Molecular dynamics studies of trinucleotide repeat DNA involved in neurodegenerative disorders.

Expansion of trinucleotide repeat DNA of the classes CAG�·CTG, CGG�·CCG and GAA�·TTC are found to be associated with several neurodegenerative disorders. Different mechanisms have been attributed to the expansion of triplets, mainly involving the formation of alternate secondary structures by such repeats. This paper reports the molecular dynamics simulation of triplet repeat DNA sequences to study the basic structural features of DNA that are responsible for the formation of structures such as hairpins and slip-strand DNA leading to expansion. All the triplet repeat sequences studied were found to be more flexible compared to the control sequence unassociated with disease. Moreover, flexibility was found to be in the order CAG�·CTG > CGG�·CCG = GAA�·TTC, the highly flexible CAG�·CTG repeat being the most common cause of neurodegenerative disorders. In another simulation, a single G�·C to T�·A mutation at the 9th position of the CAG�·CTG repeat exhibited a reduction in bending compared to the pure 15-mer CAGâ�¢CTG repeat. EPM1 dodecamer repeat associated with the pathogenesis of progressive myoclonus epilepsy was also simulated and showed flexible nature suggesting a similar expansion mechanism.

Molecular basis for estrogen receptor alpha deficiency in BRCA1-linked breast cancer

Background BRCA1-mutant breast tumors are typically estrogen receptor alpha (ER alpha) negative, whereas most sporadic tumors express wild-type BRCA1 and are ER alpha positive. We examined a possible mechanism for the observed ER alpha-negative phenotype of BRCA1-mutant tumors.

Methods We used a breast cancer disease-specific microarray to identify transcripts that were differentially expressed between paraffin-embedded samples of 17 BRCA1-mutant and 14 sporadic breast tumors. We measured the mRNA levels of estrogen receptor 1 (ESR1) ( the gene encoding ER alpha), which was differentially expressed in the tumor samples, by quantitative polymerase chain reaction. Regulation of ESR1 mRNA and ER alpha protein expression was assessed in human breast cancer HCC1937 cells that were stably reconstituted with wild-type BRCA1 expression construct and in human breast cancer T47D and MCF-7 cells transiently transfected with BRCA1-specific short-interfering RNA ( siRNA). Chromatin immunoprecipitation assays were performed to determine if BRCA1 binds the ESR1 promoter and to identify other interacting proteins. Sensitivity to the antiestrogen drug fulvestrant was examined in T47D and MCF-7 cells transfected with BRCA1-specific siRNA. All statistical tests were two-sided.

Results Mean ESR1 gene expression was 5.4-fold lower in BRCA1-mutant tumors than in sporadic tumors ( 95% confidence interval [CI]=2.6-fold to 40.1-fold, P =.0019). The transcription factor Oct-1 recruited BRCA1 to the ESR1 promoter, and both BRCA1 and Oct-1 were required for ER alpha expression. BRCA1-depleted breast cancer cells expressing exogenous ER alpha were more sensitive to fulvestrant than BRCA1-depleted cells transfected with empty vector ( T47D cells, the mean concentration of fulvestrant that inhibited the growth of 40% of the cells [IC40] for empty vector versus ER alpha: > 10(-5) versus 8.0 x 10(-9) M [ 95% CI=3.1x10(-10) to 3.2 x 10(-6) M]; MCF-7 cells, mean IC40 for empty vector versus ER alpha : > 10(-5) versus 4.9 x 10(-8) M [ 95% CI=2.0 x 10(-9) to 3.9 x 10(-6) M]).

Conclusions BRCA1 alters the response of breast cancer cells to antiestrogen therapy by directly modulating ER alpha expression.

Controlling dissociation processes in the D-2(+) molecular ion using high-intensity, ultrashort laser pulses

A novel technique is proposed to control the dissociation mechanism of small diatomic molecules. This technique, relying upon the creation of a coherent nuclear wavepacket, uses intense (> 10(14) W cm(-2)), ultrashort (similar to 10 fs) infrared laser pulses in a pump and probe scheme. In applying this technique to D-2(+) good agreement has been observed between a quantum simulation and experiment. This represents a major step towards quantum state control in molecules, using optical fields.

Stabilization of Ti-molecular sieve catalysts used in selective sulfoxidation reactions by ionic liquids

Sulfoxidation reactions of 4,6-dimethyl-2-methylthiopyrimidine have been performed using titanosilicate catalysts in ionic liquids, dioxane and ethanol. The ionic liquid reactions showed superior reactivity compared with molecular solvents. Moreover, on examination of the recycling of the catalyst, a significant increase in the stability of catalyst was found both in terms of recycling activity and leaching of the titanium from the catalyst. The mechanism by which the ionic liquid reduces the solubilisation of the catalysts is explored.

The mechanism of N2O formation via the (NO)(2) dimer: A density functional theory study

Catalytic formation of N2O via a (NO)(2) intermediate was studied employing density functional theory with generalized gradient approximations. Dimer formation was not favored on Pt(111), in agreement with previous reports. On Pt(211) a variety of dimer structures were studied, including trans-(NO)(2) and cis-(NO)(2) configurations. A possible pathway involving (NO)(2) formation at the terrace near to a Pt step is identified as the possible mechanism for low-temperature N2O formation. The dimer is stabilized by bond formation between one O atom of the dimer and two Pt step atoms. The overall mechanism has a low barrier of approximately 0.32 eV. The mechanism is also put into the context of the overall NO+H-2 reaction. A consideration of the step-wise hydrogenation of O-(ads) from the step is also presented. Removal of O-(ads) from the step is significantly different from O-(ads) hydrogenation on Pt(111). The energetically favored structure at the transition state for OH(ads) formation has an activation energy of 0.63 eV. Further hydrogenation of OH(ads) has an activation energy of 0.80 eV. (C) 2004 American Institute of Physics.

Mechanism of H-2 metabolism on Fe-only hydrogenases

The metabolism of hydrogen (H-2 2H(+) + 2e(-)) constitutes a central process in the global biological energy cycle. Among all the enzymes that can mediate this process, Fe-only hydrogenases are unique in their particular high reactivity. Recently, some important progresses have been achieved. Following our previous paper [Z.-P. Liu and P. Hu, J. Am. Chem. Soc. 124, 5175 (2002)] that characterizes the individual redox state of the active site of Fe-only hydrogenase, in this work we have determined the feasible reaction pathways and energetics for the H-2 metabolism on the active site of Fe-only hydrogenases, using density functional theory. We show that H-2 metabolism possesses very low reaction barriers and a proximal base from a nearby protein plays an important role in H-2 metabolism. (C) 2002 American Institute of Physics.

Insight into why the Langmuir-Hinshelwood mechanism is generally preferred

In heterogeneous catalysis, the two main reaction mechanisms which have been proposed are the Langmuir-Hinshelwood and the Eley-Rideal. For the vast majority of surface catalytic reactions, it has been accepted that the Langmuir-Hinshelwood mechanism is preferred. In this study, we investigate catalytic CO oxidation on Pt(111). It is found that reaction barriers for Langmuir-Hinshelwood mechanisms actually tend to be higher than those for Eley-Rideal ones. An explanation is presented as to why it is still more probable for the reaction to proceed via the Langmuir-Hinshelwood mechanism, despite its higher reaction barrier. (C) 2002 American Institute of Physics.

Quantum chessboards in the deuterium molecular ion

We present a new algorithm for vibrational control in deuterium molecules that is feasible with current experimental technology. A pump mechanism is used for creating a coherent superposition of the D-2(+) vibrations. A short, intense infrared control pulse is applied after a chosen delay time to create selective interferences. A 'chessboard' pattern of states can be realized in which a set of even- or odd-numbered vibrational states can be selectively annihilated or enhanced. A technique is proposed for experimental realization and observation of this effect using 5 fs pulses of lambda = 790 nm radiation, with intermediate intensity (5 x 10(13) W cm(-2)).

Pathways to state-selective control of vibrational wavepackets in the deuterium molecular ion

The capability of intense ultrashort laser pulses to initiate, control and image vibrational wavepacket dynamics in the deuterium molecular ion has been simulated with a view to inform and direct future femtosecond pump-control-probe experiments. The intense-field coherent control of the vibrational superposition has been studied as a function of pulse intensity and delay time, to provide an indication of key constraints for experimental studies. For selected cases of the control mechanism, probing of the subsequent vibrational wavepacket dynamics has been simulated via the photodissociation (PD) channel. Such PD probing is shown to elucidate the modified wavepacket dynamics where the position of the quantum revival is sensitive to the control process. Through Fourier transform analysis the PD yield is also shown to provide a characterisation of the vibrational distribution. It has been shown that a simple 'critical R cut-off' approximation can be used to reproduce the effect of a probe pulse interaction, providing a convenient and efficient alternative to intensive computer simulations of the PD mechanism in the deuterium molecular ion.

On the mechanism for optomechanical entanglement and its revelation

An intuitive and accurate picture of the occurrence of optomechanical entanglement in a system of great current experimental interest is provided. At the optimal working point for entanglement generation, the interaction of a light field with a micromechanical oscillator is described in terms of simple SU( 2) transformations. This allows the analysis of a recent proposal for the revelation of quantumness in the state of a massive mirror from a clear and experimentally biased viewpoint.