Electron Localization in Metallic Quasicrystals

Bulk icosahedral-quasicrystalline aluminum-palladium-rhenium alloys of high structural quality and thermal stability are found to exhibit low-temperature electrical resistivities that are four orders of magnitude larger than those found in disordered metals and metallic glasses. Experiments suggest that these quasiperiodic alloys, which have a semimetallic electron density, are insulators at low temperature. The findings are discussed in light of theories on electron localization and band-gap formation in ordered metallic systems.

[Percutaneous hot water injection therapy (PHoT) for hepatic tumors: a clinical study]

Percutaneous ethanol injection therapy (PEIT) has become widely used in the treatment of HCC. However, the indications for this method are limited by the toxicity of ethanol itself. Against this background, the authors turned their attention to the heat coagulation necrosis effect induced by boiled physiological saline (hot water) and devised percutaneous hot water injection therapy (PHoT) as a new local treatment method. PHoT was performed a total of 41 times in 13 patients (16 nodules) with HCCs measuring < or = 3 cm. Changes in AFP values, CT findings, angiographic findings before and after treatment, and histopathological findings of needle biopsy or resected specimen were investigated. AFP values decreased in all of the seven patients who initially showed high values. On CT, all lesions receiving PHoT became hypodense, with this change thought to indicate necrosis. Disappearance of the tumor stain was confirmed in the four patients in whom follow-up angiography was performed. In the six patients in whom needle biopsy was performed, disappearance and scaring of tumor cells were observed, while in the one patient in whom the tumor was resected, complete necrosis of the tumor was confirmed. PHoT, despite a small number of punctures, shows good anti-tumor effects, and has promise not only as a curative local treatment method for small HCCs but also in combination with TAE for large HCCs.

Structure of a parallel-stranded tetramer of the Oxytricha telomeric DNA sequence dT4G4

We report here the determination of the solution structure of the single-copy tetramer of the sequence dT4G4, the unit repeat in telomeres of the ciliated protozoan Oxytricha, in the presence of potassium ions. This is accomplished by a combination of sequential assignments and distance determinations from 2D proton NMR with model building, based on conformational analysis of the structure using a full-matrix NOESY simulation and molecular dynamics. Each strand in this tetramer structure has an identical environment and conformation: a parallel-stranded, right-handed helix, with all nucleotides in the C2'-endo, anti configuration. The T flanking the G cluster stacks in a 4-fold symmetrical helical array, while the remaining T's become increasingly flexible and sample multiple stacked configurations.

Segmental transcatheter hepatic artery chemoembolization with iodized oil for hepatocellular carcinoma: antitumor effect and influence on normal tissue

PURPOSE

Segmental transcatheter arterial embolization (TAE) with use of iodized oil mixed with an anticancer drug, followed by injection of gelatin sponge particles, was undertaken to evaluate its antitumor effect and its influence on normal tissue in patients with hepatocellular carcinoma (HCC).

PATIENTS AND METHODS

Histologic findings in 12 patients who underwent hepatectomy after segmental TAE were compared with findings on plain radiographs and computed tomographic (CT) scans. Visualization of the portal veins contiguous to the tumor on radiographs and the pattern of iodized oil accumulation in the tumor and vicinity on CT scans after TAE were assessed.

RESULTS

Complete necrosis of the tumor was achieved in 10 cases (83%), while complete necrosis of daughter nodules and capsular invasion was observed histologically in eight of these 10 patients (80%). The degree of tumor necrosis correlated with the pattern of iodized oil accumulation in and near the tumor. Partial necrosis of normal tissue near the tumor correlated with accumulation of iodized oil.

CONCLUSION

Segmental TAE may be an excellent therapeutic method for treatment of HCC that is localized in one or a few segmental or subsegmental regions.

[CO2US via an implantable port--drug distribution in intraarterial chemotherapy for hepatic tumors and evaluation of effect]

The distribution of blood flow was determined from the distribution of CO2 by US performed during the infusion of CO2 microbubbles via an implantable port (IP-CO2US) in intraarterial chemotherapy for hepatic tumor, and the usefulness of this method in determining tumor vascularity and evaluating the effects of therapy was investigated. A total of 16 patients, 12 of whom had metastatic liver tumor, two hepatocellular carcinoma, one gall bladder carcinoma, and one cholangiocellular carcinoma were studied. The enhanced areas in the liver in 16 patients in whom IP-CO2US was performed a total of 24 times were consistent in all cases with the enhanced areas demonstrated by IP-RI angiography performed a total of 10 times within 10 days, and were also consistent with one exception with the enhanced areas demonstrated by IP-CTA performed 14 times. The tumor detection rate was markedly higher with IP-CO2US than with plain US or IP-DSA, and was similar to that of IP-CTA. Evaluation of the vascularity of individual nodules by IP-CO2US surpassed that by IP-DSA, and was similar to that of IP-CTA. It was demonstrated that blood flow distribution (intrahepatic drug distribution) can be equally well grasped with IP-CO2US, which is a simple and convenient method, as with IP-RI angiography. It was also suggested that IP-CO2US is useful in the evaluation of tumor vascularity and the effect of therapy.

Effect of thymine tract length on the structure and stability of model telomeric sequences

DNA from the telomeres at the ends of eukaryotic chromosomes contains a stretch of simple tandemly repeated sequences in which clusters of G residues alternate with clusters of T/A sequences along one DNA strand. Model telomeric G-clusters form four-stranded structures in Na+ or K+, stabilized by Hoogsteen pairing between G bases. DNA containing a single copy of the G-cluster can self-associate to form tetramers, with a parallel-stranded, right-handed helical structure. Two copies of the 3'-terminal G strand form a folded-back hairpin that dimerizes to create an antiparallel quadruplex structure. We show here that the tetrameric structure is strongly influenced by the T residue flanking either side of the G-cluster. The parallel tetraplex formed by single copies of the sequences dTnG4 is most stable for n = 1 and least stable for n = 8, the longest tract we have studied. At least two thymine residues are required to allow formation of antiparallel folded-back hairpin dimers from two-copy oligomers of sequence d(TnG4)2 in Na+; additional T's destabilize this structure. In K+, the predominant structure formed is the four-stranded parallel tetramer in all cases. Kinetic analysis indicates that the quadruplex structure formed by Oxytricha telomeric DNA overhangs in the presence of Na+ arises by dimerization of two Hoogsteen base-paired hairpins, with a relatively low energy barrier.

[Study on the evaluation of recurrence of HCC and the effect after transcatheter hepatic arterial embolization--fluctuations in AFP values]

To determine the usefulness of alpha-fetoprotein (AFP) in determining recurrence of HCC after interventional angiography (IVA) and to define the relation between AFP and the imaging diagnosis of HCC recurrence, changes in AFP values in 160 patients with hepatocellular carcinoma who were treated by IVA > or = two times were classified into four patterns: A: the AFP value was decreased after the first IVA, increased at recurrence and decreased again after the second IVA; B: the AFP value was unchanged after the first IVA, but increased at recurrence and decreased after the second IVA; C: the AFP value was decreased after the first IVA, but was not increased at recurrence; D: the AFP value showed no change. The frequency of each AFP pattern and the diagnosis of recurrence by AFP were determined. The relation between tumor type and AFP was defined. Pattern A was the most frequently detected. In 62.6%, AFP was increased at recurrence (A and B), and there was a positive correlation between changes in the AFP value and the findings of imaging diagnosis. In another 37.5%, AFP was not increased at recurrence (C and D), and therefore, the diagnosis of HCC recurrence by imaging methods was very important.

Electrophysiological and pathological observations on experimental coxsackie B-3 viral myocarditis in mice

Electrophysiological action of right ventricular myocardium examined by standard intracellular microelectrode technique and real-time microcomputer data processor system and histological and ultrastructural changes of myocardium in BALB/c mice infected with coxsackie B-3 virus from 3 days to 9 months were observed. It was found that electrophysiologic parameters of action potential changed very quickly at the early stage (3 days to 1 month) of the disease. Those abnormalities became most apparent by the 5-30th day, and 7 patterns of abnormal action potential occurred frequently within the same period. These changes were basically parallel to the myocardial lesions. At the late stage (3-9 months) the electrophysiological parameters were nearly normal, while the myocardial lesions decreased gradually. However, the abnormal patterns of action potential were still detected, even though they were improved gradually. The results suggest that myocardial damages caused by viral infection may lead to changes of cardiac electric action, which may be one of the factors in arrhythmias in the episode of viral myocarditis.

Thermodynamics of G-tetraplex formation by telomeric DNAs

Telomeres are structures at the ends of eukaryotic chromosomes, the DNA of which contains stretches of tandemly repeated sequences with G clusters along one strand. Model telomeric G-rich DNAs can form different tetraplex structures, stabilized by cyclic hydrogen bonding of four guanines in the presence of metal ions such as Na+ or K+. Oligonucleotides with a single copy of the Oxytricha sequence dT4G4 form a tetramer, with a parallel-stranded, right-handed helical structure. Additional copies favor folded-back structures that associate to form an antiparallel dimer. The parallel-stranded tetramer has all G's in the anti configuration, while the folded-back dimer has alternating syn and anti nucleotide conformations along each strand. Here we have constructed two G-tetraplex structures, containing identical G-tetrad base pairs, from oligonucleotides. One has the truncated telomeric sequence from Oxytricha, dG4T4G4, which forms an antiparallel G-quartet structure; the second is constrained to form a parallel G-strand arrangement by insertion of a 5'-p-5' linkage between two dT2G4 sequences. Each oligomer forms a defined G-tetraplex dimeric structure in the presence of Na+. The standard-state enthalpies, entropies, and free energy for formation of these tetraplexes have been determined. The parallel strand structure is thermodynamically more stable than the antiparallel one, primarily because of both greater enthalpy and entropy of formation. In addition, the two molecules differ in their interaction with sodium ions, reflecting a difference in ion binding and therefore in structure between the two forms.

[Tear malate dehydrogenase, lactate dehydrogenase, and their isoenzymes in normal Chinese subjects and patients of ocular surface disorders]

Levels of malate dehydrogenase (MDH), lactate dehydrogenase (LDH) and their isoenzymes in tears of normal Chinese subjects and patients with ocular surface disorders were determined. The normal values of tear LDH and MDH were found to be 45.51 +/- 23.00-81.35 +/- 37.84 mumol.s-1/L and 11.00 +/- 5.33-19.50 +/- 9.17 mumol.s-1/L respectively, disregarding sex or eye distinction. The LDH/MDH ratio reflected sensitively the metabolism of corneal and conjunctival epithelium. The MDH isoenzymes comprised MDHs and MDHm, the former accounting for 80.0%-89.1%. The LDH isoenzymes comprised 5 varieties, of which the ratio H/M of subunit H to subunit M was 0.196 +/- 0.02. The changes in LDH isoenzymes were helpful to the differential diagnosis of external eye diseases, and the increase of MDHm reflected sensitively the degree of injury to the corneal epithelium.

Effect of verapamil on acute coxsackievirus B3 murine myocarditis

The effect of verapamil (Ver) on CVB3 murine myocarditis was investigated. It was found that Ver could aggravate the myocardial inflammation, increase the viral replication in myocardium, and raise mortality in mice with viral myocarditis when the drug was injected within the first 6 days after the CVB3 inoculation.

Adenine affects the structure and stability of telomeric sequences

Adenine occurs in the strand containing repeated G clusters in the telomeric DNA of a variety of organisms, including that of humans. The role of adenine has been investigated by constructing two sets of oligonucleotides each with one, two, or four copies of the telomeric sequence dTTTAGGG together with a control sequence in which T replaces the A residue, dTTTTGGG. Comparison of the stability and spectral properties of these two sequences in the presence of Na+ or K+ affords a basis for defining the role of adenine in these structures. In Na+, the A residue stabilizes the structure formed by each oligomer significantly, presumably by a base-pairing interaction with T. In K+, by contrast, there is little difference in stability. In two- and four-copy oligomers, the A sequence has a different structure from its T analog, as detected by CD spectroscopy. In the presence of either Na+ or K+, the tetraplexes of A and T interact with intercalators.

A tyrosyl-tRNA synthetase binds specifically to the group I intron catalytic core

The Neurospora CYT-18 protein, the mitochondrial tyrosyl-tRNA synthetase, functions in splicing group I introns in mitochondria. Here, we show that CYT-18 binds strongly to diverse group I introns that have minimal sequence homology and recognizes highly conserved structural features of the catalytic core of these introns. Inhibition experiments indicate that the intron RNA and tRNA(Tyr) compete for the same or overlapping binding sites in the CYT-18 protein. Considered together with functional analysis, our results indicate that the CYT-18 protein promotes splicing by binding to the intron core and stabilizing it in a conformation required for catalytic activity. Furthermore, the specific binding of the synthetase suggests that the group I intron catalytic core has structural similarities to tRNAs, which could reflect either convergent evolution or an evolutionary relationship between group I introns and tRNAs.

Conformational properties of B-Z junctions in DNA

The structural consequences of specific base sequences in DNA can exert a strong influence on the function of DNA. It has previously been reported that the presence of multiple B-Z conformational junctions in constructed DNA oligomers results in unusually enhanced electrophoretic gel mobilities of these oligomers [Winkle, S. A., & Sheardy, R. D. (1990) Biochemistry 29, 6514-6521]. In order to investigate this phenomenon further, we designed and synthesized several DNA oligomers capable of pure Z or B-Z junction formation for polyacrylamide gel electrophoresis studies. The results indicate that both pure Z-DNA and polymorphic B-Z-DNA oligomers exhibit unusual gel migratory properties. The results of gel mobility studies in the absence and presence of cobalt hexamine indicate that a B-Z junction corresponds to a stiff bend of the helix axis, with two or more conformers accessible at the junction site. This is a different bend and mechanism than that in oligo(A) tracts.

Structure and stability of sodium and potassium complexes of dT4G4 and dT4G4T

The ends of eukaryotic chromosomes contain specialized structures that include DNA with multiple tandem repeats of simple sequences containing clusters of G on one strand, together with proteins which synthesize and bind to these sequences. The unit repeat in the protozoan Oxytricha with the cluster dT4G4 can form structures containing tetrads of guanine residues, referred to G4 DNA, in the presence of metal ions such as Na+ or K+. We show here that, in the presence of Na+, dT4G4 forms a tetramer with parallel strands by means of a UV cross-linking assay. In the presence of K+, two further interactions are observed: at low temperature, higher order complexes are formed, provided the 3' end of the strand is G; a single 3'T inhibits this association in dT4G4T. At high temperature, these complexes dissociate, leading to a tetramer with a different ordered structure that melts only at very high temperatures. These results suggest that the cohesive properties of DNA containing G clusters might depend on associative interactions driven by a free 3'G terminus in the presence of K+, as well as by connecting antiparallel G hairpins as has been postulated.

Interaction of the dye ethidium bromide with DNA containing guanine repeats

DNA containing one or more copies of the motifs repeated in telomere sequences has unusual conformational properties. The isolated sequence from the protozoan Oxytricha, dT4G4 has the potential to form tetramers in the presence of sodium or potassium ions. We report here that these tetramers bind ethidium tightly, with an interaction that fulfills several criteria for an intercalative mechanism in the G sequence. By contrast, the 4-fold tandem repeat of this subunit, d(T4G4)4, does not interact specifically with ethidium in the presence of Na+. This difference might have a simple structural basis: the tetramer of dT4G4 forms a stack of four G-quartets in the presence of Na+ or K+, whereas the constraint imposed by the T4 "tethers" in the repeat d(T4G4)4 allows only two layers to form in the presence of Na+. In the presence of sufficient K+, the latter can partially form a four-layer G-quartet structure, which interacts with ethidium. This idea is supported by analysis of a "relaxed" sequence, dT4G4(T7G4)3, which allows formation of four G-quartets and binds ethidium in the presence of Na+ as well as K+. Ethidium (and intercalators generally) should thus be able to retard or inhibit the action of telomerase in the presence of K+.

Thermodynamics of DNA branching

Branched DNA molecules arise transiently as intermediates in genetic recombination or on extrusion of cruciforms from covalent circular DNA duplexes that contain palindromic sequences. The free energy of these structures relative to normal DNA duplexes is of interest both physically and biologically. Oligonucleotide complexes that can form stable branched structures, DNA junctions, have made it possible to model normally unstable branched states of DNA such as Holliday recombinational intermediates. We present here an evaluation of the free energy of creating four-arm branch points in duplex DNA, using a system of two complementary junctions and four DNA duplexes formed from different combinations of the same set of eight 16-mer strands. The thermodynamics of formation of each branched structure from the matching pair of intact duplexes have been estimated in two experiments. In the first, labeled strands are allowed to partition between duplexes and junctions in a competition assay on polyacrylamide gels. In the second, the heats of forming branched or linear molecules from the component strands have been determined by titration microcalorimetry at several temperatures. Taken together these measurements allow us to determine the standard thermodynamic parameters for the process of creating a branch in an otherwise normal DNA duplex. The free energy for reacting two 16-mer duplexes to yield a four-arm junction in which the branch site is incapable of migrating is + 1.1 (+/- 0.4) kcal mol-1 (at 18 degrees C, 10 mM-Mg2+). Analysis of the distribution of duplex and tetramer products by electrophoresis confirms that the free energy difference between the four duplexes and two junctions is small at this temperature. The associated enthalpy change at 18 degrees C is +27.1 (+/- 1.3) kcal mol-1, while the entropy is +89 (+/- 30) cal K-1 mol-1. The free energy for branching is temperature dependent, with a large unfavorable enthalpy change compensated by a favorable entropy term. Since forming one four-stranded complex from two duplexes should be an entropically unfavorable process, branch formation is likely to be accompanied by significant changes in hydration and ion binding. A significant apparent delta Cp is also observed for the formation of one mole of junction, +0.97 (+/-0.05) kcal deg-1 mol-1.

The use of Imagent BP in diagnostic imaging research and 19F magnetic resonance for PO2 measurements

Imagent BP (90% w/v perflubron emulsion) is radiopaque and serves as an X-ray contrast medium. Quantitative X-ray Computed Tomography, provides the means to non-invasively estimate tissue perflubron concentration providing three unique capabilities: 1) The use of the same animal for biodistribution and elimination analysis; 2) The precise geographic distribution of the agent to more accurately quantitate localized accumulations; and 3) The ability to gather physiologic data by monitoring the time dependent distribution of perflubron. It is known that the T1(-1) of 19F of perfluorochemicals is linearly related to the dissolved oxygen which allows the quantitation of PO2 in-vivo. We showed using perflubron in phanta that not only was T1(-1) linearly related to PO2 but also T2(-1) and both were insensitive to perflubron concentration. Since flow interferes with signal, the first in-vivo experiments have focused on stationary perflubron located within phagocytes. T1(-1) measured from this environment suggested a PO2 of 15-25 Torr. T1(-1) increased by nearly 50% when the FIO2 was increased from 20 to 100% reflecting an increase in intracellular PO2 on the order of 25 Torr.

Drug binding to a DNA BZ molecule: analysis by chemical footprinting

The polymorphism in a DNA 16-mer (designated BZ-II) has been investigated by means of circular dichroism (CD) spectroscopy and chemical footprinting. CD spectra indicate that, in low salt, the oligomer is fully right-handed whereas, in high salt, it possesses a B-Z conformational junction: half of the duplex is right-handed while the other half is left-handed. Treatment of BZ-II with diethyl pyrocarbonate (DEPC) confirms the existence of a left-handed segment of the duplex in high salt: enhanced DEPC scission occurs at the G residues in the alternating CG sequence. The scission patterns of the upper and lower strands in BZ-II by the reactive chemical probe MPE.Fe(II), and the antitumor antibiotics dynemicin and Fe-(II).bleomycin, are different under low salt conditions. The 3'-terminal region of both upper and lower strands and the middle region of the upper strand of BZ-II are preferential cleavage sites in low salt. This result suggests that the methylated cytosines or the alternating CG domain in the molecule perturbs the DNA structure. Under high salt conditions, the reactivity of the Z-DNA segment of BZ-II for MPE.Fe(II) and Fe(II).bleomycin is dramatically enhanced, while it is reduced in the case of dynemicin. Excess propidium (PI) eliminates preferential cleavage by each of these chemical probes in high salt conditions. This is due in part to conversion of the BZ-DNA molecule into B-DNA, as is seen by a DEPC modification experiment.(ABSTRACT TRUNCATED AT 250 WORDS)

Parallel and antiparallel Holliday junctions differ in structure and stability

Two Holliday junction analogs, JA and JP, containing identical base-paired arms have been constructed from oligonucleotides. The former is constrained to adopt an antiparallel Sigal-Alberts structure, and the latter a parallel structure, by means of single strand d(T)9 tethers. We evaluate here the free energy difference between JA and JP using two different methods. One is a direct measurement of the ratio of the equilibrium constants for formation of branched structures from intact duplexes using one labeled strand and a competition assay. The second method estimates the difference in stability from the difference in thermal denaturation temperatures of JA and JP, using urea to shift the tm of the complexes. Both methods reveal a small free energy difference between the two complexes: JA is more stable than JP by -1.1(+/- 0.4) kcal (mol junction)-1, at 25 degrees C, 5 mM-Mg2+, from the first method, and by -1.6(+/- 0.3) kcal (mol junction)-1, according to the second. DNase I and the resolvase, endonuclease I from phage T7, cleave JA differently from JP in the vicinity of the branch, indicating that the structures of these two models differ at this site. Diethyl pyrocarbonate also reveals a difference in the major grooves. Comparison of the scission patterns of JA and JP by the reactive chemical probes methidium-propyl-EDTA..Fe(II), [MPE.Fe(II)] and Cu(I)-[o-phenanthroline]2,[(OP)2Cu(I)], indicates that in both cases the branch point is a site of enhanced binding for drugs, as it is in the untethered four-arm junction containing the same core sequence at the branch.

Determination of DNA cleavage specificity by esperamicins

The esperamicins are members of a class of potent antitumor antibiotics that contain stained diacetylenic ring systems capable of forming DNA-cleaving diradicals upon reaction with thiols. Here we show that the diacetylenic ring core itself determines the sequence specificity for scission of duplex DNA): esperamicin A1, and three products of hydrolysis of the glycon, esperamicins C, D, and E, are found to retain a common sequence preference. The sugar residues exert a strong influence on the cleavage efficiency, presumably by interacting nonspecifically with DNA. The presence of a branch in the DNA is found locally to inhibit scission by esperamicins, and this effect is shown to be due to the core also.

Site-specific interaction of the antitumor antibiotic dynemicin with branched DNA molecules

A specific interaction of stable branched DNA molecules with the antitumor antibiotic dynemicin is reported. Dynemicin contains an anthraquinone and an enediyne unit, and belongs to the family of enediyne antitumor agents. DNA strand scission by dynemicin appears to involve interaction of the anthraquinone core with DNA and release of a phenyl diradical from the enediyne core that can abstract hydrogen atoms from the sugar phosphate backbone of DNA. The cleavage patterns of each labeled strand in two branched tetramers of four 16-mers are compared with those of the same strands in unbranched duplex controls. Differences between the profiles corresponding to scission of branched and duplex DNA molecules can be detected in most of the strands. The strongest differences define a specific site flanking the branch in each of two branched structures. At 18 degrees C, cleavage at strand positions demarcating the site of enhanced affinity in both junctions is observed to be 70-100% more efficient than at the corresponding sequence positions in the control duplex DNA molecules. The patterns of preferential cleavage at these sites are significantly altered in the presence of excess propidium diiodide, an intercalative drug.

Effect of dexamethasone on Coxsackievirus B2-infected rat beating heart cells in culture

The effects of dexamethasone on cultured rat beating heart cells experimentally infected with coxsackievirus B2 were investigated at an early stage (1-3 days) post challenge. Changes in the release of the cardiac enzyme, aspartate amino-transferase (AST), beating %, cytopathic effect (CPE), virus titre, ultrastructure and alterations of the electrical activity were evaluated. The protective effects of dexamethasone on infected cells were abolished except the release of AST at 5 days post infection. These results suggest that steroids may benefit patients with severe myocarditis if conventional therapy for protection of the myocardium and modulation of immunologic function are concomitantly given.

Effect of sequence on the structure of three-arm DNA junctions

We have investigated the geometry of a number of three-arm branched DNA molecules by measuring the relative electrophoretic mobilities of analogues of each junction in which one pair of arms is extended. In general, the mobilities of three species of three-arm junctions in which the duplex arms are extended pairwise differ in the presence of Mg2+. This effect is eliminated by the absence of Mg2+ or by an increase in temperature, leading us to conclude that the three-arm DNA junctions are not 3-fold symmetric, because of either preferential stacking or asymmetric kinking of the arms at the branch that occurs in the presence of Mg2+. The geometry of the junction is governed by the base sequence at the branch and 1 bp removed from the branch. The pairwise elongated analogues of junctions that contain identical base pairs at the branch or 1 bp from the branch show mobility differences; when both positions have the same sequence no mobility differences are detected even in the presence of Mg2+. Formation of a branch in three-arm DNA junctions can be seen to produce a strain or deformation that propagates about one turn of the helix from the branch, leading thymines in this region to become hyperreactive to osmium tetraoxide. Surprisingly, the effect is independent of the presence or absence of metal cations. The structure of the three-arm junction is thus quite different in character from that of four-arm junctions both in the presence and absence of high concentrations of metal cations.

Conformational preference and ligand binding properties of DNA junctions are determined by sequence at the branch

Four-arm DNA branched junctions are stable analogues of Holliday recombinational intermediates. A number of four-arm DNA junctions synthesized from oligonucleotides have now been studied. Gel mobility or chemical footprinting experiments on several immobile four-arm junctions indicate that in the presence of Mg2+, they assume a preferred conformation consisting of two helical domains, each formed by stacking a particular pair of arms on each other. We show here that a junction we designate as J1c that has the same chemical composition as one we have previously studied in detail, J1, but is formed from the four strands complementary to those of the latter, exhibits the reverse stacking preference. The pattern of self-protection of the strands of J1c exposed to Fe(II).EDTA-induced scission reveals that twofold symmetry is preserved, but the opposite pair of strands preferentially cross over. Moreover, the Fe(II).EDTA scission profiles of J1c indicate that this junction exhibits a weaker bias as to which strands cross over than is observed in J1. The preference for the dominant species in J1 is 1.3 times greater than in J1c at 4 degrees C and in the presence of 10 mM Mg2+, based on chemical reactivity data. This is confirmed by a cleavage experiment using the resolvase enzyme, endonuclease I, from bacteriophage T7. This difference could reflect either sequence-dependent differences in the equilibrium among isomers, or in the structure of these junctions. Chemical footprinting experiments using the probes MPE.Fe(II) and (OP)2Cu(I) show that the high-affinity ligand binding site in immobile junctions is determined by junction geometry.

Resolution of branched DNA substrates by T7 endonuclease I and its inhibition

Endonuclease I is a multipurpose enzyme implicated in the breakdown of host DNA, packaging of phage DNA, and recombination during the lytic cycle of bacteriophage T7. We investigate here some aspects of the substrate requirements for its activity in resolving branched intermediates similar to Holliday junctions (Holliday, R. (1964) Genet. Res. 5, 282-304) that arise in recombination. The enzyme is able to resolve branched substrates containing very short duplex arms: 4 base pairs suffice. It cleaves 5' to the branch, with a distinct preference for the non-crossover strands in Holliday-like model junctions. Ligands that interact strongly with the branch site can inhibit the enzyme, with KI values in the 10-50 microM range.

NMR angiography with enhanced quasi-half-echo scanning

Flow dephasing effects in NMR images can be significantly reduced by the use of gradient quasi-half-echo signals. They can also be reduced by moment-nulling techniques. In this paper, an efficient imaging pulse sequence, the flow-insensitive enhanced quasi-half-echo method is developed in which these two techniques are combined. This pulse sequence is used to reduce dephasing effects in images acquired to enhance blood vessels in gradient echo subtraction angiography. Both phase corrected and uncorrected quasi-half-echo reconstruction techniques are used to determine the effect on image resolution and vessel enhancement.

Asymmetric structure of a three-arm DNA junction

We present here experimental evidence that three-arm branched DNA molecules form an asymmetric structure in the presence of Mg2+. Electrophoretic mobility and chemical and enzymatic footprinting experiments on a three-arm branched DNA molecule formed from three 16-mer strands are described. The electrophoretic mobilities of three species of a three-arm junction in which pairs of arms are extended are found to differ in the presence of Mg2+: one combination of elongated arms migrates significantly faster than the other two. This effect is eliminated in the absence of Mg2+, leading us to suggest that the three-arm DNA junction forms an asymmetric structure due to preferential stacking of two of the arms at the junction in the presence of Mg2+. The pattern of self-protection of each 16-mer strand of the core complex exposed to Fe(II).EDTA and DNase I scission is unique, consistent with formation of an asymmetric structure in the presence of Mg2+. We conclude that three-arm junctions resemble four-arm junctions in showing preferential stacking effects at the branch site. Comparison of the scission patterns of linear duplexes and the branched trimer by the reactive probes methidiumpropyl-EDTA.Fe(II) [MPE.Fe(II)] and Cu(I)-[o-phenanthroline]2 [(OP)2CuI] further indicates that the branch point represents a site of enhanced binding for drugs, as it does in the four-arm case. Reaction with diethyl pyrocarbonate (DEPC), a purine-specific probe sensitive to conformation, is enhanced at the branch site, consistent with loosening of base pairing or unpairing at this point.(ABSTRACT TRUNCATED AT 250 WORDS)

Characterization of a bimobile DNA junction

We present here a chemical and enzymatic footprinting analysis of a branched DNA molecule formed from four complementary 50-mer strands. These strands are designed to form a stable junction, in which two steps of branch point migration freedom are possible. Exposure of the junction to Fe(II).EDTA shows protection of 3 or 4 residues in each strand at the branch, while two resolvase enzymes (endonuclease VII from phage T4 and endonuclease I from phage T7), cleave all four strand near the branch. Chemical footprinting of this junction using the reagents MPE.Fe(II) and (OP)2Cu(I) shows that the branch site is hyper-reactive to cutting induced by these probes as it is in an immobile four-arm junction. The effects involve more residues than in the immobile case. In the absence of divalent cations, the structure of the junction alters, sites of enhanced cleavage by MPE.Fe(II) and (OP)2Cu(I) disappear, and purines at the branch become reactive to diethyl pyrocarbonate. Our interpretation of these results is based on the properties of immobile junction analogs and their response to these probes. In the presence of Mg2+, the three migrational isomers coexist, each probably in the form of a 2-fold symmetric structure with two helical arms stacked.

Charge dependence of Fe(II)-catalyzed DNA cleavage

The effect of charge of the Fe(II) reagent used to induce DNA strand cleavage reactions in the presence of a source of reducing equivalents is investigated using two oligonucleotide models. The first consists of the two strands dA20 and dT20, and an equimolar complex between them. The second is a short four-arm branched DNA complex composed of four 16-mer strands. In the former case, cleavage of the 1:1 complex by three reagents with different formal charge, Fe(II).EDTA2-, Fe(II).EDDA and Fe2+, is comparable in rate to that of the individual dT20 and the dA20 strands. While the three reagents show similar cleavage rates for the duplex and single stranded molecules, they give distinctive cutting patterns in the DNA tetramer, consistent with the presence of a site of excess negative charge at the branch point. Scission induced by Fe(II).EDTA2- shows lower reactivity at the branch site relative to duplex controls, whereas Fe(II)2+ shows enhanced reactivity. Formally neutral Fe(II).EDDA shows weak loss of cutting reactivity at the branch. The position of attack by Fe(II)2+ in the branched tetramer is shifted with respect to those of Fe(II).EDTA2- or Fe(II).EDDA; a slower migrating species is also detected in the scission of dA20.dT20 duplex by Fe(II) reaction. These results suggest that the Fe(II)2+ reaction proceeds by a different mechanism from the other agents. The difference in cutting profiles induced by the neutral and negatively charged chelated complexes is consistent with a local electrostatic repulsion of a negatively charged source of radicals, not a positively charged one.

Construction and analysis of parallel and antiparallel Holliday junctions

The Holliday junction is a four-stranded DNA intermediate that arises during recombination reactions. We have designed and constructed a set of Holliday junction analogs that model each of the ideal conformations available to a 2-fold symmetric four-arm junction. The strategy used is to connect two arms of a junction molecule with a short tether of thymidines. These DNA molecules share a common core sequence but have different arms that are connected so that each molecule is constrained in either an antiparallel or a parallel structure. For tethered antiparallel molecules the identity of the crossover strands is determined by which arms are connected. Different arm connections gave molecules representing each of the two antiparallel crossover isomers. Two parallel molecules that differ in the length and position of the tether exhibit opposite biases in their choice of crossover strands. Thus, a physical constraint applied at a distance from the branch point can determine the conformation of a junction.

Drug binding by branched DNA: selective interaction of the dye stains-all with an immobile junction

The thiacarbocyanine dye Stains-All (4,5:4',5'-dibenzo-3,3'-diethyl-9-methylthiacarbocyanine bromide) is one of a large number of cyanine dyes introduced as photosensitizers in the photographic industry. Stains-All is used in histology as a stain for nucleic acids, proteins, polysaccharides, and lipids. We report here that the dye colors branched DNA molecules differently from linear duplexes and use footprinting experiments with methidiumpropyl-EDTA-Fe(II) [MPE.Fe(II)] and bis(o-phenanthroline)copper(I) [(O-P)2Cu(I)] to show that Stains-All interacts preferentially at the branch point of a four-arm DNA structure. A titration experiment allows us to estimate that the interaction of the dye with the branch has a dissociation constant below 45 nM, tighter than that of ethidium or methidium by over 2 orders of magnitude. Probing the interaction with the purine-specific reagent diethyl pyrocarbonate (DEPC) implies that the dye induces an asymmetric distortion near the branch in the major grooves of double helix in the junction.

Drug binding by branched DNA: selective interaction of tetrapyridyl porphyrins with an immobile junction

The differential binding of a number of water-soluble cationic porphyrins to a branched DNA molecule is reported. Tetrakis(4-N-methylpyridiniumyl)porphine (H2TMpyP-4) interacts near the branch point with an immobile DNA junction formed from four 16-mer strands. Its Cu(II) and Ni(II) derivatives show stronger preferential binding in the neighborhood of the branch point. Axially liganded derivatives, Zn, Co, and Mn, also interact near this branch point, but in a different way. We use the reagents methidiumpropyl-EDTA.Fe(II) [MPE.Fe(II)] and bis(o-phenanthroline)copper(I) [(OP)2Cu(I)] to cleave complexes of DNA duplex controls and the junction with these porphyrins. The resulting cleavage patterns are consistent with previous evidence that the branch point provides a strong site for intercalative binding agents, which is not available in unbranched duplexes of identical sequence. The preferential scission by (OP)2Cu(I) in the presence of Ni and Cu porphyrins near the branch point exceeds that seen for any agents we have studied. This hyperreactivity is not seen in the case of porphyrins with axial ligands, ZnTMpyP-4, CoTMpyP-4, and MnTMpyP-4, although these also interact near the branch point. The Zn derivative tends to protect sites close to the branch point from cutting, while the Co and Mn porphyrins moderately enhance cleavage of sites in this region.

Drug binding by branched DNA molecules: analysis by chemical footprinting of intercalation into an immobile junction

Branched DNA structures interact with drugs differently from unbranched control duplexes of similar sequence. A specific interaction between the reagent (methidiumpropyl-EDTA).Fe(II) [MPE.Fe(II)] and a branched DNA molecule formed from 16-mer oligonucleotide strands has been reported [Guo, Q., Seeman, N. C., & Kallenbach, N. R. (1989) Biochemistry 28, 2355-2359]. The structure of the branched molecule is thought to be made up of two double-helical stacking domains with an overall twofold symmetry across the branch site. The MPE-Fe(II) interaction occurs predominantly at or adjacent to the branch site and is eliminated by a second intercalator, propidium iodide. Further studies on the nature and properties of this site are presented here. Comparison of the patterns of scission of linear duplex and branched tetramer by EDTA.Fe(II), MPE.Fe(II), and Cu(I)-(o-phenanthroline)2 [(OP)2Cu(I)] provides a higher resolution picture of the site of enhanced binding. In particular, the sensitive footprinting afforded by (OP)2Cu(I) allows us to localize the major site of preferential interaction with propidium precisely to the branch point itself, with a roughly twofold symmetric pattern of cuts resulting. In detail, the differential pattern with respect to each duplex control is distinct for each arm of the junction. Excess propidium results in apparent reversal of the crossover isomer of the junction, indicating a possible additional avenue for the action of drugs in biological systems--effects on the products of recombination.

Investigation of blood flow dynamics by NMR angiography

Gradient-echo sequences with different amount of flow velocity compensation have been studied using cardiac gating in cine mode MR angiography. The initial results on the leg of a healthy volunteer indicate that the circulatory dynamics may be studied qualitatively by means of these flow-sensitive angiograms.

Treatment of experimental Coxsackie B-3 viral myocarditis with Astragalus membranaceus in mice

A murine model system for observing the effect of Astragalus Membranaceus (AM) on experimental myocarditis caused by Coxsackie B-3 virus (CB3V) was developed in 4-week-old male BALB/C mice. Gross, histopathologic and ultrastructural examinations of the infected-AM treated group showed that the severity and involved area of the myocardial lesions became milder and smaller than those in the infected-NS treated mice. The total lesion area, and the total lesion area/total myocardial area examined (%) and virus titer in the former group were also smaller and lower than those in the latter group. The results suggest that AM is effective in the inhibition of Coxsackie B virus propagation and protection of myocardium in mouse myocarditis.

DNase I cleavage of branched DNA molecules

We report here a potentially useful signature of branched DNA structures. The base 5' to the branch and the five bases flanking the 3' side of the branch site are protected from cleavage by DNase I in both three- and four-arm branched DNA molecules. Our procedure is to measure the cleavage profile for each 5' -labeled strand in a control duplex and compare this with that of the same strand in a branched structure under conditions yielding less than one cut per strand. The resulting cleavage pattern in an immobile four-arm junction is roughly 2-fold symmetric, consistent with the pattern of Fe(II).EDTA-induced cleavage that has been observed previously. In the three-arm junction, the DNase I cleavage pattern is asymmetric, indicating lack of 3-fold symmetry. A variable pattern of protection occurs to the 5' side of the branch in some strands only for both three- and four-arm junctions, extending 2-4 residues 5' to the branch.

[Treatment of ulcerative colitis by traditional Chinese medicine and dynamic study of immune functions]

The effect of the traditional Chinese medicinal herbs enema and enteric-coated capsules in the treatment of ulcerative colitis (UC) were compared in 260 cases. The immune complexes and the dynamic change of autoantibodies were monitored in 28 out of the 260 cases before and after treatment. The following results were observed. (1) There was no significant difference in the total effective rate between the enema group and the oral capsule group (93.3% and 87.5% respectively), but the recovery rates of purulent hemafecia, mucusfecia and erosion accompanying colitis, etc. in the former group were higher than those in the latter (P less than 0.01). (2) The circulating immune complexes were found 43 times above the normal range in 17 cases with positive rate 60.7%, and tended to decrease as the condition became better after treatment. Antinuclear antibodies were determined by the indirect fluorescent immune method and the indirect enzyme labelling method and the positive rates were 53.6% and 64.7% respectively, both being much higher than those in the controls (P less than 0.01).

[Effect of dexamethasone on Coxsackie B-2 virus-infected rat beating heart cells in culture]

The effects of dexamethasone (Dex) on cultured rat beating heart cells infected with 100 TCID-50 Coxsackie virus B-2 (CB2V) were observed. The beating % began to decrease in the infected group 2 or 3 d post-challenge. Meanwhile, the cytopathic effect (CPE) appeared rapidly from 1+ to 3+. In the infected and Dex-treated group 1 h after inoculation, the beating % and CPE in the whole flask were significantly higher and less, respectively, than that in the group infected (P less than 0.05) at the same intervals. At 5 d after challenge, the beating % in the whole flask was significantly higher than that in the infected group. The cardiac enzyme-aspartate aminotransferase (AST) in the infected group was higher than that in the infected and Dex-treated group (P less than 0.01) through 3-5 d post-challenge. Moreover, the AST levels in these 2 groups were also higher than that in the uninfected group, Dex control group at the same intervals (P less than 0.01). Ultrastructural findings were parallel to the results of CPE through 1-5 d post-challenge in these 4 groups. It is suggested that the protective effect of Dex on cultured beating heart cells infected with CB2V occurred in the early stages after infection. It is surmised that steroids can probably save the lives of patients with severe myocarditis if the conventional therapy for protecting the myocardium and improving immunity were administered together.

Site-specific interaction of intercalating drugs with a branched DNA molecule

The interaction of a stable branched DNA molecule with an intercalative drug is probed by hydroxyl radical scission. Methidiumpropyl-EDTA.Fe(II) [MPE.Fe(II)], consisting of an intercalating ring system tethered to EDTA.Fe(II), produces the hydroxyl radicals by means of a Fenton reaction. The cleavage patterns of each labeled strand in a branched tetramer of four 16-mers are compared with those of the same strands in unbranched duplex controls. Strong differences between the profiles corresponding to scission of branched and duplex DNA molecules are seen in each of the strands at low MPE/DNA ratios. A specific site in the branched structure interacts preferentially with the drug, while other regions of the molecule are protected from cleavage. At 4 degrees C, cutting at strand positions demarcating the site of enhanced affinity is observed to be 60-100% more efficient than at the corresponding sequence positions in the control duplex DNA molecules; the degree of protection is comparable. Cleavage in the vicinity of the preferred site occurs at residues flanking the branch point. The reactive Fe(II) group appears to be centered within two residues of the branch point, and the site of preferential intercalation may be between the two base pairs abutting the branch point in one of the two helical domains. The pattern of preferential cutting at this site is eliminated in the presence of excess propidium diiodide, another intercalative drug.