Biomedical subjects

V Fritsch

Publications and source records attributed to V Fritsch.

9 recordsLinked to original sources

PubMed2005

Orbital freezing and orbital glass state in FeCr2S4.

Low-temperature specific heat measurements and dielectric spectroscopy have been performed on polycrystalline and single-crystalline FeCr2S4, the single crystals showing a transition into a low-temperature orbital glass phase. The freezing of the orbital moments is revealed by a glasslike specific heat anomaly and by a clear relaxational behavior of the dielectric permittivity, exhibiting several hallmark features of glassy dynamics. The orbital relaxation dynamics continuously slows down over six decades in time, before at the lowest temperatures the glass transition becomes suppressed by quantum tunneling.

Journal Article↗

PubMed2004

Spin and orbital frustration in MnSc2S4 and FeSc2S4.

Crystal structure, magnetic susceptibility, and specific heat were measured in the normal cubic spinel compounds MnSc2S4 and FeSc2S4. Down to the lowest temperatures, both compounds remain cubic and reveal strong magnetic frustration. Specifically the Fe compound is characterized by a Curie-Weiss (CW) temperature ThetaCW = -45 K and does not show any indications of order down to 50 mK. In addition, the Jahn-Teller ion Fe2+ is orbitally frustrated. Hence, FeSc2S4 belongs to the rare class of spin-orbital liquids. MnSc2S4 is a spin liquid for temperatures T>TN approximately 2 K.

Journal Article↗

PubMed2003

Evidence for Jahn-Teller distortions at the antiferromagnetic transition in LaTiO3.

LaTiO3 is known as a Mott insulator which orders antiferromagnetically at T(N)=146 K. We report on results of thermal expansion and temperature dependent x-ray diffraction together with measurements of the heat capacity, electrical transport measurements, and optical spectroscopy in untwinned single crystals. At T(N) significant structural changes appear, which are volume conserving. Concomitant anomalies are also observed in the dc resistivity, in bulk modulus, and optical reflectivity spectra. We interpret these experimental observations as evidence of orbital order.

Journal Article↗

PubMed2000

RNA folding: beyond Watson-Crick pairs.

Several crystal structures of RNA fragments, alone or in complex with a specific protein, have been recently solved. In addition, the structures of an artificial ribozyme, the leadzyme, and the cleavage product of a human pathogen ribozyme, have extended the structural diversity of ribozyme architectures. The attained set of folding rules and motifs expand the repertoire seen previously in tRNA structures.

Base Pairing↗

PubMed1995

Molecular mechanics and dynamics studies on two structurally related amide-modified DNA backbones for antisense technology.

The effect of the replacement of the natural phosphodiester linkage -C3'-O-PO2-O-CH2-C4'- in the DNA strand of RNA.DNA hybrid duplexes by either of the two amide linkages -C3'-CH2-CO-NH-CH2-C4'- or -C3'-CH2-NH-CO-CH2-C4' has been investigated by molecular mechanics (MM) and molecular dynamics (MD) simulations. Conformational analysis has been used to assess various low-energy conformers of the amide-modified backbones. MD simulations have been carried out to study the dynamic behavior of the modified duplexes. The modified RNA.DNA hybrid double helices kept a conservative base pairing scheme during the MD simulations. Although the general behavior has been found to be similar to that of the corresponding wild-type hybrid duplexes, some notable differences, especially regarding the sugar puckering in the amide-modified DNA strands, have been observed. The behavior of the RNA strands in the hybrid duplexes has not been affected by the modified DNA strands and is similar to that in wild-type RNA.DNA duplexes.

Amides↗

PubMed1994

Molecular dynamics simulations of a r(GA12G).d(CT12C) hybrid duplex.

RNA.DNA hybrid duplexes are relevant in various biological mechanisms like transcription and replication. Enzymes like RNase H cleave specifically the RNA strand in RNA.DNA duplexes. In antisense technology the complexation of mRNA with "modified" oligo(deoxy)-nucleotides leads to new hybrid duplexes. The knowledge about structure and dynamical behavior on an atomic level is fundamental for the understanding of any process involving hybrid duplexes. Therefore, molecular dynamics studies (200 picoseconds of trajectory) on a hybrid duplex structure r(GA12G).d(CT12C) were performed. During the stimulations, the deoxyribose residues assumed a puckering state between C2'-endo and C3'-endo, with an average mode around O4'-endo-C1'-exo, whereas the riboses of the RNA strand remained in the C3'-endo puckering domain. The results are compared to those obtained for the DNA.DNA duplex d(GA12G).d(CT12C) under identical simulation conditions. The DNA strand in the hybrid duplex behaves similar to that in a standard B-type DNA duplex. The helical parameters of the hybrid duplex however are closer to A- than to B-type. These observations suggest that RNA.DNA hybrid double helices are neither clearly A-form nor B-form. The furanoses in both strands can assume different puckering modes without the appearance of major geometrical constraints. The simulation results are in excellent agreement with recent experimental data.

Base Sequence↗

PubMed1993

Molecular dynamics simulations of poly(dA).poly(dT): comparisons between implicit and explicit solvent representations.

The program AMBER 3.0 has been used to generate molecular dynamics trajectories of a poly(dA).poly(dT) decamer. The simulations were performed using different methods to treat solvent effects. Results of a simulation including 18 counterions NH4+ and 4109 water molecules under (N, P, T) conditions were compared to simulation runs with implicit solvent representation in which solvent screening effects were represented by the use of a sigmoidal distance-dependent dielectric function. In the latter case, the system was simulated under microcanonical (N, V, E) and canonical (N, V, T) conditions. For the fully hydrated system simulation, a preequilibration protocol was developed since it was observed that long and progressive periods of heating and equilibration on the overall system were necessary in order to avoid energetic collisions between the solute and the solvent molecules, leading to severe irreversible deformation of the solute. A detailed analysis of DNA conformations, sugar puckers, and stability of the hydrogen bonds, Watson-Crick and three-center H bonds, is reported. The results show that DNA remains essentially in the B conformer with a tendency in the hydrated model to adopt a slightly distorted, unwound, and stretched conformation in comparison to standard B-DNA. Concerning sugar puckers, the mean pseudorotation phases of the adenine residues are systematically higher than those of the thymine residues, except in the case of the hydrated model for which a articular behavior is observed for the adenine strand. In this case, the terminal bases oscillate between C2'-endo and O4'-endo and the central ones stay in the C3'-endo domain. The mean lifetimes of the internal Watson-Crick H-bond (A) HN6...O4(T) are also dependent on the base pairs included in the calculation, excepted for the implicit solvent simulation at constant temperature. The three-center H bonds have very small mean lifetimes in all three cases of MD simulation. In the minor groove of the hydrated model, a spine of hydration is found as observed by x-ray crystallography and other theoretical simulations. On the basis of the rms deviations, it appears that the fully hydrated simulation has not reached a plateau at the end of the run, while the implicit simulation at constant energy seems to have converged. At constant temperature, very large oscillations in rms deviations are observed.

Base Sequence↗

PubMed1992

Investigations on the dynamic structures of adenine- and thymine-containing DNA.

The structures of poly(dA-dT), poly(dA-dBr5U) and of poly(dA).poly(dT) have been investigated in solution and in fibers, by Raman spectroscopy. Both the alternating poly(dA-dT), poly(dA-dBr5U) and non-alternating poly(dA).poly(dT) exhibit, in the region of sugar phosphate backbone vibrations, two bands of almost equal intensity at about 841 cm-1 and 817 cm-1. The analysis of the characteristic bands of thymine residues that are sensitive to sugar puckers gives indication of a significant displacement from the C(2')-endo conformer suggesting the adoption of alternative conformers such as O(4')-endo. In contrast, the diagnostic Raman bands for the sugar pucker of adenine residues suggest, instead, predominant adoption of C(2')-endo conformations. These Raman results are compatible with rapid dynamic changes of sugar puckers between C(2')-endo and O(4')-endo for the thymidine (and uridine) residues, whereas in adenine residues the sugar puckers fluctuate around the C(2')-endo pucker in all synthetic DNA molecules studied. Molecular dynamics simulations, performed on six different starting models using two distance-dependent dielectric functions epsilon(r) = 4 r and a sigmoidal dependence), all gave similar dynamic behavior in agreement with these Raman data and their interpretation. The mean calculated pseudorotation phases of the adenine residues are systematically higher (around C(2')-endo) than those of the thymine residues (close to O(4')-endo-C(1')-exo). Besides, the mean lifetimes of the thymine residues are 1.5 to 2.0-fold higher in the O(4')-endo than in the C(2')-endo domain, while those of the adenine residues are two to threefold higher in the C(2')-endo than in the O(4')-endo domain. In the Raman spectra of the alternating poly(dA-dBr5U), the splitting of a band into two components arising from the two contributions of ApBr5U and Br5UpA provides strong evidence for a repeating dinucleotide structure in solution. The calculated twist values averaged over the simulation runs are also systematically higher in the 5'T-A3' step (39 degrees) than in the 5'A-T3' step (33 degrees). Simultaneously, the calculated roll values are positive in the 5'T-A3' step (6 degrees) and negative in the 5'A-T3' step (-9 degrees), while the propeller twist values are about the same (-11 degrees to -16 degrees). On the other hand, in the homopolymer, the average twist value is close to 36 degrees with the roll angle close to 0 degrees and large propeller twist values (-20 degrees).

Adenine↗

PubMed1992

Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex.

The oligonucleotides d[(G-A)7G] and d[(G-A)12G] self-associate under physiological conditions (10 mM MgCl2, neutral pH) into a stable double-helical structure (psRR-DNA) in which the two polypurine strands are in a parallel orientation in contrast to the antiparallel disposition of conventional B-DNA. We have characterized psRR-DNA by gel electrophoresis, UV absorption, vacuum UV circular dichroism, monomer-excimer fluorescence of oligonucleotides end-labelled with pyrene, and chemical probing with diethyl pyrocarbonate and dimethyl sulfate. The duplex is stable at pH 4-9, suggesting that the structure is compatible with, but does not require, protonation of the A residues. The data support a model derived from force-field analysis in which the parallel-stranded d(G-A)n helix is right-handed and constituted of alternating, symmetrical Gsyn.Gsyn and Aanti.Aanti base pairs with N1H...O6 and N6H...N7 hydrogen bonds, respectively. This dinucleotide structure may be the source of a negative peak observed at 190 nm in the vacuum UV CD spectrum, a feature previously reported only for left-handed Z-DNA. The related sequence d[(GAAGGA)4G] also forms a parallel-stranded duplex but one that is less stable and probably involves a slightly different secondary structure. We discuss the potential intervention of psRR-DNA in recombination, gene expression and the stabilization of genomic structure.

Base Sequence↗