The formation pathway of i-motif tetramers

The i-motif is a four-stranded structure formed by two intercalated parallel duplexes containing hemiprotonated C•C+ pairs. In order to describe the sequence of reactions by which four C-rich strands associate, we measured the formation and dissociation rates of three [TCn]4 tetramers (n = 3, 4 and 5), their dissociation constant and the reaction order for tetramer formation by NMR. We find that TCn association results in the formation of several tetramers differing by the number of intercalated C•C+ pairs. The formation rates of the fully and partially intercalated species are comparable but their lifetimes increase strongly with the number of intercalated C•C+ pairs, and for this reason the single tetramer detected at equilibrium is that with optimal intercalation. The tetramer half formation times vary as the power −2 of the oligonucleotide concentration indicating that the reaction order for i-motif formation is 3. This observation is inconsistent with a model supposing association of two preformed duplex and suggests that quadruplex formation proceeds via sequential strand association into duplex and triplex intermediate species and that triplex formation is rate limiting

Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference

Through binding and fluorescence studies of oligonucleotides covalently attached to a pyrene group via one carbon linker at the sugar residue, we previously found that pyrene-modified RNA oligonucleotides do not emit well in the single-stranded form, yet the attached pyrene emits with a significantly high quantum yield upon binding to a complementary RNA strand. In sharp contrast, similarly modified pyrene–DNA probes exhibit very weak fluorescence both in the double-stranded and single-stranded forms. The pyrene-modified RNA oligonucleotides therefore provide a useful tool for monitoring RNA hybridization. The purpose of this paper is to present the structural basis for the different fluorescence properties of pyrene-modified RNA/RNA and pyrene-modified DNA/DNA duplexes. The results of absorption, fluorescence anisotropy and circular dichroism studies all consistently indicated that the pyrene attached to the RNA duplex is located outside of the duplex, whereas the pyrene incorporated into the DNA duplex intercalates into the double helix. (1)H NMR measurements unambiguously confirmed that the pyrene attached to the DNA duplex indeed intercalates between the base pairs of the duplex. Molecular dynamics simulations support these differences in the local structural elements around the pyrene between the pyrene–RNA/RNA and the pyrene–DNA/DNA duplexes

Semihemoglobins, High Oxygen Affinity Dimeric Forms of Human Hemoglobin Respond Efficiently to Allosteric Effectors without Forming Tetramers

Significant reduction in oxygen affinity resulting from interactions between heterotropic allosteric effectors and hemoglobin in not only the unligated derivative but also the fully ligated form has been reported (Tsuneshige, A., Park, S. I., and Yonetani, T. (2002) Biophys. Chem. 98, 49-63; Yonetani, T., Park, S. I., Tsuneshige, A., Imai, K., and Kanaori, K. (2002) J. Biol. Chem. 277, 34508-34520). To further investigate this effect in more detail, alpha- and beta-semihemoglobins, namely, alpha(heme)beta(apo) and alpha(apo)beta(heme), respectively, were prepared and characterized with respect to the impact of allosteric effectors on both conformation and ligand binding properties. Semihemoglobins are dimers characterized by a high affinity for oxygen and lack of cooperativity. We found that, compared with stripped conditions, semihemoglobins responded to effectors (inositol hexaphosphate and L35) by decreasing the affinity for oxygen by 60- and 130-fold for alpha- and beta-semihemoglobins, respectively. 1H NMR and sedimentation velocity experiments carried out with their ligated and unligated forms in the absence and presence of effectors revealed that semihemoglobins always remain as single-heme-carrying dimers. Recombination kinetics of their photolyzed CO derivatives showed that effectors did indeed interact with their ligated forms. Measurements of the Fe-His stretching mode show that the semihemoglobins undergo a large ligand binding-induced conformational shift and that both ligand-free and ligand derivatives respond to the presence of effectors. Contradictions to the Monod-Wyman-Changeaux/Perutz allosteric model arise since 1) the modulation of ligand affinity is not achieved in semihemoglobins by the formation of a low affinity T conformation (quaternary effect) but by direct interaction with effectors, 2) effectors do interact significantly with ligated forms of high affinity semihemoglobins, and 3) modulation of the ligand affinity and the cooperativity are not necessarily linked but instead can be separated into two distinct phenomena that can be isolated

Solution structure and stability of the DNA undecamer duplexes containing oxanine mismatch

Solution structures of DNA duplexes containing oxanine (Oxa, O) opposite a cytosine (O:C duplex) and opposite a thymine (O:T duplex) have been solved by the combined use of 1H NMR and restrained molecular dynamics calculation. One mismatch pair was introduced into the center of the 11-mer duplex of [d(GTGACO6CACTG)/d(CAGTGX17GTCAC), X = C or T]. 1H NMR chemical shifts and nuclear Overhauser enhancement (NOE) intensities indicate that both the duplexes adopt an overall right-handed B-type conformation. Exchangeable resonances of C17 4-amino proton of the O:C duplex and of T17 imino proton of O:T duplex showed unusual chemical shifts, and disappeared with temperature increasing up to 30°C, although the melting temperatures were >50°C. The O:C mismatch takes a wobble geometry with positive shear parameter where the Oxa ring shifted toward the major groove and the paired C17 toward the minor groove, while, in the O:T mismatch pair with the negative shear, the Oxa ring slightly shifted toward the minor groove and the paired T17 toward the major groove. The Oxa mismatch pairs can be wobbled largely because of no hydrogen bond to the O1 position of the Oxa base, and may occupy positions in the strands that optimize the stacking with adjacent bases

Japan Sea, opening history and mechanism: A synthesis

Laurent Jolivet est Professeur à l'Université d'Orléans au 1er Septembre 2009International audienceThe respective tectonic effects of back arc spreading and continental collision in Asia are considered either as two independent processes or as closely interrelated. Extrusion tectonics assumes that the opening of the South China Sea and the left-lateral motion along the Red River fault are geometrically linked in a pull-apart manner. This model is not accepted by several workers because the structural link between the two processes is not clearly demonstrated. In the case of the Japan Sea, we can show without ambiguity that back arc opening was controlled by large intracontinental strike-slip faults which can be easily understood as effects of the India-Asia collision far from the indenter. The Japan Sea opened in the early Miocene in a broad pull-apart zone between two major dextral strike-slip shear zones. The first one extends from north Sakhalin to central Japan along 2000 km, it has accommodated about 400 km of finite displacement. Deformation along it varies from dextral transpression in the north to dextral transtension in the south. The second is between Korea and SW Japan and has accommodated a smaller displacement of about 200 km. The extensional domain in between lies in the back arc region of Japan. Distributed stretching of the arc crust resulted in the formation of most of the Japan Sea, while localized oceanic spreading at the southern termination of the eastern transpressional shear zone shaped the Japan Basin. The first oceanic crust was formed in a small triangle based on the eastern shear zone, and spreading propagated westward inside the pull-apart region. Timing of oceanic crust formation, of formation of the dextral shear zones and of block rotation in between, as well as the internal structure of the basins and the geometry of deformation along the master shear zones are used to reconstruct the opening history. This evolution is discussed by comparison to other manifestations of the arc and back arc activity, such as the history of sedimentation and volcanism. The paper then suggests that the collision of India can have tectonic consequences as far north as Japan and Sakhalin and describes the geometrical relation of back arc opening there and diffuse extrusion

Source distribution of acoustic emissions during an in-situ direct shear test: Implications for an analog model of seismogenic faulting in an inhomogeneous rock mass

We monitored acoustic emission (AE) events during an in-situ direct shear test on a specimen composed of a slate-dominant alternation of slate and sandstone, measuring 0.5 m long, 0.5 m wide and 0.2 m high. The test was conducted in a survey tunnel for an underground powerhouse in central Japan. The AE epicenters located on a fractured plane are compared with the locations of joints and a loosening seam, the height distribution of the fractured plane, and the horizontal movement of the test block prior to failure. We conclude that an initially intact region of rock bounded by the joints and the seam is fractured, generating the AE. Considering these results in connection with asperity models of seismogenic faulting for a subduction-zone earthquake, the significant contrast of stress conditions derived from the geological inhomogeneity and the uneven fractured plane is analogous to that due to subducted seamounts and horst-graben structures on a subducted oceanic plate. For an inland earthquake, the intact regions on an expected shear plane can be considered to be a portion of the fault asperity that causes strong ground motion, while the weakened portion can be considered to correspond to a region of aseismic creep. Consequently, large-scale inhomogeneous rock fracturing experiments such as the in-situ direct shear test may provide useful insights as analog models of seismogenic faulting. Furthermore, understanding of inhomogeneous rock-mass fracturing obtained from such experiments will not only contribute to a better understanding of the mechanism of earthquakes but also provide valuable knowledge for AE monitoring applications in rock engineering, such as the predictions of rockbursts in mines and the monitoring of fractures around large underground chambers