Terminal contributions for duplex oligonucleotide thermodynamic properties in the context of nearest neighbor models.

Additive physical properties of DNA polymer duplexes have been expanded in terms of eight irreducible parameters that ultimately lead to consistency relations among the corresponding 10 duplex dimer contributions. End parameters are often added to allow for oligomer analysis which would add four extra degrees of freedom to the aforementioned parameters. Analysis of sufficient experimental data on oligomer duplexes allows for the unambiguous recovery of irreducible parameters. Values for free energy, enthalpy, and entropy are thus obtained, in terms of either irreducible or dimer decomposition sets. Here, a better adjust for the entropic (and enthalpic) irreducible parameters are obtained as we consider the more precise melting temperature data for the sequences of a given dataset. However, still large error estimates, and no clear distinction between the orientations of the terminal base pairs could yet be found. Finally, statistical mechanics approaches are applied for to connect the nearest neighbor approach to the two states model. Ad hoc end effects can be thus correlated to nucleation phenomena, leading to a critique for its role in nearest neighbor modeling.

The role played by exons in genomic DNA sequence correlations.

The codon structure inside exons imposes a strong modulation with period-3 for genomic composition correlations. A new formalism for calculating nucleotide correlations along DNA sequences in terms of an irreducible set of six correlation functions is presented. New procedures to extract the corresponding period-3 modulations are also developed. These modulations are seen to be stronger for the irreducible self-correlation C(zz)(k), which accounts only for the binding strength of dinucleotides (z stands for adenine or thymine minus cytosine or guanine concentrations). We investigate and model the relationship between exon distribution and genomic period-3 correlations for the D. melanogaster genome.

Irreducible representation for nucleotide sequence physical properties and self-consistency of nearest-neighbor dimer sets.

A compact representation of usual DNA/RNA four-nucleotide sets based on molecular affinity classes is proposed. In a geometrical correspondence to this formulation, it follows that intrinsic tetrahedral symmetry correlates nucleotide properties. This representation also leads to a proper decomposition frame for any sequence-dependent physical expectation. Thermodynamic and other physical properties of nucleotide sequences are most often stated within the scope of nearest-neighbor models and decomposed in terms of dimer properties. The inverse problem of obtaining dimer set properties is, however, well known to be ill-posed due to sequence composition closure relations. Analysis of the dimer set composition and structure within the novel tetrahedral formulation provides important self-consistency relations, solving the ill posed nature of the original formulation. As an applied example, we analyze DNA oligomer duplex free energy data available on the literature. It is shown that imposition of stringent self-consistency relations does not decrease fit quality to the experimental data set. On the other hand, an improved dimer set with physically consistent free energies is obtained. Meaningful corrections to previous determinations are found when the self-consistent set is applied to calculate free energies for sequences with composition order bias.

Scattering from dilute ferrofluid suspensions in soft polymer gels.

Small angle neutron and x-ray scattering methods are used to investigate the structure of dilute suspensions of two different ferrofluid systems dispersed in soft polyacrylamide hydrogels. It is found that the particles in the fluid are fractal aggregates composed of smaller particles of radius ca. 5 nm. The fractal dimension is strongly dependent on sample, taking the value 1.7 in the first sample and 2.9 in the second sample. In the presence of a magnetic field the aggregates orient, but are restricted in both their translational and rotational freedom. The effect of the gel elasticity is treated as a hindrance to the orientation process.