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At least 811 records · Page 45Linked to original sources
PubMed1996

Stability of intrastrand hairpin structures formed by the CAG/CTG class of DNA triplet repeats associated with neurological diseases.

Expansions of trinucleotide repeats in DNA, a novel source of mutations associated with human disease, may arise by DNA replication slippage initiated by hairpin folding of primer or template strands containing such repeats. To evaluate the stability of single-strand folding by repeating triplets of DNA bases, thermal melting profiles of (CAG)10, (CTG)10, (GAC)10 and (GTC)10 strands are determined at low and physiological salt concentrations, and measurements of melting temperature and enthalpy change are made in each case. Comparisons are made to strands with three times as many repeats, (CAG)30 and (CTG)30. Evidence is presented for stable intrastrand folding by the CAG/CTG class of triplet repeats. Relative to the GAC/GTC class not associated with disease, the order of folding stability is found to be CTG > GAC approximately = CAG > GTC for 10 repeats. Surprisingly, the folds formed by 30 repeats of CTG or CAG have no higher melting temperature and are only 40% more stable in free energy than those formed by 10 repeats. This finding suggests that triplet expansions with higher repeat number may result from the formation of more folded structures with similar stability rather than fewer but longer folds of greater stability.

Base Sequence↗
PubMed1997

Relative stability of triplexes containing different numbers of T.AT and C+.GC triplets.

We have used DNase I footprinting to compare the stability of parallel triple helices containing different numbers of T.AT and C+. GC triplets. We have targeted a fragment containing the 17mer sequence 5'-AGGAAGAGAAAAAAGAA with the 9mer oligonucleotides 5'-TCCTTCTCT, 5'-TTCTCTTTT and 5'-TTTTTTCTT, which form triplexes at the 5'-end, centre and 3'-end of the target site respectively. Quantitative DNase I footprinting has shown that at pH 5.0 the dissociation constants of these oligonucleotides are 0.13, 4.7 and >30 microM respectively, revealing that increasing the proportion of C+.GC triplets increases triplex stability. The results suggest that the positive charge on the protonated cytosine contributes to triplex stability, either by a favourable interaction with the stacked pisystem or by screening the charge on the phosphate groups. In the presence of a naphthylquinoline triplex binding ligand all three oligonucleotides bind with similar affinities. At pH 6.0 these triplexes only form in the presence of the triplex binding ligand, while at pH 7.5 footprints are only seen with the oligonucleotide which generates the fewest number of C+.GC triplets (TTTTTTCTT) in the presence of the ligand.

Adenine↗
PubMed1998

Comparison of the solution structures of intramolecular DNA triple helices containing adjacent and non-adjacent CG.C+ triplets.

The solution conformations of the intramolecular triple helices d(AGAAGA-X-TCTTCT-X-TC+TTC+T) and d(AAGGAA-X-TTCCTT-X-TTC+C+TT) (X = non-nucleotide linker) have been determined by NMR.1H NMR spectra in H2O showed that the third strand cytosine residues are fully paired with the guanine residues, each using two Hoogsteen hydrogen bonds. Determination of the13C chemical shifts of the cytosine C6 and C5 and their one-bond coupling constants (1 J CH) conclusively showed that the Hoogsteen cytosine residues are protonated at N3. The global conformations of the two molecules determined with >19 restraints per residue are very similar (RMSD = 0.96 A). However, some differences in local conformation and dynamics were observed for the central two base triplets of the two molecules. The C N3H were less labile in adjacent CG.C+triplets than in non-adjacent ones, indicating that the adjacent charge does not kinetically destabilize these triplets. The sugar conformations of the two adjacent cytosine residues were different and the 5'-residue was atypical of protonated cytosine. Hence, there are subtle effects of the interaction between two adjacent cytosine residues. The central two purines in each sequence showed non-standard backbone conformations, averaging between gamma approximately 60 degrees and gamma approximately 180 degrees. This may be related to the difference in the dependence of the thermodynamic stability on pH observed for these two sequences.

Base Sequence↗
PubMed2002

Effects of triplet repeat sequences on nucleosome positioning and gene expression in yeast minichromosomes.

Triplet repeat sequences that cause human hereditary diseases can form a variety of DNA conformations. Since DNA structures act as determinants of chromatin structure, chromatin may be involved in mechanisms of these diseases. To address this issue, we examined effects of triplet repeat sequences on chromatin structure and gene expression in Saccharomyces cerevisiae. We show here that (1) (CTG)12 promotes nucleosome formation, (2) (CGG)12 disrupts an array of positioned nucleosomes, and (3) (GAA)12 has little effect on nucleosome formation. Also, we show that insertion of (CGG)12 increases gene expression of a UAS-less promoter about 10-fold, while (CTG)12 and (GAA)12 have no effect. Thus, expansion of triplet repeat sequences may cause improper expression of disease related genes, through their effects on chromatin structure.

Chromosomes, Fungal↗
PubMed2002

Dual role of triplet localization on the accessory chlorophyll in the photosystem II reaction center: photoprotection and photodamage of the D1 protein.

Infrared absorption and electron spin resonance studies have shown that the excited triplet state of chlorophyll formed by radical pair recombination in the PSII reaction center is mainly localized on the accessory chlorophyll, which is most probably located in the D1 protein (Chl(1)). This triplet localization plays two contrasting roles, depending on the redox state of Q(A), in the process of acceptor-side photoinhibition of PSII. In the early stage of photoinhibition, in which singly reduced Q(A) is reversibly stabilized, the triplet state of Chl(1) ((3)Chl(1)*) is rapidly quenched (t(1/2) = 2-20 micro s) by the interaction with Q(A)(-), preventing formation of harmful singlet oxygen. In the next inhibitory stage, in which Q(A) is doubly reduced and then irreversibly released from the Q(A) pocket, the lifetime of (3)Chl(1)* becomes longer by more than two orders of magnitude (t(1/2) = 1-3 ms). As a result, singlet oxygen is produced around Chl(1) in the D1 protein, causing damage preferably to the D1 protein, which induces subsequent proteolytic degradation. Thus, (3)Chl(1)* functions as a switch to change from the protective to the degradative phase of the PSII reaction center by sensing either reversible or irreversible inhibited state at the Q(A) site.

Chlorophyll↗
PubMed2002

Origin of the oscillator strength of the triplet state of a trion in a magnetic field.

The dynamics of the spin-triplet trion state, under high magnetic field in a GaAs/AlGaAs quantum well, are studied using time resolved spectroscopy. The oscillator strength of the triplet transition is shown to rise with increasing electron density, in good agreement with a theoretical model where the trion interacts with excess electrons in the quantum well. This analysis suggests that the spin-triplet trion state, which is expected to be an optically "dark" state, is experimentally observable due to the interactions with the excess electrons, demonstrating that X- cannot be regarded as an isolated three particle complex.

Journal Article↗
PubMed2003

Triplet-to-singlet exciton formation in poly(p-phenylene-vinylene) light-emitting diodes.

The triplet to singlet exciton formation ratio in a MEH-PPV light-emitting diode is measured by comparing the triplet-induced absorptions with optical and electric excitations at the same singlet exciton density. The ratio is a strong universal decreasing function of the averaged electric field. Using 4 ns for singlet to triplet intersystem crossing time, the ratio is significantly larger than the spin-independent value 3 at intermediate field but is reduced to about 2 for higher field.

Journal Article↗
PubMed2004

Odd-parity triplet pair induced by Hund's rule coupling.

We discuss microscopic aspects of the odd-parity triplet pair in orbital degenerate systems. From the concept of off-diagonal long-range order, a pair state is unambiguously defined as the eigenstate with the maximum eigenvalue of a pair correlation function. Performing this scheme by a numerical technique, we clarify that the odd-parity triplet pair occurs as an out-of-phase combination of local triplets induced by Hund's rule coupling for the lattice including two sites in the unit cell.

Journal Article↗
PubMed2004

Off-site repulsion-induced triplet superconductivity: a possibility for chiral p(x+y)-wave pairing in Sr2RuO4.

In order to probe the effect of charge fluctuations on triplet pairing, we study the pairing symmetry in the one-band Hubbard model having the off-site Coulomb repulsion (V) on top of the on-site repulsion as a model for the gamma band of Sr2RuO4, a strong candidate for a triplet pairing superconductor. The result, obtained with the dynamical cluster approximation combined with the quantum Monte Carlo method, and confirmed from the fluctuation exchange approximation, shows that while d(x(2)-y(2)) pairing dominates over p in the absence of V, introduction of V makes p(x+y) and d(xy) dominant. The gap function for the chiral p(x+y)+ip(x-y) has nodes that are consistent with the recent measurement of specific heat in rotated magnetic fields in the ruthenate. This suggests that the off-site repulsion may play an essential role in triplet superconductivity in this material.

Journal Article↗
PubMed2004

Singlet-triplet splitting of geminate electron-hole pairs in conjugated polymers.

The singlet-triplet splitting of geminate polaron pairs in a ladder-type conjugated polymer has been studied by the thermally stimulated luminescence technique. The energy gap separating the singlet and triplet states of the geminate pairs is measured to be in the range of 3-6 meV, depending on the polymer morphology. The results of correlated quantum-chemical calculations on a long ladder-type oligomer are fully consistent with the observed values of the geminate polaron pair singlet-triplet gap. Such low splitting values have important implications for the spin-dependent exciton formation in conjugated polymers.

Journal Article↗
PubMed2005

Ferromagnetic fluctuation and possible triplet superconductivity in NaxCoO2.yH2O: fluctuation-exchange study of the multiorbital Hubbard model.

Spin and charge fluctuations and superconductivity in NaxCoO2.yH(2)O are studied based on a multiorbital Hubbard model. Tight-binding parameters are determined to reproduce the results of band calculations. By applying the fluctuation-exchange approximation, we show that the Hund's-rule coupling between the Co t(2g) orbitals causes ferromagnetic (FM) spin fluctuation. Triplet fy((y(2)-3x(2)))-wave and p-wave pairings are favored by this FM fluctuation on the hole-pocket band. We propose that, in NaxCoO2.yH(2)O, the Co t(2g) orbitals and interorbital Hund's-rule coupling play important roles on the triplet pairing, and this compound can be a first example of the triplet superconductor in which the orbital degrees of freedom play substantial roles.

Journal Article↗
PubMed2006

S-wave spin-triplet order in superconductors without inversion symmetry: Li2Pd3B and Li2Pt3B.

We investigate the order parameter of noncentrosymmetric superconductors Li2Pd3B and Li2Pt3B via the behavior of the penetration depth lambda(T). The low-temperature penetration depth shows BCS-like behavior in Li2Pd3B, while in Li2Pt3B it follows a linear temperature dependence. We propose that broken inversion symmetry and the accompanying antisymmetric spin-orbit coupling, which admix spin-singlet and spin-triplet pairing, are responsible for this behavior. The triplet contribution is weak in Li2Pd3B, leading to a wholly open but anisotropic gap. The significantly larger spin-orbit coupling in Li2Pt3B allows the spin-triplet component to be larger in Li2Pt3B, producing line nodes in the energy gap as evidenced by the linear temperature dependence of lambda(T). The experimental data are in quantitative agreement with theory.

Journal Article↗
PubMed2006

Coexistence of triplet superconductivity and spin density waves.

We discuss the possibility of the coexistence of spin density waves (antiferromagnetism) and triplet superconductivity as a particular example of a broad class of systems where the interplay of magnetism and superconductivity is important. We focus on the case of quasi-one-dimensional metals, where it is known that antiferromagnetism is in close proximity to triplet superconductivity in the pressure versus temperature phase diagram. Over a range of pressures, we propose an intermediate nonuniform phase consisting of antiferromagnetic and triplet superconducting orders. In the coexistence region, we propose a flop transition in the spin density wave order parameter vector, which affects the nature of the superconducting state and leads to the appearance of several new phases.

Journal Article↗
PubMed2003

Improving triplet-phase accuracy by symmetry observations in reference-beam diffraction measurements.

The reference-beam X-ray diffraction technique allows parallel measurements of many three-beam interference profiles in a modified rotating-crystal experiment. Because of the unique symmetry relations that exist in the reference-beam geometry, a complete 360 degrees rotation leads to a fourfold redundancy of any given triplet phase delta(H) involving primary reflection H, reference reflection G and coupling reflection H-G, measured in a data set. Two such redundant measurements correspond to simple duplications with the reciprocal node H going into and coming out of the Ewald sphere, while the other two correspond to the Friedel mate G-H of the coupling reflection H-G passing through the Ewald sphere in a similar fashion. It is shown that substantial differences may exist between the H and the G-H cases, with an enhanced triplet-phase interference effect in one of them. These symmetry-related observations, coupled with inverse-beam triplet measurements, would improve the phase measurement accuracy of the reference-beam diffraction technique.

Crystallography, X-Ray↗
PubMed2003

Accurate triplet phase determination in non-perfect crystals--a general phasing procedure.

A completely different approach to the problem of physically measuring the invariant triplet phases by three-beam X-ray diffraction is proposed. Instead of simulating the three-beam diffraction process to reproduce the experimental intensity profiles, the proposed approach makes use of a general parametric equation for fitting the profiles and extracting the triplet phase values. The inherent flexibility of the parametric equation allows its applicability to be extended to non-perfect crystals. Exploitation of the natural linear polarization of synchrotron radiation is essential for eliminating systematic errors and to provide accurate triplet phase values. Phasing procedures are suggested and demonstrative examples from simulated data are given.

Journal Article↗
PubMed1999

Three-wave grazing-incidence X-ray diffraction from thin crystal surface layers: determination of triplet phase invariants.

Numerical calculation of the angular and spectral distributions of the intensities of the specularly diffracted waves in the case of three-wave grazing-incidence X-ray diffraction is carried out using the dynamical theory. The angular and spectral distributions are shown to be uniquely and continuously dependent upon the value of the triplet phase invariant. A method of determining the value of the triplet phase invariant for thin crystal surface layers is developed, based on the comparison of experimentally measured three-wave peak profiles with the profiles calculated for different values of the triplet phase invariant. An analysis scheme of the phase sensitivity of the reflection coefficients is proposed taking into account the interference of the directly excited and the 'Umweg'-excited specularly diffracted waves.

Journal Article↗
PubMed1998

Application of known triplet phases in the crystallographic study of bovine pancreatic trypsin inhibitor. II: study at 2.0 A resolution.

Direct methods strengthened by the application of about 130 triplet phases, assumed known with a mean error of about +/- 20 degrees, were used to re-determine the structure of BPTI with data at 2.0 A resolution. The triplet phases served to shift the mean direction and enhance the concentration parameter in the corresponding Cochran distributions. These phases were used in combination with the partial structure extracted from successive density maps to control the gradual expansion and refinement of Fourier coefficients. Single phases were developed iteratively from tangent-formula estimation following the path of the convergence map. The a priori triplet phase information was sufficient to initiate solution of the structure at 2.0 A.

Algorithms↗
PubMed1998

Structure of the DNA decamer d(GGCAATTGCG) contains both major- and minor-groove binding G.(G.C) base triplets.

The crystal structure of the decamer d(GGCAATTGCG) has been determined at 2.4 A resolution. The central eight bases of each DNA single-strand base pair with a self-complementary strand to form an octamer B-DNA duplex. These duplexes lie end-to-end within the unit cell. The terminal 5'-G and G-3' bases of each decamer strand are unpaired, and interact with the neighbouring duplexes via interactions within both the major and minor groove. This results in base triplets of the type G-(G.C) and G*(G.C), with the third guanine base binding to a Watson-Crick G.C base pair from the major groove and the minor groove, respectively. The triplet interaction of the type G-(G.C) involves Hoogsteen hydrogen-bonding interactions between the two guanine bases. The minor- and major-groove base triplet interactions which exist within this structure act to stabilize the d(GCAATTGC)2 B-DNA octamer duplex.

Crystallization↗