Engineering new limits to magnetostriction through metastability in iron-gallium alloys.

Magnetostrictive materials transduce magnetic and mechanical energies and when combined with piezoelectric elements, evoke magnetoelectric transduction for high-sensitivity magnetic field sensors and energy-efficient beyond-CMOS technologies. The dearth of ductile, rare-earth-free materials with high magnetostrictive coefficients motivates the discovery of superior materials. Fe1-xGax alloys are amongst the highest performing rare-earth-free magnetostrictive materials; however, magnetostriction becomes sharply suppressed beyond x = 19% due to the formation of a parasitic ordered intermetallic phase. Here, we harness epitaxy to extend the stability of the BCC Fe1-xGax alloy to gallium compositions as high as x = 30% and in so doing dramatically boost the magnetostriction by as much as 10x relative to the bulk and 2x larger than canonical rare-earth based magnetostrictors. A Fe1-xGax - [Pb(Mg1/3Nb2/3)O3]0.7-[PbTiO3]0.3 (PMN-PT) composite magnetoelectric shows robust 90° electrical switching of magnetic anisotropy and a converse magnetoelectric coefficient of 2.0 × 10-5 s m-1. When optimally scaled, this high coefficient implies stable switching at ~80 aJ per bit.

Probing protein binding spectra with Fourier microfluidics.

New developments in microfluidic chip technology enable the construction of chemical spectrum analyzers that can probe the binding interactions between chemical entities. In this paper we report the implementation of a microfluidic chip suitable for Fourier transform measurements of biochemical interactions. The chip consists of a chemical signal generator, a flow cell and a binding sensor surface. The microfluidic signal generator produces a periodic stream of protein plugs in solution flowing at constant velocity through the cell. This flow produces periodic association and dissociation cycles of the protein to a functionalized gold sensing surface placed inside the cell. The sensor activity corresponding to the phasor response of the chemical interaction at the excitation frequency is measured optically using surface plasmon resonance (SPR) imaging. We demonstrated the feasibility of the technique using a model system of carbonic anhydrase-II (CA-II) and immobilized 4-(2-Aminoethyl) benzenesulfonamide (ABS) ligand. The observed transfer function showed a dominant pole at 10.2 mHz corresponding to association and dissociation constants of 4.8 × 10(3) M(-1)·s(-1), and 3.5 × 10(-2) s(-1) respectively.

Locating monovalent cations in the grooves of B-DNA.

Here we demonstrate that monovalent cations can localize around B-DNA in geometrically regular, sequence-specific sites in oligonucleotide crystals. Positions of monovalent ions were determined from high-resolution X-ray diffraction of DNA crystals grown in the presence of thallium(I) cations (Tl(+)). Tl(+) has previously been shown to be a useful K(+) mimic. Tl(+) positions determined by refinement of model to data are consistent with positions determined using isomorphous F(Tl) - F(K) difference Fouriers and anomalous difference Fouriers. None of the observed Tl(+) sites surrounding CGCGAATTCGCG are fully occupied by Tl(+) ions. The most highly occupied sites, located within the G-tract major groove, have estimated occupancies ranging from 20% to 35%. The occupancies of the minor groove sites are estimated to be around 10%. The Tl(+) positions in general are not in direct proximity to phosphate groups. The A-tract major groove appears devoid of localized cations. The majority of the observed Tl(+) ions interact with a single duplex and so are not engaged in lattice interactions or crystal packing. The locations of the cation sites are dictated by coordination geometry, electronegative potential, avoidance of electropositive amino groups, and cation-pi interactions. It appears that partially dehydrated monovalent cations, hydrated divalent cations, and polyamines compete for a common binding region on the floor of the G-tract major groove.

X-ray crystallography of DNA-drug complexes.

Here we have stressed important differences between protein and DNA crystallography. Crystal growth and data collection methodologies are not directly transferable between the two subfields. In addition, we note that analysis of symmetry and packing of DNA crystals can be useful and a uniquely aesthetic exercise.

Influence of the dynamic positions of cations on the structure of the DNA minor groove: sequence-dependent effects.

Different models for minor groove structures predict that the conformation is essentially fixed by sequence and has an influence on local ion distribution or alternatively that temporal positions of ions around the minor groove can affect the structure if they neutralize cross-strand phosphate charges. Our previous studies show that the minor groove in an AATT dodecamer responds to local sodium ion positions and is narrow when ions neutralize cross-strand phosphate-phosphate charges [J. Am. Chem. Soc. 2000, 122, 10513-10520]. Previous results from a number of laboratories have shown that G-tracts often have a wider minor groove than A-tracts, but they do not indicate whether this is due to reduced flexibility or differences in ion interactions. We have undertaken a molecular dynamics study of a d(TATAGGCCTATA) duplex to answer this question. The results show that the G-tract has the same amplitude of minor groove fluctuations as the A-tract sequence but that it has fewer ion interactions that neutralize cross-strand phosphate charges. These results demonstrate that differences in time-average groove width between A- and G-tracts are due to differences in ion interactions at the minor groove. When ions neutralize the cross-strand phosphates, the minor groove is narrow. When there are no neutralizing ion interactions, the minor groove is wide. The population of structures with no ion interactions is larger with the GGCC than with the AATT duplex, and GGCC has a wider time-average minor groove in agreement with experiment.

The discrepancy-attribution hypothesis: II. Expectation, uncertainty, surprise, and feelings of familiarity.

In the accompanying article (B. W. A. Whittlesea & L. D. Williams, 2001), surprising violation of an expectation was observed to cause an illusion of familiarity. The authors interpreted that evidence as support for the discrepancy-attribution hypothesis. This article extended the scope of that hypothesis, investigating the consequences of surprising validation of expectations. Subjects were shown recognition probes as completions of sentence stems. Their expectations were manipulated by presenting predictive, nonpredictive, and inconsistent stems. Predictive stems caused an illusion of familiarity, but only when the subjects also experienced uncertainty about the outcome. That is, as predicted by the discrepancy-attribution hypothesis, feelings of familiarity occurred only when processing of a recognition target caused surprise. The article provides a discussion of the ways in which a perception of discrepancy can come about, as well as the origin and nature of unconscious expectations.

The discrepancy-attribution hypothesis: I. The heuristic basis of feelings of familiarity.

B. W. A. Whittlesea and L. D. Williams (1998, 2000) proposed the discrepancy-attribution hypothesis to explain the source of feelings of familiarity. By that hypothesis, people chronically evaluate the coherence of their processing. When the quality of processing is perceived as being discrepant from that which could be expected, people engage in an attributional process; the feeling of familiarity occurs when perceived discrepancy is attributed to prior experience. In the present article, the authors provide convergent evidence for that hypothesis and show that it can also explain feelings of familiarity for nonlinguistic stimuli. They demonstrate that the perception of discrepancy is not automatic but instead depends critically on the attitude that people adopt toward their processing, given the task and context. The connection between the discrepancy-attribution hypothesis and the "revelation effect" is also explored (e.g., D. L. Westerman & R. L. Greene, 1996).

Electrostatic mechanisms of DNA deformation.

The genomes of higher cells consist of double-helical DNA, a densely charged polyelectrolyte of immense length. The intrinsic physical properties of DNA, as well as the properties of its complexes with proteins and ions, are therefore of fundamental interest in understanding the functions of DNA as an informational macromolecule. Because individual DNA molecules often exceed 1 cm in length, it is clear that DNA bending, folding, and interaction with nuclear proteins are necessary for packaging genomes in small volumes and for integrating the nucleotide sequence information that guides genetic readout. This review first focuses on recent experiments exploring how the shape of the densely charged DNA polymer and asymmetries in its surrounding counterion distribution mutually influence one another. Attention is then turned to experiments seeking to discover the degree to which asymmetric phosphate neutralization can lead to DNA bending in protein-DNA complexes. It is argued that electrostatic effects play crucial roles in the intrinsic, sequence-dependent shape of DNA and in DNA shapes induced by protein binding.

The source of feelings of familiarity: the discrepancy-attribution hypothesis.

Many investigators have observed that the feeling of familiarity is associated with fluency of processing. The authors demonstrated a case in which the feeling of familiarity did not result from fluency per se; they argued that it resulted instead from perceiving a discrepancy between the actual and expected fluency of processing (B. W. A. Whittlesea & L. D. Williams, 1998). In this article, the authors extend that argument. They observed that stimuli that are experienced as strongly familiar when presented in isolation are instead experienced as being novel when presented in a rhyme or semantic context. They interpreted that result to mean that in those other contexts, the subjects brought a different standard to bear in evaluating the fluency of their processing. This different standard caused the subjects to perceive their performance not as discrepant, but as coherent in one case and incongruous in the other. The authors suggest that the perception of discrepancy is a major factor in producing the feeling of familiarity. They further suggest that the occurrence of that perception depends on the task in which the person is engaged when encountering the stimulus, because that task affects the standard that the person will apply in evaluating their processing.

Effects of cationic charge on three-dimensional structures of intercalative complexes: structure of a bis-intercalated DNA complex solved by MAD phasing.

We characterize intercalative complexes as either "high charge" and "low charge". In low charge complexes, stacking interactions appear to dominate stability and structure. The dominance of stacking is evident in structures of daunomycin, nogalamycin, ethidium, and triostin A/echinomycin. By contrast in a DNA complex with the tetracationic metalloporphyrin CuTMPyP4 [copper (II) meso-tetra(N-methyl-4-pyridyl)porphyrin], electrostatic interactions appear to draw the porphyrin into the duplex interior, extending the DNA along its axis, and unstacking the DNA. Similarly, DNA complexes of tetracationic ditercalinium and tetracationic flexi-di show significant unstacking. Here we report x-ray structures of complexes of the tetracationic bis-intercalator D232 bound to DNA fragments d(CGTACG) and d(BrCGTABrCG). D232 is analogous to ditercalinium but with three methylene groups inserted between the piperidinium groups. The extension of the D232 linker allows it to sandwich four base pairs rather than two. In comparison to CuTMPyP4, flexi-di and ditercalinium, stacking interactions of D232 are significantly improved. We conclude that it is not sufficient to characterize intercalators simply by net charge. One anticipates strong electrostatic forces when cationic charge is focused to a small volume or region near DNA and so must consider the extent to which cationic charge is focused or distributed. In sum, ditercalinium, with a relatively short linker, focuses cationic charge more narrowly than does D232. So even though the net charges are equivalent, electrostatic charges are expected to be of greater structural significance in the ditercalinium complex than in the D232 complex.

Preschoolers' and adults' reliance on object shape and object function for lexical extension.

We investigated the developmental progression of reliance on object function versus object shape to extend novel words. In 3 experiments, 3-year-olds, 5-year-olds, and adults were presented with sets of objects consisting of a target, a same-shape/different-function match, a different-shape/same-function match, and a distracter. In Experiments 1 and 2, function was emphasized during the word learning phase and participants were given direct experience with the functions of target and test objects. In Experiment 3, function was emphasized both during the learning phase and when requesting a referent of the novel labels. Across all 3 experiments, 3- and 5-year-olds focused on shape while adults focused on function when extending the novel words. These results suggest a developmental change in the consideration of shape and function in lexical extension.

A double-blind, placebo-controlled study of oral nalmefene for alcohol dependence.

BACKGROUND: Nalmefene is a newer opioid antagonist that is structurally similar to naltrexone but with a number of potential pharmacological advantages for the treatment of alcohol dependence, including no dose-dependent association with toxic effects to the liver, greater oral bioavailability, longer duration of antagonist action, and more competitive binding with opioid receptor subtypes that are thought to reinforce drinking. METHODS: A double-blind, placebo-controlled trial was conducted to evaluate the safety and efficacy of 2 doses of oral nalmefene for alcohol dependence. The 105 outpatient volunteers were abstinent for a mean of 2 weeks prior to random assignment to the placebo or 20- or 80-mg/d dose nalmefene groups for 12 weeks. Cognitive behavioral therapy was provided weekly during treatment. Self-reported drinking or abstinence was confirmed by determinations of breath alcohol concentration and by collateral informant reports. RESULTS: Outcomes did not differ between the 20- and 80-mg dose nalmefene groups. Significantly fewer patients treated with nalmefene than patients given placebo relapsed to heavy drinking through 12 weeks of treatment (P<.02), with a significant treatment effect at the first weekly study visit (P<.02). The odds ratio of relapsing to heavy drinking was 2.4 times greater with placebo compared with nalmefene (95% confidence interval, 1.05-5.59). Patients treated with nalmefene also had fewer subsequent relapses (P<.03) than patients given placebo. CONCLUSIONS: Treatment with nalmefene was effective in preventing relapse to heavy drinking relative to placebo in alcohol-dependent outpatients and was accompanied by acceptable side effects.

DNA structure: cations in charge?

Recent X-ray diffraction, NMR spectroscopy and molecular mechanics results suggest that monovalent cations selectively partition into the minor groove of AT-tracts in DNA. These observations are consistent with DNA deformation by electrostatic collapse around areas of uneven cation density. This model predicts the occurrence of known DNA deformations, such as AT-tract bending and changes in the minor-groove width.

Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations.

The potassium form of d(CGCGAATTCGCG) solved by X-ray diffraction to 1.75 A resolution indicates that monovalent cations penetrate the primary and secondary layers of the "spine of hydration". Both the sodium [Shui, X., McFail-Isom, L., Hu, G. G., and Williams, L. D. (1998) Biochemistry 37, 8341-8355] and the potassium forms of the dodecamer at high resolution indicate that the original description of the spine, only two layers deep and with full occupancy by water molecules, requires substantive revision. The spine is merely the bottom two layers of a four layer solvent structure. The four layers combine to form a repeating motif of fused hexagons. The top two solvent layers were not apparent from previous medium-resolution diffraction data. We propose that the narrow minor groove and axial curvature of A-tract DNA arise from localization of cations within the minor groove. In general, the results described here support a model in which most or all forces that drive DNA away from canonical B-conformation are extrinsic and arise from interaction of DNA with its environment. Intrinsic forces, originating from direct base-base interactions such as stacking, hydrogen bonding, and steric repulsion among exocyclic groups appear to be insignificant. The time-averaged positions of the ubiquitous inorganic cations that surround DNA are influenced by DNA bases. The distribution of cations depends on sequence. Regions of high and low cation density are generated spontaneously in the solvent region by heterogeneous sequence or even within the grooves of homopolymers. The regions of high and low cation density deform DNA by electrostatic collapse. Thus, the effects of small inorganic cations on DNA structure are similar to the effects of proteins.

Oxyanion-mediated inhibition of serine proteases.

Novel aryl derivatives of benzamidine were synthesized and tested for their inhibitory potency against bovine trypsin, rat skin tryptase, human recombinant granzyme A, human thrombin, and human plasma kallikrein. All compounds show competitive inhibition against these proteases with Ki values in the micromolar range. X-ray structures were determined to 1.8 A resolution for trypsin complexed with two of the para-substituted benzamidine derivatives, 1-(4-amidinophenyl)-3-(4-chlorophenyl)urea (ACPU) and 1-(4-amidinophenyl)-3-(4-phenoxyphenyl)urea (APPU). Although the inhibitors do not engage in direct and specific interactions outside the S1 pocket, they do form intimate indirect contacts with the active site of trypsin. The inhibitors are linked to the enzyme by a sulfate ion that forms an intricate network of three-centered hydrogen bonds. Comparison of these structures with other serine protease structures with noncovalently bound oxyanions reveals a pair of highly conserved oxyanion-binding sites in the active site. The positions of noncovalently bound oxyanions, such as the oxygen atoms of sulfate, are distinct from the positions of covalent oxyanions of tetrahedral intermediates. Noncovalent oxyanion positions are outside the "oxyanion hole." Kinetics data suggest that protonation stabilizes the ternary inhibitor/oxyanion/protease complex. In sum, both cations and anions can mediate Ki. Cation mediation of potency of competitive inhibitors of serine proteases was previously reported by Stroud and co-workers [Katz, B. A., Clark, J. M., Finer-Moore, J. S., Jenkins, T. E., Johnson, C. R., Ross, M. J., Luong, C., Moore, W. R., and Stroud, R. M. (1998) Nature 391, 608-612].

Divalent cations stabilize unstacked conformations of DNA and RNA by interacting with base pi systems.

Nucleic acid structure, stability, and reactivity are governed substantially by cations. We propose that magnesium and other biological inorganic ions unstack bases of DNA and RNA. This unstacking function of cations opposes their previously accepted role in stabilizing DNA and RNA duplexes and higher assemblies. We show that cations interact favorably with pi-systems of nucleic acid bases. These cation-pi interactions require access of cations or their first hydration shells to faces of nucleic acid bases. We observe that hydrated magnesium ions located in the major groove of B-DNA pull cytosine bases partially out from the helical stack, exposing pi-systems to positive charge. A series of critical cation-pi interactions contribute to the stability of the anticodon arm of yeast-tRNAphe, and to the magnesium core of the Tetrahymena group I intron P4-P6 domain. The structural consequences of divalent cation-pi interactions are clearly distinct from, and some cases in opposition to, cation-electron lone pair interactions. These observations of cation-pi interactions suggest a number of new mechanistic roles for cations in DNA bending, DNA-protein recognition, base-flipping, RNA folding, and catalysis.

Migration of electrons and holes in crystalline d(CGATCG)-anthracycline complexes X-irradiated at 4 K.

Electrons and holes generated in irradiated DNA migrate to stable trapping sites. Protonation and deprotonation reactions at these sites promote the trapping of electrons and holes, thereby inhibiting further migration. The extent of migration determines the final distribution of damage in irradiated DNA. In this study, electron and hole migration is investigated in a crystalline DNA hexamer intercalated with an anthracycline drug. The intercalator is no further than 2 base pairs away from any DNA base. From EPR measurements, there is no evidence of DNA-centered radicals in the irradiated DNA hexamer. The aromatic region of the anthracycline intercalator evidently sequesters most or all of the electrons and most of the holes. Further hole trapping and radical stabilization appear to occur on the anthracycline's amino sugar group, which is nestled in the minor groove of the hexamer. The relatively large yield of this proposed amino sugar radical suggests that holes generated in the DNA solvation shell migrate to the amino sugar, where they become trapped. This would be the first observation of a radical formed by the direct effect of low-dose, low-LET radiation that is trapped within the DNA helix, yet lies outside of the stacked bases. With respect to holes generated in the DNA bases at 4 K, we conclude that most, if not all, are capable of migrating to an intercalator < or = 2 base pairs away. With respect to dry electrons, we conclude that anthracycline competes effectively for electron trapping over a region of at least 2 base pairs; our experiments cannot distinguish between electron attachment to the bases followed by transfer to the intercalator and direct attachment to the intercalator.

Why do strangers feel familiar, but friends don't? A discrepancy-attribution account of feelings of familiarity.

Recent articles on familiarity (e.g. Whittlesea, B.W.A, 1993. Journal of Experimental Psychology 19, 1235) have argued that the feeling of familiarity is produced by unconscious attribution of fluent processing to a source in the past. In this article, we refine that notion: We argue that is not fluency per se, but rather fluent processing occurring under unexpected circumstances that produces the feeling. We demonstrate cases in which moderately fluent processing produces more familiarity than does highly fluent processing, at least when the former is surprising.

The B-DNA dodecamer at high resolution reveals a spine of water on sodium.

We describe a very accurate addition (called structure X here) to the B-DNA dodecamer family of X-ray structures. Our results confirm the observation of Drew and Dickerson [(1981) J. Mol. Biol. 151, 535-556] that the spine of hydration in AT tract DNA is two layers deep. However, our results suggest that the primary spine is partially occupied by sodium ions. We suggest that many sequence-dependent features of DNA conformation are mediated by site specific binding of cations. For example, preferential localization of cations, as described here within the minor groove of structure X, is probably the structural origin of AT tract bending and groove narrowing. The secondary spine, which does not interact directly with the DNA, is as geometrically regular as the primary spine, providing a model for transmission of sequence information into solvent regions. A fully hydrated magnesium ion located in the major groove of structure X appears to pull cytosine bases partially out from the helical stack, exposing pi-systems to partial positive charges of the magnesium ion and its outer sphere. A partially ordered spermine molecule is located within the major groove of structure X. Dodecamer structures are derived from crystals of [d(CGCGAATTCGCG)]2 in space group P212121 (a = 25 A, b = 40 A, and c = 66 A). On average, those crystals diffracted to around 2.5 A resolution with 2500 unique reflections. Structure X, with the same space group, DNA sequence, and crystal form as the "Dickerson dodecamer", is refined against a complete, low-temperature, 1.4 A resolution data set, with over 11000 reflections. Structure X appears to be conformationally more ordered than previous structures, suggesting that at least a portion of the conformational heterogeneity previously attributed to DNA sequence in fact arises from experimental error.

Melting of a DNA hairpin without hyperchromism.

UV absorbance spectroscopy is the most common method for detecting nucleic acid structural transitions and obtaining thermodynamic parameters. UV-detected melting has been used to determine stabilities of nucleic acid hairpins, duplexes, triplexes, and higher order structures and to determine thermodynamic effects of unusual or modified bases and mismatched base-pairs. We report that in some cases UV absorbance spectroscopy is an inadequate analytical technique for these purposes. Some critical transitions are invisible to UV absorbance spectroscopy. For example, the conversion of dodecamer d(CGCAAATTCGCG) from hairpin to random coil is not accompanied by hyperchromism. Circular dichroism (CD) spectroscopy (263 nm) clearly detects two transitions for this dodecamer, each giving a pronounced change in ellipiticity. The concentration dependence of the low-temperature transition and the concentration independence of the high-temperature transition indicate that the predominant state converts from duplex to hairpin to random coil as the temperature increases. These assignments are confirmed by comparison to oligonucleotides of similar sequence that undergo a hairpin to coil transition only. In contrast to CD spectroscopy, UV absorbance spectroscopy shows only a single transition. The transition detected by UV absorbance spectroscopy corresponds to the low-temperature transition detected by CD. UV absorbance spectroscopy does not detect the second transition at any wavelength (from 218 to 310 nm) (by changes) in either absorbance or its derivative with temperature.