The mixture of the short segments of double-stranded DNA and a flexible polymer are addressed. It is shown that in the condensed phase, rigid DNA molecules exhibit transition between isotropic and orientationally ordered phases. It is shown that orientational ordering stabilizes the secondary structure of double-stranded DNA that could be relevant for the regulation of the gene expression at the condensed state of DNA.

No abstract

Motivated by the prospects of developing DNA field-effect transistors, as tools for a variety of application fields such as medical diagnostics, environmental pollutants monitoring, biological weapons defense, and taking into account that the efficiency of DNA-sensors depends on the precise prediction of experimental parameters responsible for thermostability of nucleic acids duplexes and specific times of formation of DNA duplexes, we analyze the factors influencing both the thermodynamics of hybridization and the stability of DNA–DNA and DNA–RNA duplexes. In this work the case of competition-free DNA hybridization is analyzed. It is shown how the intercalating ligands effectively increase the binding constant for the target sequences and thus affects the sensitivity of the DNA-chip.