Probing the role of structural water in a duplex oligodeoxyribonucleotide containing a water-mimicking base analog

Characterization of the conformational ensemble from bioactive N-acylhydrazone derivatives

The search for bioactive conformations from prototypes is mostly referenced on crystallographic ligand-receptor complexes, in which the molecule conformation is already caged inside its binding site. However, the complexation process is a thermodynamic event depending on both complexed and uncomplexed states. As ligand affinity originates from such equilibrium, the development of novel computational models capable of supplying data on ligand dynamics in biological solutions is potentially applicable in more efficient methods for prediction of compounds binding and affinity. In this context, the current work employs a series of molecular dynamics simulations on three N-acylhydrazone derivatives, already shown to present promising cardioinotropic and vasodilatory activities, in order to obtain a precise characterization of each compound conformational ensemble in aqueous solutions, instead of a single minimum energy conformation. Consequently, we were able to observe the influence of each functional group of the studied molecules on the conformation of the entire compounds and thus on the exposure of functional groups that might potentially bind to target receptors. Additionally, the differences between the molecules conformational behavior were characterized, supporting a spatial and temporal image of each ligand, which may be potentially correlated to their biological activities. So in the context of conformational selection, such strategy may represent a useful methodology to contribute in the choice of ligands conformations for both 3D-QSAR and docking calculations.

Endonucleolytic mutation analysis by internal labeling (EMAIL)

Mismatch-specific endonucleases are efficient tools for the targeted scanning of populations for subtle DNA variations. Conventional protocols involve 5'-labeled amplicon substrates and the detection of digestion products by LIF electrophoresis. A shortcoming of such protocols, however, is the limited 5'-signal strength. Normally the sensitivity of fluorescent DNA analyzers is superior to that of intercalating dye/agarose systems, however, pooling capacities of the former and latter approaches to mismatch scanning are somewhat similar. Detection is further limited by significant background. We investigated the activity of CEL nucleases using amplicon substrates labeled both internally and at each 5'-terminus. The amplicons were generated from exon 8 of the rice starch synthase IIa encoding gene. Signal of both 5'-labels was significantly reduced by enzyme activity, while that of the internal label was largely unaffected. In addition, background resulting from internal labeling was a significant improvement on that associated with 5'-labeling. Sizing of the multilabeled substrates suggests that 5'-modification enhances exonucleolytic activity, resulting in the removal of the dye-labeled terminal nucleotides. We have developed an alternative approach to mismatch detection, in which amplicon labeling is achieved via the incorporation of fluorescently labeled deoxynucleotides, which we have named Endonucleolytic Mutation Analysis by Internal Labeling (EMAIL). The strength of the EMAIL assay was demonstrated by the reclassification of a rice line as being heterozygous for the starch gene. This cultivar was assigned as being homozygous by a previous resequencing study. EMAIL shows potential for the clear identification of multiple mutations amongst allelic pools.

Conformational model of the Holliday junction transition deduced from molecular dynamics simulations

Homologous recombination plays a key role in the restart of stalled replication forks and in the generation of genetic diversity. During this process, two homologous DNA molecules undergo strand exchange to form a four-way DNA (Holliday) junction. In the presence of metal ions, the Holliday junction folds into the stacked-X structure that has two alternative conformers. Experiments have revealed the spontaneous transitions between these conformers, but their detailed pathways are not known. Here, we report a series of molecular dynamics simulations of the Holliday junction at physiological and elevated (400 K) temperatures. The simulations reveal new tetrahedral intermediates and suggest a schematic framework for conformer transitions. The tetrahedral intermediates bear resemblance to the junction conformation in complex with a junction-resolving enzyme, T7 endonuclease I, and indeed, one intermediate forms a stable complex with the enzyme as demonstrated in one simulation. We also describe free energy minima for various states of the Holliday junction system, which arise during conformer transitions. The results show that magnesium ions stabilize the stacked-X form and destabilize the open and tetrahedral intermediates. Overall, our study provides a detailed dynamic model of the Holliday junction undergoing a conformer transition.

Molecular dynamics simulation of nucleic acids

We review molecular dynamics simulations of nucleic acids, including those completed from 1995 to 2000, with a focus on the applications and results rather than the methods. After the introduction, which discusses recent advances in the simulation of nucleic acids in solution, we describe force fields for nucleic acids and then provide a detailed summary of the published literature. We emphasize simulations of small nucleic acids ( approximately 6 to 24 mer) in explicit solvent with counterions, using reliable force fields and modern simulation protocols that properly represent the long-range electrostatic interactions. We also provide some limited discussion of simulation in the absence of explicit solvent. Absent from this discussion are results from simulations of protein-nucleic acid complexes and modified DNA analogs. Highlights from the molecular dynamics simulation are the spontaneous observation of A B transitions in duplex DNA in response to the environment, specific ion binding and hydration, and reliable representation of protein-nucleic acid interactions. We close by examining major issues and the future promise for these methods.

A new crystal form for the dodecamer C-G-C-G-A-A-T-T-C-G-C-G: symmetry effects on sequence-dependent DNA structure

The dodecanucleotide d(CGCGAATTCGCG) has been crystallised in the space group P3(2)12, representing a new crystal form for this sequence. The structure has been solved by molecular replacement and refined at 1.8 A resolution. The present structure contrasts with previous ones for this sequence since it is situated on a crystallographic 2-fold axis, and the crystal symmetry reflects the palindromic nature of this sequence. Some features accord with previous observations, notably that the minor groove is hydrated with a continuous spine of solvent. There is no evidence of alkali metal ions within this spine. The minor groove retains its narrow width, although it is now symmetric and extends over the A/T tract. Various base and base-pair morphological parameters have been examined. Their values do not show significant correlations with earlier reports, suggesting that crystal packing effects on them are more dominant than has been hitherto realised.