Structural polymorphism in a tubercidin analogue of the DNA double helix

The neurotoxic beta-amyloid (Abeta) peptide fragment Abeta(25-35) has been suggested to exert its deleterious effects on cells via production of hydrogen peroxide. In human platelets and in the presence of DMSO to prevent production of hydroxyl radicals from hydrogen peroxide, both Abeta(25-35) and hydrogen peroxide were found to increase intracellular calcium levels. Hydrogen peroxide in addition reduced the calcium response to thrombin, whereas this was not seen with Abeta(25-35). A similar pattern of effects to those seen with hydrogen peroxide were also seen with the neurotoxic aldehyde lipid peroxidation product 4-hydroxy-2-nonenal (HNE). The initial increase in calcium produced by hydrogen peroxide was not affected by EGTA, but was partially prevented by dithiothreitol. The calcium response to Abeta(25-35) [which was also seen with Abeta(1-40) and Abeta(1-42) but not with the inactive peptide Abeta(40-1)] consisted of an EGTA-sensitive and an EGTA-resistant component, of which the latter was also sensitive to DTT. Hydrogen peroxide increased basal phosphoinositide breakdown in rat brain miniprisms and decreased the responses to noradrenaline, carbachol and veratrine. The specific binding of [3H]inositol-1,4,5-trisphosphate ([3H]Ins(1,4,5)P3) to its receptor recognition site in human platelet membranes was increased by Abeta(25-35) but remained unchanged following hydrogen peroxide treatment. It is concluded that under conditions where production of hydroxyl radicals from hydrogen peroxide is blocked, hydrogen peroxide and Abeta(25-35) produce their effects on calcium by affecting the mobilisation of intracellular calcium. The qualitative differences in the calcium responses of these two agents can be explained (a) by an additional effect of Abeta(25-35) upon calcium entry and (b) by differences in their effects upon the Ins(1,4,5)P3 receptor.     

Sequence-specific recognition of double helical RNA and RNA.DNA by triple helix formation

The stabilities of eight triple helical pyrimidine.purine.pyrimidine structures comprised of identical sequence but different RNA (R) or DNA (D) strand combinations were measured by quantitative affinity cleavage titration. The differences in equilibrium binding affinities reveal the importance of strand composition. For the sequences studied here, the stabilities of complexes containing a pyrimidine third strand D or R and purine.pyrimidine double helical DD, DR, RD, and RR decrease in order: D + DD, R + DD, R + DR, D + DR > R + RD, R + RR > D + RR, D + RD (pH 7.0, 25 degrees C, 100 mM NaCl/1 mM spermine). These findings suggest that RNA and DNA oligonucleotides will be useful for targeting (i) double helical DNA and (ii) RNA.DNA hybrids if the purine Watson-Crick strand is DNA. However, RNA, but not DNA, oligonucleotides will be useful for sequence-specific binding of (i) double helical RNA and (ii) RNA.DNA hybrids if the purine Watson-Crick strand is RNA. This has implications for the design of artificial ligands targeted to specific sequences of double helical RNA and RNA.DNA hybrids.     

Analysis of the stability of hemoglobin S double strands

The deoxyhemoglobin S (deoxy-HbS) double strand is the fundamental building block of both the crystals of deoxy-HbS and the physiologically relevant fibers present within sickle cells. To use the atomic-resolution detail of the hemoglobin-hemoglobin interaction known from the crystallography of HbS as a basis for understanding the interactions in the fibers, it is necessary to define precisely the relationship between the straight double strands in the crystal and the twisted, helical double strands in the fibers. The intermolecular contact conferring the stability of the double strand in both crystal and fiber is between the beta6 valine on one HbS molecule and residues near the EF corner of an adjacent molecule. Models for the helical double strands were constructed by a geometric transformation from crystal to fiber that preserves this critical interaction, minimizes distortion, and makes the transformation as smooth as possible. From these models, the energy of association was calculated over the range of all possible helical twists of the double strands and all possible distances of the double strands from the fiber axis. The calculated association energies reflect the fact that the axial interactions decrease as the distance between the double strand and the fiber axis increases, because of the increased length of the helical path taken by the double strand. The lateral interactions between HbS molecules in a double strand change relatively little between the crystal and possible helical double strands. If the twist of the fiber or the distance between the double strand and the fiber axis is too great, the lateral interaction is broken by intermolecular contacts in the region around the beta6 valine. Consequently, the geometry of the beta6 valine interaction and the residues surrounding it severely restricts the possible helical twist, radius, and handedness of helical aggregates constructed from the double strands. The limitations defined by this analysis establish the structural basis for the right-handed twist observed in HbS fibers and demonstrates that for a subunit twist of 8 degrees, the fiber diameter cannot be more than approximately 300 A, consistent with electron microscope observations. The energy of interaction among HbS molecules in a double strand is very slowly varying with helical pitch, explaining the variable pitch observed in HbS fibers. The analysis results in a model for the HbS double strand, for use in the analysis of interactions between double strands and for refinement of models of the HbS fibers against x-ray diffraction data.     

Identification of hydroxyhydroquinone in coffee as a generator of reactive oxygen species that break DNA single strands

A component in instant coffee that caused DNA single strand breaks was isolated by successive ethyl acetate:ethanol extraction, silica gel column chromatography and high performance liquid chromatography using a reversed phase column. The active component was identified as hydroxyhydroquinone (HHQ). Incubation of supercoiled pBR 322 DNA with HHQ at 0.1 mM in phosphate buffer (pH 7.4) at 37 degreesC for 1 h caused single strand breaks, and reactive oxygen species, hydrogen peroxide and hydroxyl radical, were involved in DNA breaking by HHQ. Genotoxic effects of HHQ including DNA breaking activity through generation of reactive oxygen species have been well-demonstrated because the component is considered to be an important genotoxic intermediate metabolite of benzene. Occurrence of HHQ in coffee must have an important significance to consider genotoxicity of coffee.     

The conducting form of gramicidin A is a right-handed double-stranded double helix

The linear pentadecapeptide antibiotic, gramicidin D, is a naturally occurring product of Bacillus brevis known to form ion channels in synthetic and natural membranes. The x-ray crystal structures of the right-handed double-stranded double-helical dimers (DSDH) reported here agree with 15N-NMR and CD data on the functional gramicidin D channel in lipid bilayers. These structures demonstrate single-file ion transfer through the channels. The results also indicate that previous crystal structure reports of a left-handed double-stranded double-helical dimer in complex with Cs+ and K+ salts may be in error and that our evidence points to the DSDH as the major conformer responsible for ion transport in membranes.     

Design and clinical application of a double helix electrode for functional electrical stimulation

Disrupting bacterial biofilms is necessary for a wide application domains such as reusable medical devices, or systems of pipes for water or fluids in cosmetics, food and chemicals industry. Bacterial cells embedded in a biofilm are less susceptible to disinfectants than suspended cells. This property is referable to the structure of the biofilm itself. The gangue of exopolymers and the thickness of a 5-day-old biofilm of Escherichia coli (more than 200 layers of bacteria), contribute to this decrease of susceptibility. The present work deals with the release of an Escherichia coli biofilm by the sequential action of enzymes and a phenolic disinfectant on the one hand, and by the sequential or simultaneous action of surfactants and the previous disinfectant on the other hand. The decrease of bacteria count per mm2 and the Scanning Electron Microscope observations exhibited a synergic action in every case. Nevertheless, Escherichia coli biofilms quickly reconstructed even after exposition to the previous treatment.     

Both DNA strands of antibody genes are hypermutation targets

During the maturation of the immune response, antibody genes are subjected to localized hypermutation. Mutations are not evenly distributed along the V gene; intrinsic hot spots exist that are correlated with primary sequence motifs. Although the mechanism of hypermutation remains unknown, it has been proposed to exhibit DNA strand polarity because purine residues on the coding strand are more frequently targeted for mutation than pyrimidines. However, this polarity may not be an intrinsic property of the hypermutation mechanism but a consequence of evolutionary-selected peculiarities of V gene sequences. Furthermore, the possibility that both strands are hypermutation targets has received little attention. To discriminate between these possibilities, we have analyzed the average frequency of mutations of each of the three bases of all nucleotide triplets by using large databases taken from both V and non-V mutation targets. We also have reassessed the sequence motifs associated with hot spots. We find that even in non-Ig sequences, A mutates more than T, consistent with a strand-dependent component to targeting. However, the mutation biases of triplets and of their inverted complements are correlated, demonstrating that there is a sequence-specific but strand-independent component to mutational targeting. Thus, there are two aspects of the hypermutation process that are sensitive to local DNA sequences, one that is DNA strand-dependent and the other that is not.     

Structure-based discovery of ligands targeted to the RNA double helix

Ligands capable of specific recognition of RNA structures are of interest in terms of the principles of molecular recognition as well as potential chemotherapeutic applications. We have approached the problem of identifying small molecules with binding specificity for the RNA double helix through application of the DOCK program [Kuntz, I. D., Meng, E. C., and Shoichet, B. K. (1994) Acc. Chem. Res. 27, 117-123], a structure-based method for drug discovery. A series of lead compounds was generated through a database search for ligands with shape complementarity to the RNA deep major groove. Compounds were then evaluated with regard to their fit into the minor groove of B DNA. Those compounds predicted to have an optimal fit to the RNA groove and strong discrimination against DNA were examined experimentally. Of the 11 compounds tested, 3, all aminoglycosides, exhibited pronounced stabilization of RNA duplexes against thermal denaturation with only marginal effects on DNA duplexes. One compound, lividomycin, was examined further, and shown to facilitate the ethanol-induced B to A transition in calf thymus DNA. Fluorine NMR solvent isotope shift measurements on RNA duplexes containing 5-fluorouracil provided evidence that lividomycin binds in the RNA major groove. Taken together, these results indicate that lividomycin recognizes the general features of the A conformation of nucleic acids through deep groove binding, confirming the predictions of our DOCK analysis. This approach may be of general utility for identifying ligands possessing specificity for additional RNA structures as well as other nucleic acid structural motifs.     

Reliability of closed double helix electrode for functional electrical stimulation

The reliability of a closed double helix electrode in the lower limbs was studied. This electrode is an implanted intramuscular electrode and is used for a totally implantable functional electrical stimulation system. Eighty electrodes were evaluated retrospectively with a mean period of 15 months. The total implant time was 1222 electrode months. The cumulative proportion surviving was 0.934 at 6 months, 0.855 at 1 year, 0.765 at 2 years, and 0.730 after 30 months. Fifteen of 80 electrodes failed, seven showed increasing electrode impedance, and eight had undesirable changes in recruitment. Of the failed electrodes, 2/3 failed during the first 10 months. The reliability was 0.91 at 6 months and 0.80 at 1 year after implantation in all muscle groups. The closed double helix electrode displayed an increased reliability when compared with the open double helix electrode at 6 months, and an equivalent reliability as compared with the electrodes developed by Handa and colleagues at 6 months and 1 year, using the chi squared test for independence. This study suggests that the closed double helix electrode has an acceptable reliability and can be used as a part of a totally implantable functional electrical stimulation system.     

Enzymatic DNA methylation as an aging mechanism

By analysis of 70 functional parameters of organism it has been shown that the senescence of human organs starts from the age of 20 +/- 10 years and it has more or less a linear character in the most cases. Judging by the averaged aging rate, human maximal lifespan can be equal to about 145 years. An aging model has been proposed according to it the functional involution is caused by cells destructing and is a result of gradual accumulation of special mutations in genome. The evidences has been obtained that enzymatic DNA methylation is a powerful generator for the 5mC-->T+C transition, constantly occurring with each cell division. It has been found that the age-related loss of the most part or all 5mC residues from DNA coincides with both the Hayflick limit in cell lines and the maximal lifespan of different animal species studied. The rate of DNA hypomethylation is proportional to the cell aging rate in vitro and in vivo. The 5mC-->T transitions contribute more than half of all point mutations, accumulated in genome of vertebrates during evolution. These substitutions occur ten times more often in the methylated sites than in other positions of DNA and they disproportional contribute to the general mutagenesis and to the hereditary human diseases. The conclusion has been made that DNA methylation meet the requirements of the main criterions of an aging biomarker and it can be considered as a mechanism for genetically programmed accumulation of mutations with aging. In immortal cell lines this mechanism starts working in the reverse direction, increasing the 5mC content in DNA.