Molecular Dynamics Simulation of a PNA·DNA·PNA Triple Helix in Aqueous Solution

Molecular dynamics simulations have been used to explore the conformational flexibility of a PNA·DNA·PNA triple helix in aqueous solution. Three 1.05 ns trajectories starting from different but reasonable conformations have been generated and analyzed in detail. All three trajectories converge within about 300 ps to produce stable and very similar conformational ensembles, which resemble the crystal structure conformation in many details. However, in contrast to the crystal structure, there is a tendency for the direct hydrogen-bonds observed between the amide hydrogens of the Hoogsteen-binding PNA strand and the phosphate oxygens of the DNA strand to be replaced by water-mediated hydrogen bonds, which also involve pyrimidine O2 atoms. This structural transition does not appear to weaken the triplex structure but alters groove widths and so may relate to the potential for recognition of such structures by other ligands (small molecules or proteins). Energetic analysis leads us to conclude that the reason that the hybrid PNA/DNA triplex has quite different helical characteristics from the all-DNA triplex is not because the additional flexibility imparted by the replacement of sugar−phosphate by PNA backbones allows motions to improve base-stacking but rather that base-stacking interactions are very similar in both types of triplex and the driving force comes from weak but definate conformational preferences of the PNA strands.

Molecular Dynamics Simulations of the d(TAT) Triple Helix

Molecular dynamics (MD) simulations have been used to study the dynamical and time-averaged characteristics of the DNA triple helix d(T)10âd(A)10âd(T)10. The structures sampled during the trajectory resemble closely the B-type model for the DNA triplex proposed on the basis of NMR data, although there are some subtle differences. Alternative P- and A-type conformations for the triplex, suggested from X-ray experiments, are not predicted to contribute significantly to the structure of the DNA triplex in solution. Comparison with the best available experimental data supports the correctnes of the MD-generated structures. The analysis of the collected data gives a detailed picture of the characteristics of triple-helix DNA. A new and interesting pattern of hydration, specific for triplex DNA, is an important observation. The results suggest that molecular dynamics can be useful for the study of novel nucleic acid structures.

Decompression during Late Proterozoic Al2SiO5 Triple-Point Metamorphism at Cerro Colorado, New Mexico

An outstanding problem in understanding the late Proterozoic tectonic assembly of the southwest is identifying the tectonic setting associated with regional metamorphism at 1.4 Ga. Both isobaric heating and cooling, and counter-clockwise looping PT paths are proposed for this time. We present a study of the Proterozoic metamorphic and deformation history of the Cerro Colorado area, southern Tusas Mountains, New Mexico, which shows that the metamorphism in this area records near-isothermal decompression from 6 to 4 kbar at ca. 1.4 Ga. We do not see evidence for isobaric heating at this time. Decompression from peak pressures is recorded by the reaction Ms + Grt = St + Bt, with a negative slope in PT space; the reaction Ms + Grt = Sil + Bt, which is nearly horizontal in PT space; and partial to total pseudomorphing of kyanite by sillimanite during the main phase of deformation. The clearest reaction texture indicating decompression near peak metamorphic temperature is the replacement of garnet by clots of sillimanite, which are surrounded by halos of biotite. The sillimanite clots, most without relict garnet in the cores and with highly variable aspect ratios, are aligned. They define a lineation that formed with the dominant foliation. An inverted metamorphic gradient is locally defined by sillimanite-garnet schists (625 degrees C) structurally above staurolite-garnet schists (550 degrees C) and implies ductile thrusting during the main phase of deformation. The exhumation that led to the recorded decompression was likely in response to crustal thickening due to ductile thrusting and subsequent denudation.

Influence of V5/6-His Tag on the Properties of Gap Junction Channels Composed of Connexin43, Connexin40 or Connexin45

HeLa cells expressing wild-type connexin43, connexin40 or connexin45 and connexins fused with a V5/6-His tag to the carboxyl terminus (CT) domain (Cx43-tag, Cx40-tag, Cx45-tag) were used to study connexin expression and the electrical properties of gap junction channels. Immunoblots and immunolabeling indicated that tagged connexins are synthesized and targeted to gap junctions in a similar manner to their wild-type counterparts. Voltage-clamp experiments on cell pairs revealed that tagged connexins form functional channels. Comparison of multichannel and single-channel conductances indicates that tagging reduces the number of operational channels, implying interference with hemichannel trafficking, docking and/or channel opening. Tagging provoked connexin-specific effects on multichannel and single-channel properties. The Cx43-tag was most affected and the Cx45-tag, least. The modifications included (1) V j-sensitive gating of I j (V j, gap junction voltage; I j, gap junction current), (2) contribution and (3) kinetics of I j deactivation and (4) single-channel conductance. The first three reflect alterations of fast V j gating. Hence, they may be caused by structural and/or electrical changes on the CT that interact with domains of the amino terminus and cytoplasmic loop. The fourth reflects alterations of the ion-conducting pathway. Conceivably, mutations at sites remote from the channel pore, e.g., 6-His-tagged CT, affect protein conformation and thus modify channel properties indirectly. Hence, V5/6-His tagging of connexins is a useful tool for expression studies in vivo. However, it should not be ignored that it introduces connexin-dependent changes in both expression level and electrophysiological properties.

Irregularities below the Enamel-Dentin Junction May Predispose for Fissure Caries

This study investigated the structure of the fissure fundus on occlusal surfaces with respect to the detection of possible irregularities below the enamel-dentin junction (EDJ). Occlusal surfaces were examined by micro-computed tomography (µCT). In total, 203 third molars with clinically sound occlusal fissures or non-cavitated lesions were selected. All specimens were scanned with µCT. Subsequently, each tooth was sectioned, and each slice was investigated by stereomicroscopy. In 7 of 203 molars (3.4%), demarcated radiolucencies below the EDJ were detected by µCT. These defects were obviously of non-carious origin, because the µCT images revealed no gradient of demineralization in the dentin. In all cases, a direct pathway between the oral cavity and the dentin was evident. The comparison of the µCT sites with conventional histological images also revealed defects in the dentin. These results demonstrate that demarcated radiolucencies below the EDJ may not necessarily be caries lesions according to µCT images and may be classified as possible developmental irregularities. To avoid misinterpreting µCT data, dental researchers should carefully consider this condition when analyzing µCT images. The clinical significance of this finding is that these defects may predispose molar teeth to early-onset caries in occlusal pits and fissures.

The IS/OS junction layer in the natural history of type 2 idiopathic macular telangiectasia

To document the progression of a break in the photoreceptor inner segment/outer segment (IS/OS) junction layer and its functional correlates over time in the natural history of type 2 idiopathic macular telangiectasia (type 2 MacTel).

"En face" OCT imaging of the IS/OS junction line in type 2 idiopathic macular telangiectasia

We investigated abnormalities of the photoreceptor inner/outer segment (IS/OS) junction layer viewed "en face" and their functional correlates in type 2 idiopathic macular telangiectasia (type 2 MacTel).

Triple innominate osteotomy for Legg-Calvé-Perthes disease in children: does the lateral coverage change with time?

Triple innominate osteotomy (TIO) is one of the modalities of surgical containment in Legg-Calvé-Perthes disease (LCPD). However, overcoverage with TIO can lead to pincer impingement.