Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes

NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients (r²) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization.     

Electron microscopical localization of nucleic acids by means of nuclease-gold complexes

Summary Nucleic acids can be specifically localized at the electron microscope level by means of enzyme-gold complexes. Two enzymes RNAase A and DNAase I were labelled with colloidal gold, and the enzyme-gold complexes obtained applied on thin sections of glutaraldehyde-fixed and Epon-embedded tissues. Using RNAase-gold, the rough endoplasmic reticulum and the nucleolus of different cells appeared densely labelled. With the DNAase-gold the labelling was present over the euchromatin and the mitochondria. The quantitative evaluation, performed on different cellular compartments of the pancreatic acinar cells, confirmed the qualitative observations and ascertained the specificity of the labelling. The application of this technique, for the demonstration of nucleic acids in different tissues, is illustrated.     

Binding of N-methyl isatin beta-thiosemicarbazone-copper complexes to proteins and nucleic acids.

N-Methyl isatin beta-thiosemicarbazone-copper complexes interact with nucleic acids and proteins as shown by ultraviolet (UV) and visible spectroscopy and Sephadex exclusion chromatography. The Cu++ ions are most effective; Co++ ions have less albeit significant activity. Chelating agents, such as Tris and histidine, high NaCl concentration, and dimethyl sulfoxide reduce the binding of the drug-metal complex. The binding constant of the drug-copper complex to calf-thymus DNA was calculated to range between 6.9 x 10(4) and 2.7 x 10(5) M-1.     

Modeling nucleic acids

Nucleic acids are an important class of biological macromolecules that carry out a variety of cellular roles. For many functions, naturally occurring DNA and RNA molecules need to fold into precise three-dimensional structures. Due to their self-assembling characteristics, nucleic acids have also been widely studied in the field of nanotechnology, and a diverse range of intricate three-dimensional nanostructures have been designed and synthesized. Different physical terms such as base-pairing and stacking interactions, tertiary contacts, electrostatic interactions and entropy all affect nucleic acid folding and structure. Here we review general computational approaches developed to model nucleic acid systems. We focus on four key areas of nucleic acid modeling: molecular representation, potential energy function, degrees of freedom and sampling algorithm. Appropriate choices in each of these key areas in nucleic acid modeling can effectively combine to aid interpretation of experimental data and facilitate prediction of nucleic acid structure.     

Extracellular nucleic acids

Extracellular nucleic acids are found in different biological fluids in the organism and in the environment: DNA is a ubiquitous component of the organic matter pool in the soil and in all marine and freshwater habitats. Data from recent studies strongly suggest that extracellular DNA and RNA play important biological roles in microbial communities and in higher organisms. DNA is an important component of bacterial biofilms and is involved in horizontal gene transfer. In recent years, the circulating extracellular nucleic acids were shown to be associated with some diseases. Attempts are being made to develop noninvasive methods of early tumor diagnostics based on analysis of circulating DNA and RNA. Recent observations demonstrated the possibility of nucleic acids exchange between eukaryotic cells and extracellular space suggesting their participation in so far unidentified biological processes.     

Macromolecular complexes of BSA with gelatin

This work studies the effect of the helix-coil transition in gelatin on the structure development in the complex forming water-gelatin-BSA system using dynamic light scattering, environment scanning electron microscopy, rheometry, differential scanning microcalorimetry, circular dichroism, fluorescence, and absorption measurements. It was established that the structure of the complexes formed and the mechanism of intermacromolecular interaction are different in the case of two conformation states of gelatin. Above the temperature of the conformational transition (40 °C) intermacromolecular interaction leads to collapse gelatin macromolecules and formation compact (30 nm in radius) BSA-gelatin complexes (～6:1, mole/mole), partial stabilization of the secondary structure (increase the mean helix content), and stabilization of BSA molecules against thermo aggregation. At the same time it does not leads to an appreciable change in the thermodynamic parameters of the thermal transitions for BSA and gelatin. Below the temperature of the conformation transition (at 18 °C) the interaction results in formation of the large (600-1000 nm in radius) complex particles due to trapping BSA molecules into the meshes of the gelatin network and, as consequence, a substantial increase in the storage and loss moduli of the system.