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. Fe_1-xGa_x 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 Fe_1-xGa_x 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 Fe_1-xGa_x - [Pb(Mg_1/3Nb_2/3)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.

Selectivity of binding of PEGs and PEG-like oligomers to anti-PEG antibodies induced by methoxyPEG-proteins

The use of methoxypoly(ethylene glycol) (mPEG) in PEG conjugates of proteins and non-protein therapeutic agents has led to the recognition that the polymer components of such conjugates can induce anti-PEG antibodies (anti-PEGs) that may accelerate the clearance and reduce the efficacy of the conjugates. Others have classified anti-PEGs as "methoxy-specific" or "backbone-specific". The results of our previous research on anti-PEGs in the sera of rabbits immunized with mPEG or hydroxyPEG (HO-PEG) conjugates of three unrelated proteins were consistent with that classification (Sherman, M.R., et al., 2012. Bioconjug. Chem. 23, 485-499). Enzyme-linked immunosorbent assays (ELISAs) were performed on rabbit antisera and rabbit monoclonal anti-PEGs with competitors including 10 kDa mPEG, 10 kDa PEG diol and six linear or cyclic oligomers of oxyethylene (CH2CH2O), with molecular weights of ca. 150-264 Da. Our results demonstrate that (1) the binding affinities of anti-mPEGs depend more on the backbone lengths of the polymers and the hydrophobicities of their end-groups than on their resemblance to the methoxy terminus of the immunogenic polymer; (2) anti-PEGs raised against HO-PEG-proteins are not directed against the terminal hydroxy group, but against the backbone; (3) rabbit anti-PEGs bind to and distinguish among PEG-like oligomers with as few as three oxyethylene groups; and (4) none of the monoclonal or polyclonal anti-PEGs was absolutely "methoxy-specific" or "backbone-specific", but displayed distinct relative selectivities. If these results are relevant to human immune responses, the clinical use of stable conjugates of HO-PEG with proteins and non-protein therapeutic agents would be expected to produce fewer and less intense immune responses than those induced by conjugates with mPEG or PEGs with larger alkoxy groups.

Role of the methoxy group in immune responses to mPEG-protein conjugates

Anti-PEG antibodies have been reported to mediate the accelerated clearance of PEG-conjugated proteins and liposomes, all of which contain methoxyPEG (mPEG). The goal of this research was to assess the role of the methoxy group in the immune responses to mPEG conjugates and the potential advantages of replacing mPEG with hydroxyPEG (HO-PEG). Rabbits were immunized with mPEG, HO-PEG, or t-butoxyPEG (t-BuO-PEG) conjugates of human serum albumin, human interferon-α, or porcine uricase as adjuvant emulsions. Assay plates for enzyme-linked immunosorbent assays (ELISAs) were coated with mPEG, HO-PEG, or t-BuO-PEG conjugates of the non-cross-reacting protein, porcine superoxide dismutase (SOD). In sera from rabbits immunized with HO-PEG conjugates of interferon-α or uricase, the ratio of titers of anti-PEG antibodies detected on mPEG-SOD over HO-PEG-SOD (“relative titer”) had a median of 1.1 (range 0.9–1.5). In contrast, sera from rabbits immunized with mPEG conjugates of three proteins had relative titers with a median of 3.0 (range 1.1–20). Analyses of sera from rabbits immunized with t-BuO-PEG-albumin showed that t-butoxy groups are more immunogenic than methoxy groups. Adding Tween 20 or Tween 80 to buffers used to wash the assay plates, as is often done in ELISAs, greatly reduced the sensitivity of detection of anti-PEG antibodies. Competitive ELISAs revealed that the affinities of antibodies raised against mPEG-uricase were c. 70 times higher for 10 kDa mPEG than for 10 kDa PEG diol and that anti-PEG antibodies raised against mPEG conjugates of three proteins had >1000 times higher affinities for albumin conjugates with c. 20 mPEGs than for analogous HO-PEG-albumin conjugates. Overall, these results are consistent with the hypothesis that antibodies with high affinity for methoxy groups contribute to the loss of efficacy of mPEG conjugates, especially if multiply-PEGylated. Using monofunctionally activated HO-PEG instead of mPEG in preparing conjugates for clinical use might decrease this undesirable effect.

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.

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.

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.

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.

Diabetes insipidus in uricase-deficient mice: a model for evaluating therapy with poly(ethylene glycol)-modified uricase

Uricase-deficient mice develop uric acid nephropathy, with high mortality rates before weaning. Urate excretion was quantitated and renal function was better defined in this study, to facilitate the use of these mice as a model for evaluating poly(ethylene glycol)-modified recombinant mammalian uricases (PEG-uricase) as a potential therapy for gout and uric acid nephropathy. The uric acid/creatinine ratio in the urine of uricase-deficient mice ranges from 10 to >30; on a weight basis, these mice excrete 20- to 40-fold more urate than do human subjects. These mice consistently develop a severe defect in renal concentrating ability, resulting in an approximately sixfold greater urine volume and a fivefold greater fluid requirement, compared with normal mice. This nephrogenic diabetes insipidus leads to dehydration and death of nursing mice but, with adequate water replacement, high urine flow protects adults from progressive renal damage. Treatment of uricase-deficient mice with PEG-uricase markedly reduced urate levels and, when initiated before weaning, preserved the renal architecture (as evaluated by magnetic resonance micros-copy) and prevented the loss of renal concentrating function. PEG-uricase was far more effective and less immunogenic than unmodified uricase. Retention of uricase in most mammals and its loss in humans and some other primates may reflect the evolution of renal function under different environmental conditions. PEG-uricase could provide an effective therapy for uric acid nephropathy and refractory gout in human patients.

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 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).

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.

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.

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.

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].

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.

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.

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.

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.

Structure of a DNA-bisdaunomycin complex

The application of detailed structural data bases has now culminated in the successful design of a new generation of bisanthracyclines that form ultratight DNA complexes [Chaires, J. B., Leng, F., Przewloka, T., Fokt, I., Ling, Y. H., Perez-Soler, R., & Priebe, W. (1997) J. Med. Chem. 40, 261-266]. Daunomycin dimers were designed to bind to DNA in complexes resembling those of monomers intercalated at adjacent sites. The goal of the work described here was to determine, with X-ray crystallography, if a potent member of this newly designed and synthesized class of bisanthracyclines (WP631) binds as intended. WP631 is composed of two daunomycin molecules, linked N3' to N3' by a xylyl group. We have solved the 2.2 A X-ray crystal structure of a complex of WP631 bound to [d(CGATCG)]2. We demonstrate, on a detailed molecular level, that the WP631 design strategy is a success. The structures of WP631 and two daunomycin molecules bound to [d(CGATCG)]2 provide the unprecedented opportunity for detailed comparison of mono- and bis-intercalated complexes of the same chromophore, allowing us to distinguish effects of mono-intercalation from those of bis-intercalation. Differences are focused primarily in the centers of the complexes. DNA unwinding and other helical distortions propagate more efficiently to the center of the WP631 complex than to the center of the daunomycin complex.

A novel assay for drug-DNA binding mode, affinity, and exclusion number: scanning force microscopy

Determining the mode-of-binding of a DNA ligand is not always straightforward. Here, we establish a scanning force microscopic assay for mode-of-binding that is (i) direct: lengths of individual DNA-ligand complexes are directly measured; (ii) rapid: there are no requirements for staining or elaborate sample preparation; and (iii) unambiguous: an observed increase in DNA length upon addition of a ligand is definitive evidence for an intercalative mode-of-binding. Mode-of-binding, binding affinity, and site-exclusion number are readily determined from scanning force microscopy measurements of the changes in length of individual drug-DNA complexes as a function of drug concentration. With this assay, we resolve the ambiguity surrounding the mode of binding of 2,5-bis(4-amidinophenyl) furan (APF) to DNA and show that it binds to DNA by nonintercalative modes. APF is a member of an important class of aromatic dicationic drugs that show significant activity in the treatment of Pneumocystis carinii pneumonia, an opportunistic infection that is the leading cause of death in AIDS patients.

Inhibition of trypsin and thrombin by amino(4-amidinophenyl)methanephosphonate diphenyl ester derivatives: X-ray structures and molecular models

X-ray structures of trypsin from bovine pancreas inactivated by diphenyl [N-(benzyloxycarbonyl)amino](4-amidinophenyl)methanephosphonate [Z-(4-AmPhGly)P(OPh)2] were determined at 113 and 293 K to 1.8 angstrom resolution and refined to R factors of 0.211 (113 K) and 0. 178 (293 K). The structures reveal a tetrahedral phosphorus covalently bonded to the O gamma of the active site serine. Covalent bond formation is accompanied by the loss of both phenoxy groups. The D-stereoisomer of Z-(4-AmPhGly)P-(OPh)2 is not observed in the complex. The L-stereoisomer of the inhibitor forms contacts with several residues in the trypsin active site. One of the phosphonate oxygens is inserted into the oxyanion hole and forms hydrogen bonds to the amides of Gly193, Asp194, and Ser195. The second phosphonate oxygen forms hydrogen bonds to N epsilon 2 of His 57. The p-amidinophenylglycine moiety binds into the trypsin primary specificity pocket, interacting with Asp189. The amide forms a hydrogen bond to the carbonyl oxygen atom of Ser214. The inhibitor moiety, from the 113 K structure of trypsin inactivated by the reaction product of Z-(4-AmPhGly)P(OPh)2, was docked into human thrombin [Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S. R., & Hofsteenge, J. (1989) EMBO J. 8, 3467-3475] and energy minimized. The inhibitor fits well into the thrombin active site, forming favorable contacts similar to those in the trypsin complex with no bad contacts.

Structure of DNA-porphyrin complex

We report the 2.4 A resolution X-ray structure of a complex in which a small molecule flips a base out of a DNA helical stack. The small molecule is a metalloporphyrin, CuTMPyP4 [copper(II) meso-tetra(N-methyl-4-pyridyl)porphyrin], and the DNA is a hexamer duplex, [d(CGATCG)]2. The porphyrin system, with the copper atom near the helical axis, is located within the helical stack. The porphyrin binds by normal intercalation between the C and G of 5' TCG 3' and by extruding the C of 5' CGA 3'. The DNA forms a distorted right-handed helix with only four normal cross-strand Watson-Crick base pairs. Two pyridyl rings are located in each groove of the DNA. The complex appears to be extensively stabilized by electrostatic interactions between positively charged nitrogen atoms of the pyridyl rings and negatively charged phosphate oxygen atoms of the DNA. Favorable electrostatic interactions appear to draw the porphyrin into the duplex interior, offsetting unfavorable steric clashes between the pyridyl rings and the DNA backbone. These pyridyl-backbone clashes extend the DNA along its axis and preclude formation of van der Waals stacking contacts in the interior of the complex. Stacking contacts are the primary contributor to stability of DNA. The unusual lack of van der Waals stacking contacts in the porphyrin complex destabilizes the DNA duplex and decreases the energetic cost of local melting. Thus extrusion of a base appears to be facilitated by pyridyl-DNA steric clashes.

Clathrate hydrates are poor models of biomolecule hydration

Clathrate hydrates form the basis of a general model of biomolecule hydration. In clathrate hydrate crystal structures, the size of hydrogen-bonded water rings is highly constrained to five members. The clathrate hydrate model predicts that the size of water rings near biomolecule surfaces is similarly constrained to five members. This report describes a test of this model of biomolecule hydration. We have demonstrated that five-membered water rings are not a general feature of protein or nucleic acid hydration. The clathrate hydrate model appears to be inappropriate for soluble biomolecules.

Asymmetry and dynamics in bis-intercalated DNA

The bis-intercalator ditercalinium (NSC 366241), composed of two 7 H-pyridocarbazoles linked by a bis(ethylpiperidinium), binds to DNA with a binding constant greater than 10(7) M-1. One distinctive aspect of the 3-D X-ray structure of a DNA-ditercalinium complex is its asymmetry. We propose here that the activity of ditercalinium may be related to structural polymorphism and dynamic conversion between conformers. It was previously reported that activity is closely related to linker composition. Activity increases with increasing conformational restraints of the linker. We suggest these conformational restraints can lead to asymmetry in DNA complexes and that this asymmetry results directly in structural polymorphism. Using the Cambridge Structural Database (CSD) as a source of information about chemical fragments that are analogous to the linker of ditercalinium, we have explored the conformational space available to ditercalinium. The results indicate that the linker is highly constrained and that the DNA complex is intrinsically asymmetric. We propose a reasonable mechanism of ring reversal that is consistent with the conformations of analogous fragments within the CSD.

A clinical and molecular genetic study of dentatorubropallidoluysian atrophy in four European families

Dentatorubropallidoluysian atrophy is a neurodegenerative disorder with characteristic pathology, chiefly described in reports from Japan, and is associated with an unstable CAG trinucleotide repeat in a gene on chromosome 12. We describe four European families, three British and one Maltese, with this mutation. All exhibited autosomal dominant inheritance, and there was evidence for anticipation associated with an increase of the expansion with paternal transmission in two families. Affected chromosomes from patients with dentatorubropallidoluysian atrophy had CAG expansions of 58 to 74 repeats, compared to 7 to 26 in control chromosomes, and the size of repeat was significantly inversely correlated with age of onset. The clinical features were diverse, even within individual families, and comprised a combination of a movement disorder (chorea, myoclonus, dystonia, or parkinsonism), cerebellar ataxia, epilepsy, psychosis, and dementia. A clinical diagnosis of Huntington's disease had been made in affected individuals from all families. Neuropathological examination of 2 patients showed no specific abnormality in one and degenerative changes predominantly affecting the spinal cord in the other. Investigation of 55 patients who might represent sporadic examples of dentatorubropallidoluysian atrophy did not detect any expanded alleles. Dentatorubropallidoluysian atrophy is likely to be more common than previously recognized in non-Japanese populations, and should be considered in any patient with a dominantly inherited neurodegenerative disorder with the above-mentioned clinical features.

X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine

We have determined the x-ray structure of a DNA fragment containing 7,8-dihydro-8-oxoguanine (G(O)). The structure of the duplex form of d(CCAGOCGCTGG) has been determined to 1.6-A resolution. The results demonstrate that GO forms Watson-Crick base pairs with the opposite C and that G(O) is in the anti conformation. Structural perturbations induced by C.G(O)anti base pairs are subtle. The structure allows us to identify probable elements by which the DNA repair protein MutM recognizes its substrates. Hydrogen bond donors/acceptors within the major groove are the most likely element. In that groove, the pattern of hydrogen-bond donors/acceptors of C.G(O)anti is unique. Additional structural analysis indicates that conversion of G to G(O) would not significantly influence the glycosidic torsion preference of the nucleoside. There is no steric interaction of the 8-oxygen of G(O) with the phospho-deoxyribose backbone.

DNA distortion in bis-intercalated complexes

The bis-intercalators Flexi-Di and ditercalinium are synthetic dimers that bis-intercalate into DNA and cause cell death in prokaryotes from futile and abortive repair of DNA. Each is composed of two 7H-pyridocarbazole units and a linker. Flexi-Di has a flexible spermine-like linker while ditercalinium has a rigid bis(ethylpiperidinium) linker. This report, describing the 2.5-A X-ray structure of Flexi-Di complexed with [d(BrCGCG)]2, appears to be the first report of a three-dimensional structure of a DNA complex with a bis-intercalator with a flexible linker. DNA complex formation with a ditercalinium analog having a flexible linker was not anticipated to yield unstacked and bent DNA as was observed in the previously reported ditercalinium.[d(CGCG)]2 complex. Surprisingly, the DNA in the Flexi-Di complex is bent to a degree exceeding that of the ditercalinium complex. A comparison of the DNA complexes of Flexi-Di and ditercalinium has allowed us to propose a mechanism by which these bis-intercalators distort DNA. We propose that this class of bis-intercalators pulls the internal base pairs into the major groove and pushes the external base pairs into the minor groove. The result is a bend toward the minor groove. It appears that hydrogen bonds between the linker and the internal guanines effectively pull the central base pairs of the complex out into the major groove. At the external regions of the complex, stacking interactions between the chromophores and terminal base pairs effectively push the terminal base pairs into the minor groove. The result of this push/pull combination is to bend the DNA.

Water ring structure at DNA interfaces: hydration and dynamics of DNA-anthracycline complexes

In crystallographic structures of biological macromolecules, one can observe many hydration rings that originate at one water molecule, pass via hydrogen bonds through several others, and return to the original water molecule. Five-membered water rings have been thought to occur with greater frequency than other ring sizes. We describe a quantitative assessment of relationships between water ring size and frequency of occurrence in the vicinity of nucleic acid interfaces. This report focuses on low-temperature X-ray crystallographic structures of two anthracyclines, adriamycin (ADRI) and daunomycin (DAUN), bound to d(CGATCG) and on several DNA structures published previously by others. We have obtained excellent low-temperature (-160 degrees C, LT) X-ray intensity data for d(CGATCG)-adriamycin and d(CGATCG)-daunomycin with a multiwire area detector. The LTX-ray data sets contain 20% (daunomycin, LT-DAUN) and 35% (adriamycin, LT-ADRI) more reflections than were used to derive the original room-temperature (15 degrees C) structures [Frederick, C.A., Williams, L.D., Ughetto, G., van der Marel, G. A., van Boom, J.H., Rich, A., & Wang, A.H.-J. (1990) Biochemistry 29, 2538-2549]. The results show that five-membered water rings are not preferred over other ring sizes. This assessment is consistent with our observation of broad dispersion W-W-W angles (sigma = 20 degrees). In addition, we report that the thermal mobility, distinct from the static disorder, of the amino sugar of daunomycin and adriamycin is significantly greater than that of the rest of the complex. This mobility implies that if the central AT base pair is switched to a CG base pair, there should be a low energy cost in avoiding the guanine amino group. The energy difference (for the sugar-binding preference) between d(CGTACG) and d(CGCGCG) could be considerably less than 20 kcal/mol, a value proposed previously from computation.

The low-temperature crystal structure of the pure-spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove

The X-ray crystal structure of the pure-spermine form of the left-handed Z-DNA duplex [d(CGCGCG)]2 has been determined at a temperature of -110 degrees C. Whereas the previously described room temperature structure of the pure-spermine form showed only the presence of a single "interhelix" spermine molecule, mediating contacts between neighboring duplexes (Egli et al., 1991), a second "intrahelix" spermine molecule as well as two hydrated sodium ions were found in the structure determined at low temperature. This second spermine molecule binds primarily within the minor groove of two hexamer duplexes that are stacked in an end-to-end fashion in the crystal lattice. Thus, the intrahelix spermine molecule interacts with a single infinite helix. The spine of hydration observed in other structures of Z-DNA hexamers is partially replaced and partially displaced by the intrahelix spermine molecule. In Z-DNA, phosphate groups are relatively closely spaced across the minor groove compared to the right-handed double-helical conformation of B-DNA. The intrahelix spermine molecule decreases cross-groove electrostatic repulsion within the Z-DNA helix, thereby increasing its relative stability. This structure may therefore provide an explanation for the role of spermine as a very effective inducer of the conformational B-DNA to Z-DNA transition with alternating dG-dC sequences in solution.

Plasma clearance and immunologic properties of long-acting superoxide dismutase prepared using 35,000 to 120,000 dalton poly-ethylene glycol

Some biological properties of bovine and recombinant human Cu,Zn superoxide dismutase (bSOD and rhSOD)-poly-ethylene glycol (PEG) adducts prepared by coupling 1-9 strands of high molecular weight PEG (35,000-120,000 daltons) are compared to SOD adducts coupled with 7 or 15 strands of low molecular weight PEG (5,000 daltons). Plasma clearance after i.v. injection was measured in mice and dogs. Conjugates of bSOD with 2 strands of PEG 40,000, 3 strands of PEG 72,000 or 1 strand of PEG 100,000 demonstrated half-lives of about 36 hours in mice, whereas the half-life of a conjugate with 7 strands of PEG 5,000 was about 24 hours. A PEG-bSOD with an average of 3.3 strands of PEG 41,000 was cleared from plasma with a terminal half-life of 36 to 48 hours after intraperitoneal injection in mice. PEG-SODs prepared from bSOD and rhSOD with 3 strands of PEG 50,000 each had plasma half-lives of approximately five days in dogs. An enzyme immunoassay (ELISA) was employed to measure cross-reactivity with a rabbit antibody directed against bSOD. A series of bSOD adducts with 2 to 9 strands of PEG 35,000-120,000 were compared to PEG-bSODs with 7 or 15 strands of PEG 5,000. Attaching larger PEG strands was at least 3 times more effective in reducing antigenicity, compared to PEG 5,000. Ability to induce sensitizing antibodies was measured using subcutaneous sensitization followed by i.v. or s.c. challenge in mice. Some bSOD conjugates with either 7 or 15 strands of PEG 5,000 induced sensitization reactions before the sixth challenge. Fewer than 1% of the animals tested with bSOD or rhSOD adducts with 3 or 4 strands of PEG 65,000, or 3 strands of PEG in the 30,000-50,000 molecular weight range, showed signs of anaphylaxis during six or seven challenges. In a passive cutaneous anaphylaxis test (optimized to measure mouse IgE), neither bSOD coupled to 2 strands of PEG 120,000 nor bSOD coupled to 9 strands of PEG 35,000 induced detectable antibodies against either of these PEG-bSOD preparations or against bSOD; however, the adduct with 2 strands of PEG 120,000 reacted weakly with pre-formed antibodies to bSOD. The high molecular weight PEG-bSODs tested were not immunogenic, but were weakly antigenic, compared to bSOD.

Death investigations on military installations

The authority to conduct a death investigation, including an autopsy examination, on a military installation depends upon the type of jurisdiction on the installation and the decedent's military connection. Exclusive federal jurisdiction gives the military authority to investigate deaths of active duty military members and, under specific conditions, of civilians with a military connection. Concurrent or shared jurisdiction gives the local civilian medical examiner the right of first refusal as to military members. Thus, the civilian medical examiner may waive jurisdiction to the military. This is not the case when a civilian dies under the same circumstances.

Jurisdiction on military installations

The death of an individual on a military installation often raises the question of who has the authority to investigate that death and perform an autopsy. The answer to this question depends upon whether jurisdiction is exclusively federal or is shared by the state and federal governments. Jurisdiction can be determined by contacting the installation's Directorate of Engineering and Housing or the legal office. When there is exclusive federal jurisdiction, the installation commander or the Armed Forces Medical Examiner may authorize an autopsy on a military member. Under certain conditions, the installation commander may authorize an autopsy on a civilian, especially where a legitimate connection exists between that civilian and the federal government. When jurisdiction is concurrent (that is, shared by the state and federal governments), the civilian medical examiner may waive jurisdiction to the military, but only as to the death of a military member. The authority to investigate the death of a civilian (whether a military dependent or not), to include autopsy examination, is exclusively civilian when jurisdiction is concurrent. Overseas locations are controlled by special agreements that in general, give the U.S. government jurisdiction over military members, their dependents, and U.S. civilian components of the assigned force.

DNA-ditercalinium interactions: implications for recognition of damaged DNA

Ditercalinium is unique among known DNA-binding chemotherapeutic agents. Ditercalinium treatment of Escherichia coli causes cell death by provoking malfunction of the (A)BC exinuclease excision DNA repair system. In this report, we describe the three-dimensional X-ray structure of a ditercalinium-[d(CGCG)]2 complex in detail with an analysis of both the structure and its implications. Ditercalinium bisintercalates in the DNA fragment; the positively-charged linker of the drug interacts with the major groove. The DNA retains an underwound, right-handed, double-helical conformation with a bend of around 15 degrees in the helical axis. One striking feature of the complex is the extensive interaction of ditercalinium with guanines in contrast to the near absence of interaction with cytosines. The terminal cytosines in particular are "unstacked" from the rest of the complex. A systematic comparison of the three-dimensional structure of the DNA-ditercalinium complex with those of triostin A and nogalamycin (chemotherapeutic agents that act by conventional mechanisms) allows us to suggest a general model for recognition by the (A)BC exinuclease excision repair system. It is commonly hypothesized that the same distorted conformation of DNA results from modification by each member of a diverse family of DNA-damaging agents. This specific conformation of DNA would then be recognized by the (A)BC exinuclease excision repair system. Alternatively, we propose that each of these damaging agents causes local instability of DNA (but not necessarily a common conformation) and that the (A)BC exinuclease excision repair system recognizes excessive or unusual deformability of damaged DNA in comparison to normal DNA.

Variable temperature infrared spectroscopy of cytosine-guanine base pairs: tautomerism versus polarization

This report describes an infrared (IR) spectroscopic study of a model cytosine-guanine base pair. This base pair is part of a self-consistent experimental system based on lipophilic ribose derivatives of cytidine (C), guanosine (G) and O6-methylguanosine (O6MeG) that are soluble in non-aqueous, low dielectric solvents at appreciable concentrations. Previous experiments on this system have revealed different rotation dynamics for the amino bonds within the CG base pair, an observation that could be explained by the presence of rare tautomers (P.O. Lowdin, Reviews of Modern Physics 35,724 (1963)), or by mutual polarization of the base pairs (L.D. Williams, N.G. Williams and B.R. Shaw,J.Am.Chem.Soc. 112,829 (1990)). The IR spectra in the OH and NH stretching region indicate formation of hydrogen-bonded CG base pairs and self associates in 1,2-dichlorobenzene over a temperature range from 10 to 290K. Changes in the lineshapes and intensities of the IR bands with temperature correlate with phase transitions of the solvent, but no evidence is seen for an OH stretching band that would indicate the formation of hydroxyl tautomers within base pairs. Similarly, the relative intensities of the C = O stretching bands of CG in cyclohexane solution remain constant over this same temperature range, confirming that within the base pair, the tautomeric states of the bases remain essentially unperturbed in the 2-amino/6-keto form of G and the 2-keto/4-amino form of C. The spectra of O6-MeG aid in the band assignments, since this molecule is frozen in an equivalent of the 2-amino/6-hydroxyl tautomer, but without the OH group and its associated stretching band. We conclude that the probability of tautomerism does not appear to be sufficient to explain the different rotation dynamics for the two amino bonds of the CG base pair. Rather it is argued that mutual polarization within the base pair, which would increase the bond order of the amino bond of C within the base pair, can explain the results without the formation of unconventional tautomers.

Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-A resolution

We describe the three-dimensional X-ray structure of a complex of spermine bound to a Z-DNA duplex, [d(CGCGCG)]2, in the absence of any inorganic polyvalent cations. We have crystallized the DNA hexamer d(CGCGCG) in the exclusion of magnesium and other polyvalent ions and solved its structure at 1.0-A resolution. In the crystal of this pure-spermine form of Z-DNA, the relative orientation, position, and interactions of the DNA differ from the arrangement uniformly observed in over a dozen previously reported Z-DNA hexamers. Moreover, the conformation of the Z-DNA hexamer in this structure varies somewhat from those found in earlier structures. The DNA is compressed along the helical axis, the base pairs are shifted into the major groove, and the minor groove is more narrow. The packing of spermine-DNA complexes in crystals suggests that the molecular basis for the tendency of spermine to stabilize compact DNA structures derives from the capacity of spermine to interact simultaneously with several duplexes. This capacity is maximized by both the polymorphic nature and the length of the spermine cation. The length and flexibility of spermine and the dispersion of charge-charge, hydrogen-bonding, and hydrophobic bonding potential throughout the molecule maximize the ability of spermine to interact simultaneously with different DNA molecules.

Implications and concepts of polyamine-nucleic acid interactions

Modeling, x-ray diffraction, and solution studies have contributed to the understanding of interactions between polyamines and nucleic acids. Polyamines stabilize a variety of unusual DNA structures and conformations in vitro, including both the left-handed Z and the right-handed A DNA. In addition, polyamines condense DNA and may be important in bending specific sequences. Investigations into the mechanisms of these effects provide support for both specific and nonspecific interactions between polyamines and DNA. Although exact relationships between the binding of polyamines and conformational changes in nucleic acids are still being clarified, polyamines remain important candidates for regulators of DNA conformation in vivo.

Drug-induced DNA repair: X-ray structure of a DNA-ditercalinium complex

Ditercalinium is a synthetic anticancer drug that binds to DNA by bis-intercalation and activates DNA repair processes. In prokaryotes, noncovalent DNA-ditercalinium complexes are incorrectly recognized by the uvrABC repair system as covalent lesions on DNA. In eukaryotes, mitochondrial DNA is degraded by excess and futile DNA repair. Using x-ray crystallography, we have determined, to 1.7 A resolution, the three-dimensional structure of a complex of ditercalinium bound to the double-stranded DNA fragment [d(CGCG)]2. The DNA in the complex with ditercalinium is kinked (by 15 degrees) and severely unwound (by 36 degrees) with exceptionally wide major and minor grooves. Recognition of the DNA-ditercalinium complex by uvrABC in prokaryotes, and by mitochondrial DNA repair systems in eukaryotes, might be related to drug-induced distortion of the DNA helix.

DNA-nogalamycin interactions

The anthracycline antibiotic nogalamycin differs from the more common daunomycin-type anthracyclines by substitution on both ends of the intercalating chromophore, giving nogalamycin the approximate shape of a dumbbell. The chromophore of daunomycin is substituted on only one end. In nogalamycin, the positively charged amino sugar substituent of daunomycin is replaced by an uncharged nogalose sugar and a methyl ester group. The other end of nogalamycin, where daunomycin is unsubstituted, is fused to a bicyclo amino sugar with a positively charged dimethylamino group. Much larger DNA fluctuations are required for intercalative entry of nogalamycin than for entry of daunomycin. This report describes the X-ray crystal structure of the complex between nogalamycin and the self-complementary DNA hexamer d(me5CGTsAme5CG). The DNA contains cytosines methylated at the 5-positions and a phosphorothioate linkage at the TpA step. Nogalamycin intercalates at the terminal CpG steps and interacts with both strands in both grooves of the DNA. Large conformational adjustments in both nogalamycin and the DNA are necessary to form a stable, intercalative complex. The interactions of the bases with the nogalamycin substituents lead to sliding of bases relative to each other along the normal to Watson-Crick hydrogen bonds. The planarities of base pairs surrounding the intercalation site are distorted. The backbones of the two strands are distorted asymmetrically by nogalamycin with large deviations from standard B-DNA geometry. The complex between nogalamycin and DNA illustrates the conformational flexibility of DNA. The hydrogen-bonding interactions between nogalamycin and DNA do not suggest a sequence-specific binding of the drug, although additional secondary effects might lead to differences between various intercalation sites.