Dynamic imaging of single DNA-protein interactions using atomic force microscopy

Atomic force microscopy (AFM) imaging of static DNA-protein complexes, in air and in liquid, can be used to directly obtain quantitative and qualitative information on the structure of different complexes. For example, DNA length, the location of preferential binding sites for proteins and bending of DNA as a result of the complexation can all be measured. Recording consecutive AFM images of DNA and protein molecules under conditions that they are still able to move and interact, or dynamic AFM imaging, however, can reveal information on the dynamic aspects of the interactions between these molecules. Here, an overview is given of the technical challenges that need to be considered for successful dynamic AFM imaging studies of individual DNA-protein interactions. Necessary technical improvements to the AFM set-up and the development of new sample preparation methods are described in this paper.     

Synthesis,Vibrational Spectrum and Structure of the Tetracyanoborate K[B(CN)4]·CH3CN

The new tetracyanoborate K[B(CN)₄]·CH₃CN was synthesized by dissolution of the solvent‐free K[B(CN)₄] in acetonitrile and subsequent careful crystallization. The crystal structure has been determined by single‐crystal X‐ray diffraction. It crystallizes in the orthorhombic space group P2₁2₁2₁ with Z = 4. Some comparisons with related structures are made, and the vibrational spectrum is discussed.     

Solvating,manipulating, damaging,and repairing DNA in a computer

This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

A Highly Stereoselective Synthesis of C(11)-Functionalized Aromatic Steroids by an Intramolecular Benzocyclobutene-Olefin -Cycloaddition. Preliminary Communication

The racemic cis-anti-trans-steroids 9 to 11 have been synthesized in a highly stereoselective manner starting from 4-methoxybenzocyclobutene carboxylic acid via the key step 8 → 9 . (cf. Scheme 2).     

Nonlinear intensity dependence of the rate coefficient in unimolecular reactions induced by monochromatic infrared radiation

It is shown that essentially incoherent, stepwise one-photon transitions arising in dense multilevel structures of polyatomic molecules irradiated with monochromatic coherent infrared radiation can give rise (under specified conditions) to a more than proportional intensity dependence of the steady-state rate coefficient in unimolecular reactions induced by monochromatic infrared radiation.     

13C-NMR studies of marine natural products II. Total assignment of the 13C-NMR spectrum of asperdiol

¹³C-nmr spectral assignments for asperdiol are made with the aid of model compounds and T₁ relaxation behavior. Overall isotropic tumbling was inferred from the latter providing a supplemental means of multiplicity determination. Utilization of the T₁ relaxation times as an assignment criterion for select resonances in asperdiol is also described.     

3,7-Dioxaazelaamides as Ionophores for Lithium Ion Selective Liquid Membrane Electrodes

Lipophilic neutral carriers were synthesized which show Li⁺/Na⁺ selectivities of up to ca. 80 in highly lipophilic liquid membranes. The sensor membranes exhibit improved response times and increased lifetimes as compared to systems described earlier. They allow reliable measurements of Li⁺ in blood serum within the clinical concentration range. A 1:1 Li⁺/ionophore complex of one representative (N,N,N′,N′-tetracyclohexyl-5,5-dimethyl-3,7-dioxaazelaamide) has been prepared, and its structure was elucidated by X-ray analysis.     

Inverted and suppressed direct response HMQC-TOCSY spectra - a convenient method of spectral editing

HMQC-TOCSY spectra provide a convenient means of establishing proton-proton connectivities in congested spectra of complex aromatic heterocycles. Advantage is taken of the greater dispersion of the ¹³C nmr spectrum to circumvent overlap which would preclude spectral interpretation through the usual COSY spectrum. A recently reported method for inverting direct responses (IDR) in HMQC-TOCSY spectra is demonstrated for [1]benzothieno[2,3-c]naphtho[2,1-g]quinoline. A modification of the IDR-HMQC-TOCSY method is also demonstrated which is capable of fully suppressing direct responses (SDR) without resorting to the timing of the onset of decoupling as in the original report of the HMQC-TOCSY experiment. SDR-HMQC-TOCSY has the further advantage of allowing the use of higher levels of digitization in F₂ than can be attained when broadband heteronuclear decoupling is employed.