Dynamic scanning force microscopy study of self-assembled DNA-protein nanostructures

Self-assembled oligomeric nanostructures consisting of bisbiotinylated DNA fragments connected by the protein streptavidin (STV) are studied by dynamic scanning force microscopy (SFM) operating in air. A comparison of the images taken in repulsive and attractive regimes is systematically made on DNA and STV structures. Stable and reproducible SFM images are obtained in the attractive regime by using a special feedback circuit, called Q-control. On the other hand, when SFM is operating in the repulsive regime, deformation of the structures that reduce the resolution and the image quality are clearly observable. The heights of both DNA and STV have been measured as a function of the tip/molecule interaction forces. This study offers the possibility to suggest a different mechanical behavior of DNA with respect to STV. Received: 24 July 2001 / Accepted: 3 December 2001 / Published online: 4 March 2002     

Loss without recovery of Gibbsianness during diffusion of continuous spins

We consider a specific continuous-spin Gibbs distribution μ_t=0 for a double-well potential that allows for ferromagnetic ordering. We study the time-evolution of this initial measure under independent diffusions. For `high temperature' initial measures we prove that the time-evoved measure μ<sub>t</sub> is Gibbsian for all t. For `low temperature' initial measures we prove that μ_t stays Gibbsian for small enough times t, but loses its Gibbsian character for large enough t. In contrast to the analogous situation for discrete-spin Gibbs measures, there is no recovery of the Gibbs property for large t in the presence of a non-vanishing external magnetic field. All of our results hold for any dimension d≥2. This example suggests more generally that time-evolved continuous-spin models tend to be non-Gibbsian more easily than their discrete-spin counterparts. Research carried out at EURANDOM and supported by Deutsche Forschungsgemeinschaft     

Über Sesquiselenide der Lanthanoide: Einkristalle von Ce2Se3 im C‐, Gd2Se3 im U‐ und Lu2Se3 im Z‐Typ

On Sesquiselenides of the Lanthanoids: Single Crystals of C‐type Ce₂Se₃, U‐type Gd₂Se₃, and Z‐type Lu₂Se₃ Single crystals of lanthanoid sesquiselenides (M₂Se₃; here: M = Ce, Gd, Lu) are accessible through conversion of the elements (lanthanoid and selenium) in molar ratios of 2:3 within seven days at 850 °C from evacuated silica ampoules if equimolar amounts of NaCl serve as a flux. In the case of Ce₂Se₃ (a = 897.74(6) pm) und Gd₂Se₃ (a = 872.56(5) pm) the cubic C‐type (I4¯3d, Z = 5.333) forms as dark red beads, whereas the orthorhombic Z‐type (Fddd, Z = 16) emerges for Lu₂Se₃ (a = 1125.1(1), b = 798.06(8), c = 2387.7(2) pm) as orange‐yellow bricks. Upon oxidation of monochloride hydrides (MClH_x or A_yMClH_x; M = Ce, Gd, Lu; x = 1; A = Li, Na; y = 0.5) with selenium in arc‐welded tantalum ampoules the same main products appear with C‐Ce₂Se₃ and Z‐Lu₂Se₃, even with a surplus of NaCl or LiCl as fluxing agent. In the case of Gd₂Se₃, however, black‐red needles of the orthorhombic U‐type (Pnma, Z = 4; a = 1118.2(1), b = 403.48(4); c = 1097.1(1) pm) are yielded instead of C‐Gd₂Se₃. C‐Ce₂Se₃ crystallizes in a cation‐deficient Th₃P₄‐type structure (Ce₂S₃ type) according to Ce_2.667□_0.333Se₄ (Z = 4) or with Z = 5.333 for the empirical formula Ce₂Se₃. Here, Ce³⁺ is coordinated by eight Se^2— anions trigon‐dodecahedrally. In U‐Gd₂Se₃ (U₂S₃ type) two crystallographically independent Gd³⁺ cations with coordination numbers of 7 (Gd1) and 7+1 (Gd2), respectively, are present, exhibiting mono‐ or bicapped trigonal prisms as coordination polyhedra. The crystal structure of Z‐Lu₂Se₃ (Sc₂S₃ type) shows two different Lu³⁺ cations as well, which now both reside in octahedral coordination of six Se^2— anions each.     

Unusual monodentate binding mode of 2,2'-dipyridylamine (L) in isomeric trans-(acac)2RuII(L)2, trans-[(acac)2RuIII(L)2]ClO4, and cis-(acac)2RuII(L)2 (acac = acetylacetonate). synthesis, structures, and spectroscopic, electrochemical, and magnetic aspects

The reaction of cis-Ru(acac)2(CH3CN)2 (acac = acetylacetonate) with 2,2'-dipyridylamine (L) in ethanolic medium resulted in facile one-pot synthesis of stable [(acac)2RuIII(L)]ClO4 ([1]ClO4), trans-[(acac)2RuII(L)2] (2), trans-[(acac)2RuIII)L)2]ClO4 ([2]ClO4), and cis-[(acac)2RuII(L)2] (3). The bivalent congener 1 was generated via electrochemical reduction of [1]ClO4. Although in [1]+ the dipyridylamine ligand (L) is bonded to the metal ion in usual bidentate fashion, in 2/[2]+ and 3, the unusual monodentate binding mode of L has been preferentially stabilized. Moreover, in 2/[2]+ and 3, two such monodentate L's have been oriented in the trans- and cis-configurations, respectively. The binding mode of L and the isomeric geometries of the complexes were established by their single-crystal X-ray structures. The redox stability of the Ru(II) state follows the order 1 < 2 < 3. In contrast to the magnetic moment obtained for [1]ClO4, mu = 1.84 muB at 298 K, typical for low-spin Ru(III) species, the compound [2]ClO4 exhibited an anomalous magnetic moment of 2.71 muB at 300 K in the solid state. The variable-temperature magnetic measurements showed a pronounced decrease of the magnetic moment with the temperature, and that dropped to 1.59 muB at 3 K. The experimental data can be fitted satisfactorily using eq 2 that considered nonquenched spin-orbit coupling and Weiss constant in addition to the temperature-independent paramagnetism. [1]ClO4 and [2]ClO4 displayed rhombic and axial EPR spectra, respectively, in both the solid and the solution states at 77 K.     

Microarray-based in vitro evaluation of DNA oligomer libraries designed in silico.

We report on the microarray-based in vitro evaluation of two libraries of DNA oligonucleotide sequences, designed in silico for applications in supramolecular self-assembly, such as DNA computing and DNA-based nanosciences. In this first study which is devoted to the comparison of sequence motif properties theoretically predicted with their performance in real-life, the DNA-directed immobilization (DDI) of proteins was used as an example of DNA-based self-assembly. Since DDI technologies, DNA computing, and DNA nanoconstruction essentially depend on similar prereguisites, in particular, large and uniform hybridization efficiencies combined with low nonspecific cross-reactivity between individual sequences, we anticipate that the microarray approach demonstrated here will enable rapid evaluation of other DNA sequence libraries.     

Chelation of carbocations by polyethers and polyamines

Chelates formed by carbocations and cyclic polyethers and polyamines are studied with semiempirical and ab initio MO methods.     

Adaptive approach for nonlinear sensitivity analysis of reaction kinetics

We present a unified approach for linear and nonlinear sensitivity analysis for models of reaction kinetics that are stated in terms of systems of ordinary differential equations (ODEs). The approach is based on the reformulation of the ODE problem as a density transport problem described by a Fokker-Planck equation. The resulting multidimensional partial differential equation is herein solved by extending the TRAIL algorithm originally introduced by Horenko and Weiser in the context of molecular dynamics (J. Comp. Chem. 2003, 24, 1921) and discussed it in comparison with Monte Carlo techniques. The extended TRAIL approach is fully adaptive and easily allows to study the influence of nonlinear dynamical effects. We illustrate the scheme in application to an enzyme-substrate model problem for sensitivity analysis w.r.t. to initial concentrations and parameter values.