Enrichment of non-B-form DNA at D. melanogaster centromeres

Centromeres are essential chromosomal regions that mediate the accurate inheritance of genetic information during eukaryotic cell division. Despite their conserved function, centromeres do not contain conserved DNA sequences and are instead epigenetically marked by the presence of the centromere-specific histone H3 variant CENP-A (centromeric protein A). The functional contribution of centromeric DNA sequences to centromere identity remains elusive. Previous work found that dyad symmetries with a propensity to adopt non-canonical secondary DNA structures are enriched at the centromeres of several species. These findings lead to the proposal that such non-canonical DNA secondary structures may contribute to centromere specification. Here, we analyze the predicted secondary structures of the recently identified centromere DNA sequences from Drosophila melanogaster. Although dyad symmetries are only enriched on the Y centromere, we find that other types of non-canonical DNA structures, including DNA melting and G-quadruplexes, are common features of all D. melanogaster centromeres. Our work is consistent with previous models suggesting that non-canonical DNA secondary structures may be conserved features of centromeres with possible implications for centromere specification.

Analytical determination of DNA melting characteristic parameters using the optimal degree polynomial regression model

The article describes a new technique for determining two main parameters of DNA melting: the melting temperature Tm and the temperature melting range ΔT, based on the plotting of an approximating polynomial function for the DNA melting curve. An algorithm is proposed for reducing the melting curve to approximation by the fourth degree polynomial function in accordance with the physical aspect of the DNA melting process. The correctness of the optimal degree choice from the condition of minimizing the value of the Akaike’s information criterion corrected has been confirmed. Analytical expressions for calculating the values of Tm and ΔT are given oriented to a polynomial function of the fourth degree. Results comparison of applying the proposed and well-known techniques based on the experimental data is performed. The advantages of the new technique are revealed.

SYBR Green I promotes melamine binding to poly-thymine DNA and FRET-based ratiometric sensing

Using SYBR Green I for DNA melting experiments, polythymine DNA binding to melamine was found to be an intramolecular reaction, allowing the design of a FRET-based biosensor and its sensitivity was enhanced by SYBR Green I.

Application of Molecular Dynamics and Monte-Carlo Methods near the Critical Points

The applicability of molecular dynamics and Monte-Carlo methods near the phase transition is discussed on the example of DNA melting.

Statistical Physics of DNA melting: Unveiling the artificial corrections for self-complementary sequences

ABSTRACTDNA hybridization is at the heart of countless biological and biotechnological processes. Its theoretical modeling played a crucial role, since it has enabled extracting the relevant thermodynamic parameters from systematic measurements of DNA melting curves. However, in its current state, hybridization modelling requires introducing an extra entropic contribution in self-complementary sequences that lacks any biophysical meaning. In this article, we propose a framework based on statistical physics to describe DNA hybridization and melting in an arbitrary mixture of DNA strands. In particular, we are able to analytically derive closed expressions of the system partition functions for any number N of strings, and explicitly calculate them in two paradigmatic situations: (i) a system made of self-complementary sequences and (ii) a system comprising two mutually complementary sequences. We derive the melting curve in the thermodynamic limit (N → ∞) of our description, which differs from the expression commonly used to evaluate the melting of self-complementary systems in that it does not require correcting terms. We provide a thorough study comprising limit cases and alternative approaches showing how our framework can give a comprehensive view of hybridization and melting phenomena.SIGNIFICANCEIn this study, we provide a transparent derivation of the melting curves of DNA duplexes using basic tools of statistical mechanics. We find that in the case of self-complementary sequences, our expression differs from the one used in literature, which is generally amended by the introduction of a phenomenological correction which in our approach becomes unnecessary. By offering a clean formal description of DNA hybridization, our approach sharpens our understanding of DNA interactions and opens the way to study the pairing of DNA oligomers away from any thermodynamic limit.