Mechanically manipulating the DNA threading intercalation rate

The dumbbell shaped binuclear ruthenium complex DeltaDelta-P requires transiently melted DNA in order to thread through the DNA bases and intercalate DNA. Because such fluctuations are rare at room temperature, the binding rates are extremely low in bulk experiments. Here, single DNA molecule stretching is used to lower the barrier to DNA melting, resulting in direct mechanical manipulation of the barrier to DNA binding by the ligand. The rate of DNA threading depends exponentially on force, consistent with theoretical predictions. From the observed force dependence of the binding rate, we demonstrate that only one base pair must be transiently melted for DNA threading to occur.     

Complex DNA binding kinetics resolved by combined circular dichroism and luminescence analysis

We recently reported that ruthenium complexes, with general structure [mu-bidppz(bipy)4Ru2](4+) (B) or [mu-bidppz(phen)4Ru2](4+) (P) (bidppz=11,11'-bi(dipyrido[3,2- a:2',3'-c]phenazinyl)), show extreme kinetic selectivity for long AT tracts over mixed-sequence calf thymus DNA (ct-DNA), a selectivity that also varies markedly with the size (between B and P) and sense of chirality of the complex. Earlier studies, exploiting the great increase in luminescence intensity when the compound intercalates, have yielded complex kinetics indicating the presence of both first- and second-order processes. Even with a homogeneous DNA sequence, such as poly(dAdT)2, the luminescence kinetics generally requires more than a single exponential for a satisfactory fit. We here reveal that at least part of the complexity is a result of the extreme sensitivity of the effective quantum yield of the complexes, so that the luminescence trajectories also reflect subtle variations in the environment and binding geometry that the complex is sampling on its path to its final binding site. By monitoring the rearrangement process using circular dichroism (CD), we show that threading of both enantiomers of B and P into poly(dAdT)2 is effectively a monoexponential process, as expected if the compounds are not affecting each other during the intercalation process. Thus, the complex luminescence trajectories may be explained by slow relaxations in the binding geometry (DNA conformation) and associated changes in the environment of the entering complexes. To further disentangle the intriguing features of the threading intercalation kinetics, and how they may depend on the flexibility and size of the ruthenium complexes, we have also designed and studied two new ruthenium complexes, [mu-dtpf(phen)4Ru2](4+) (F) (dtpf=4,5,9,12,16,17,21,25-octaaza-23 H-ditriphenyleno[2,3-b:2,3-h]fluorene), in which the bridging ligand is made totally rigid, and [mu-bidppz([12]aneS4) 2Ru2](4+) (S), which has less bulky, nonaromatic ancillary ligands. The threading of F into poly(dAdT)2, also found to be a monoexponential process, is about 3 times slower than for P, indicating that the flexibility of the bridging ligand is an important factor for the intercalation rate. Surprisingly, in contrast to all other compounds, S requires two exponentials to fit its binding kinetics as monitored by CD. Also surprisingly, in view of the smaller steric bulk, even the fastest phase is roughly 2 times slower for S than for B and P. Thus, not only the size of the ancillary ligand but also other properties that can influence the energy landscape of the threading path are rate-determining factors. With mixed-sequence ct-DNA, threading of B and that of P are both multiphasic processes when monitored with CD as well as with luminescence. The rate constants for threading into ct-DNA show much larger variations between complexes than for poly(dAdT)2, confirming earlier results based on luminescence data.     

Molecular fibers and wires in solid-state and solution self-assemblies of cyclodextrin [2]rotaxanes

Cyclodextrin [2]rotaxanes have been prepared by coupling dimethylanilines with dicarboxylic acids using DMT-MM, in aqueous solutions of alpha-cyclodextrin, and the example illustrated shows unusual fluorescence emission and other spectroscopic behavior characteristic of the formation of molecular wires in solution, similar to the fibers observed in the solid state.     

Total synthesis of solandelactones A, B, E, and F exploiting a tandem Petasis-Claisen lactonization strategy

Solandelactones A, B, E, and F were synthesized using Nozaki-Hiyama-Kishi coupling of iododiene 13 with aldehydes 14 and 99 obtained by oxidation of alcohols 92 and 94. Key steps in the synthesis of 92 and 94 were (i) a Nagao asymmetric acetate aldol reaction of aldehyde 77 with thionothiazolidine 78 to set in place an alcohol that becomes the (7 S) lactone center of solandelactones, (ii) a Simmons-Smith cyclopropanation of 80 directed by this alcohol, and (iii) Petasis methylenation of cyclic carbonate 90 in tandem with a Claisen rearrangement that generates the octenalactone portion of solandelactones. Synthesis of solandelactones A, B, E, and F confirmed their gross structure and absolute configuration at C7, 8, 10, and 14 but showed that alcohol configuration at C11 must be reversed in pairs, A/B and E/F, from the previous assignment made to these hydroid metabolites. Thus, solandelactones A and B are correctly represented by 2 and 1, respectively, whereas solandelactones E and F are 6 and 5. A biogenesis of solandelactones is proposed for these C 22 oxylipins that parallels a hypothesis put forward previously to explain the origin of C 20 cyclopropane-containing algal products.     

A Chemical Probe for the ATAD2 Bromodomain

ATAD2 is a cancer‐associated protein whose bromodomain has been described as among the least druggable of that target class. Starting from a potent lead, permeability and selectivity were improved through a dual approach: 1) using CF₂ as a sulfone bio‐isostere to exploit the unique properties of fluorine, and 2) using 1,3‐interactions to control the conformation of a piperidine ring. This resulted in the first reported low‐nanomolar, selective and cell permeable chemical probe for ATAD2.     

Binding geometry and photophysical properties of DNA-threading binuclear ruthenium complexes

The DNA binding conformation and the photophysical properties of the semiflexible binuclear ruthenium complex [micro-bidppz(phen)4Ru2]4+ (2) were studied with optical spectroscopy and compared to the rigid, planar homologue in syn conformation [micro-dtpf(phen)4Ru2]4+ (3) and the parent "light-switch" complex [Ru(phen)2dppz]2+ (1). Comparison of calculated and observed absorption bands of the bridging ligand, bidppz, confirm earlier suggestions that 2 is significantly nonplanar, both free in solution and when intercalated into poly(dAdT)2, but the conclusion that the intercalated conformation is an anti rotamer is not substantiated by comparison of linear and circular dichroism spectra of 2 and 3. The behavior of the emission quantum yield as a function of temperature is similar for the two binuclear complexes 2 and 3 in different protic solvents, and a quantitative analysis suggests that, in solution, the solvent is more strongly hydrogen bonded to the excited state of 2 than to 1. However, the observation that for 2 the radiative rate constant increases to a value similar to 1 upon intercalation into DNA suggests that the difference between 1 and 2 in accepting hydrogen bonds is less pronounced when intercalated.     

Measurement of the eta-meson mass using psi(2S) --> etaJ/psi

We measure the mass of the eta meson using psi(2S) --> etaJ/psi events acquired with the CLEO-c detector operating at the CESR e(+)e(-) collider. Using the four decay modes eta --> gamma gamma, 3pi(0), pi(+)pi(-)pi(0), and pi(+)pi(-)gamma, we find M(eta) = 547.785 +/- 0.017 +/- 0.057 MeV, in which the first uncertainty is statistical and the second systematic. This result has an uncertainty comparable to the two most precise previous measurements and is consistent with that of NA48, but is inconsistent at the level of 6.5 sigma with the much smaller mass obtained by GEM.     

Synthesis and characterization of doped lithium aluminate nanocrystalline particles by sol‐gel method

Nanocrystalline particles of Co²⁺doped lithium aluminate (Co²⁺:LAO) and Ni²⁺‐doped lithium aluminate (Ni²⁺:LAO) were synthesized by sol–gel method. The crystalline nature and particle size of the samples were characterized by X‐ray diffraction analysis (XRD). The morphology and the presence Co²⁺ and Ni²⁺ in the synthesized samples were analyzed by scanning electron microscope (SEM) and energy dispersive X‐ray analysis (EDAX). The presences of functional groups in the samples were analyzed using FT‐IR analysis. The optical absorbance of the synthesized samples were observed using UV absorption spectral analysis. The frequency dependent dielectric behaviour of the synthesized nano materials was analyzed. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Topological winding and unwinding in metastable Bose-Einstein condensates

Topological winding and unwinding in a quasi-one-dimensional metastable Bose-Einstein condensate are shown to be manipulated by changing the strength of interaction or the frequency of rotation. Exact diagonalization analysis reveals that quasidegenerate states emerge spontaneously near the transition point, allowing a smooth crossover between topologically distinct states. On a mean-field level, the transition is accompanied by formation of gray solitons, or density notches, which serve as an experimental signature of this phenomenon.