synthesized and incorporated enzymatically into defined positions of the plasmid pBR322. After storage under various conditions, the stable end products were analyzed using radio-GC, radio-HPLC, and electron microscopy. In addition, solutions of 14C-IdC-labeled DNA containing Na125I as an internal radiation source were studied to investigate the influence of internal radiolysis. Transmutation of the covalently bound 125I leads to complete destruction of the labeled nucleotide, giving rise to 14CO2 and 14CO as major products. Fragmentation of the pyrimidine base is independent of solvent and DNA configuration. Internal radiolysis caused by Na125I leads to only minor damage. Electron microscopy studies reveal that decay-induced double strand breaks (dsb) occur both at the site of decay and in areas as far as hundreds of base pairs apart from that site. Number and distribution of the breaks is strongly dependent on solvent and DNA configuration. A direct correlation exists between the extent of fragmentation of the nucleotide and the mean number of dsb.     

Sequence-dependent kinks induced in curved DNA

In certain curved DNA fragments without AA dinucleotides, the gel retardation anomaly associated with curvature passes through a maximum with fragment length, indicating length (and electric field) dependent structural transitions in the DNA. We suggest that thermally induced stereochemical kinks in DNA are stabilized in the gel, thus relieving the effects of curvature. These kinks are shown to occur specifically at CA/TG and TA/TA stacks. Other physical and biological evidence points to frequent structural dislocations at CA and TA steps. These reversible sequence dependent kinks may therefore represent a novel class of structural protein-DNA recognition elements.     

Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA.

The human centromere protein B (CENP-B), one of the centromere components, specifically binds a 17 bp sequence (the CENP-B box), which appears in every other alpha-satellite repeat. In the present study, the crystal structure of the complex of the DNA-binding region (129 residues) of CENP-B and the CENP-B box DNA has been determined at 2.5 A resolution. The DNA-binding region forms two helix-turn-helix domains, which are bound to adjacent major grooves of the DNA. The DNA is kinked at the two recognition helix contact sites, and the DNA region between the kinks is straight. Among the major groove protein-bound DNAs, this 'kink-straight-kink' bend contrasts with ordinary 'round bends' (gradual bending between two protein contact sites). The larger kink (43 degrees ) is induced by a novel mechanism, 'phosphate bridging by an arginine-rich helix': the recognition helix with an arginine cluster is inserted perpendicularly into the major groove and bridges the groove through direct interactions with the phosphate groups. The overall bending angle is 59 degrees, which may be important for the centromere-specific chromatin structure.     

Paradoxical effects of iodine-125 decays in parent and daughter DNA: a new target model for radiation damage

Chinese hamster ovary cells were synchronized at the G(1)/S-phase boundary of the cell cycle and were pulse-labeled with (125)I-iododeoxyuridine 30 min after they entered the S phase. Cell samples were harvested and frozen for accumulation of (125)I decays during the first and second G(2) phase after labeling. Cell aliquots that had accumulated the desired number of decays were thawed and plated for evaluation micronucleus formation and cell death. Cells subjected to (125)I decays during the first G(2) phase after labeling exhibited single-hit kinetics of cell killing (n = 1, D(0) 41 decays/cell). In contrast, decays accumulated during the second G(2) phase killed cells with dual-hit kinetics (n = 1.9, D(0) 81 decays/cell). A similar divergence in the action of (125)I was noted for micronucleus formation. These findings indicate that the effects of (125)I varied depending on whether the decays occurred in daughter DNA (first G(2) phase) or parent DNA (second G(2) phase). Control studies with external X rays showed no such divergence of the action of radiation. To account for this paradox, a model is proposed that invokes higher-order chromatin structures as radiation targets. This model implies differential spatial arrangements for parent and daughter DNA in the genome, with DNA strands organized such that a single (125)I decay originating in daughter DNA damages two targets during the first G(2) phase, but identical decays occurring during the second G(2) phase damage only one of the targets.     

Late considerations in the treatment of low-grade malignancy cerebral tumors with iodine-125 brachytherapy

The authors report their series of 45 patients harboring inoperable, low-grade cerebral neoplasms, treated in the past 6 years with 125I stereotactic brachytherapy. The majority of these tumors were grade I and II astrocytomas and oligodendrogliomas (82.2%). A 2.6- to 6-year follow-up shows good results in 65.6% with reduction or disappearance of the lesions on CT images and good social reentry. Nine patients (23.7%) died prior to follow-up. Young patients (less than 40 years) responded well to interstitial radiotherapy, while patients over 40 with the same histological findings of low-grade tumors responded poorly to this type of treatment. Diffuse infiltrating cortico-subcortical tumors, optochiasmatic gliomas, hypothalamic and lower brainstem neoplasms do not respond satisfactorily to 125I radioisotope implantations.     

A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.

The 3D solution structure of the GCC-box binding domain of a protein from Arabidopsis thaliana in complex with its target DNA fragment has been determined by heteronuclear multidimensional NMR in combination with simulated annealing and restrained molecular dynamic calculation. The domain consists of a three-stranded anti-parallel beta-sheet and an alpha-helix packed approximately parallel to the beta-sheet. Arginine and tryptophan residues in the beta-sheet are identified to contact eight of the nine consecutive base pairs in the major groove, and at the same time bind to the sugar phosphate backbones. The target DNA bends slightly at the central CG step, thereby allowing the DNA to follow the curvature of the beta-sheet.     

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.     

Chromosomal abnormalities induced by iodine-125 in mouse germ cells

Swiss albino male mice were injected intraperitoneally with 0, 185, 370 or 555 kBq (0, 5, 10 or 15 microCi) of iodine-125 (125I). All the animals were killed on the sixtieth day and chromosomal aberrations were screened in spermatocytes at meiotic metaphase I. A significant increase in the percentage of chromosomal aberrations including translocations (0, 1.2, 1.8 and 2.3 per cent translocations in controls, 185, 370 and 555 kBq groups respectively) was recorded at all dose levels indicating the clastogenic effects of 125I in mouse spermatocytes.     

Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution.

Molecular dynamics simulations have been performed on the glucocorticoid receptor DNA binding domain (GR DBD) in aqueous solution as a dimer in complex with DNA and as a free monomer. In the simulated complex, we find a slightly increased bending of the DNA helix axis compared with the crystal structure in the spacer region of DNA between the two half-sites that are recognized by GR DBD. The bend is mainly caused by an increased number of interactions between DNA and the N-terminal extended region of the sequence specifically bound monomer. The recognition helices of GR DBD are pulled further into the DNA major groove leading to a weakening of the intrahelical hydrogen bonds in the middle of the helices. Many ordered water molecules with long residence times are found at the intermolecular interfaces of the complex. The hydrogen-bonding networks (including water bridges) on either side of the DNA major groove involve residues that are highly conserved within the family of nuclear receptors. Very similar hydrogen-bonding networks are found in the estrogen receptor (ER) DBD in complex with DNA, which suggests that this is a common feature for proper positioning of the recognition helix in ER DBD and GR DBD.     

青菜(Brassica chinesis L.)对碘动态吸收的同位素示踪

碘是合成甲状腺激素不可缺少的元素,食物中严重缺碘可以导致人体中甲状腺功能的失调。利用同位素示踪技术研究了青菜在水培条件下对碘（^125Ⅰ）的吸收和富集特征,并在此基础上讨论了植物对碘吸收的生物学机制。研究结果表明,青菜根都能迅速吸收^125Ⅰ并向地上部分输送,青菜各部位^125Ⅰ的比活度大小顺序是根〉茎〉叶;青菜茎对碘的吸收量白天大于夜晚,青菜叶对碘的吸收夜晚大于白天;青菜植株不同部位叶片碘含量存在差异,上部嫩叶中^125Ⅰ高于下部叶片,说明青菜中^125Ⅰ的富集特征是植物对碘主动吸收和被动吸收共同作用的结果。青菜培养时间经过120h后,^125Ⅰ的消耗途径主要是作物的吸收和自然挥发,^125Ⅰ的放射性衰变丢失的量相对较少。研究为培育含碘作物提供了科学依据。     

Dominant lethal induction and testicular uptake of iodine-125 in mice

The mutagenic potential of 125I was studied using dominant lethal (DL) and testicular uptake studies. Dominant lethality (DL) represents embryonic death resulting from the chromosomal breakage in gametes of parents. When compared to controls, mice treated with different doses of 125I showed significant levels of induced DL. Significant pre-implantation losses were observed and variations in live implantations indicated total losses by the isotope. Dead implantations per pregnant female in the isotope treated groups showed a significant increase from controls indicating induced levels of post-implantation losses. All the stages of spermatogenesis, i.e., spermatozoa, spermatid, spermatocyte and spermatogonia were found to be sensitive to the induction of post-implantation losses, the spermatid stage being the most sensitive. Testicular uptake was measured from 1/2 hour to 72 hours after injection and maximum uptake was recorded at 1/2 hour, indicating the permeability of the blood/testis barrier.     

Probing DNA sequences in solution with a monomer-excimer fluorescence color change.

The use of a simple fluorescent nucleoside analogue in detection of point mutations by hybridization in solution is described. Pyrene is placed at 3' and 5' ends of a pair of oligodeoxynucleotide probes via a phosphoramidite derivative of deoxyribose with this fluorophore attached at the 1' position, replacing a DNA base. Adjacent binding of dual probes containing this fluorophore to a complementary target sequence results in a pronounced spectral change from blue pyrene monomer emission (lambdamax= 381 398 nm) to green-white excimer emission (lambdamax= 490 nm). Optimization of the relative binding positions of the two probes shows that the greatest spectral change occurs when they bind with partial end overlap. In optimum orientation, the monomer emission band for the probes decreases intensity by as much as a factor of seven and the excimer band increases up to 40-fold on binding a complementary target. Application to the detection of a single-base point mutation in solution is described.     

Toxicity of DNA-incorporated iodine-125: quantifying the direct and indirect effects

To understand the biophysical mechanism(s) underlying the induction of cell death by the decay of the Auger electron emitter iodine-125 in DNA, Chinese hamster V79 lung fibroblasts were labeled with 5-[(125)I]iodo-2'-deoxyuridine ((125)IdU) for two doubling times and frozen and stored at -135 degrees C in the presence of 0.26-3.0 M dimethyl sulfoxide (DMSO), which acts simultaneously as a cryoprotector and a hydroxyl radical scavenger. After the accumulation of (125)I decays, the cells were defrosted and their survival was determined. Within the range of the number of decays examined (up to 470 disintegrations per cell), the survival curves are exponential. The dependence of the D(37) on DMSO concentration is triphasic and seems to reach a plateau at approximately 1.3 M. By extrapolating to infinite DMSO concentration, we estimate the D(37) for maximal hydroxyl radical scavenging to be 411 +/- 36 disintegrations per cell. To determine the D(37) in the absence of DMSO, we extrapolate the D(37) curve to zero concentration, and a D(37) of 54 +/- 5 disintegrations per cell is obtained. The maximal dose modification factor, calculated as the ratio of the D(37) at infinite DMSO concentration (i.e. direct effects only) to the D(37) at zero DMSO concentration (i.e. direct and indirect effects), is 7.6 +/- 1.0. By inference, approximately 90% of the radiotoxic effects of DNA-incorporated (125)I are due to indirect mechanisms.     

The solution structure of the Sac7d/DNA complex: a small-angle X-ray scattering study.

Small-angle X-ray scattering has been used to study the structure of the multimeric complexes that form between double-stranded DNA and the archaeal chromatin protein Sac7d from Sulfolobus acidocaldarius. Scattering data from complexes of Sac7d with a defined 32-mer oligonucleotide, with poly[d(GC)], and with E. coli DNA indicate that the protein binds along the surface of an extended DNA structure. Molecular models of fully saturated Sac7d/DNA complexes were constructed using constraints from crystal structure and solution binding data. Conformational space was searched systematically by varying the parameters of the models within the constrained set to find the best fits between the X-ray scattering data and simulated scattering curves. The best fits were obtained for models composed of repeating segments of B-DNA with sharp kinks at contiguous protein binding sites. The results are consistent with extrapolation of the X-ray crystal structure of a 1:1 Sac7d/octanucleotide complex [Robinson, H., et al. (1998) Nature 392, 202-205] to polymeric DNA. The DNA conformation in our multimeric Sac7d/DNA model has the base pairs tilted by about 35 degrees and displaced 3 A from the helix axis. There is a large roll between two base pairs at the protein-induced kink site, resulting in an overall bending angle of about 70 degrees for Sac7d binding. Regularly repeating bends in the fully saturated complex result in a zigzag structure with negligible compaction of DNA. The Sac7d molecules in the model form a unique structure with two left-handed helical ribbons winding around the outside of the right-handed duplex DNA.