Stability Of DNA Molecules Research Articles

Melting of DNA in confined geometries.

The stability of DNA molecules during viral or biotechnological encapsulation is a topic of active current research. We studied the thermal stability of double-stranded DNA molecules of different lengths in a confined space. Using a statistical model, we evaluate the melting profile of DNA molecules in two geometries: conical and cylindrical. Our results show that not only the confinement, but also the geometry of the confined space plays a prominent role in the stability and opening of the DNA duplex. We find that for more confined spaces, cylindrical confinement stabilizes the DNA, but for less confined spaces conical geometry stabilizes the DNA overall. We also analyse the interaction between DNA sequence and stability, and the evenness with which strand separation occurs. Cylindrical and conical geometries enable a better controlled tuning of the stability of DNA encapsulation and the efficiency of its eventual release, compared to spherical or quasi-spherical geometries.

Evaluation of effect of functionalized gold nanoparticles with a partial negative charge on stability of DNA molecule: a study of molecular dynamics simulation

Today, understanding the interaction between DNA molecule with nanoparticles and functionalized nanoparticles has a significant importance in medical applications and targeted drug delivery. Molecular dynamics simulation on double-stranded molecule with the structure of the double helix and sequence of (CCTCAGGCCTCC) was performed in three states. The aim was to evaluate the effect of gold nanoparticles (GNPs) with partial negative charge on the stability of a DNA molecule. During the simulation process, the GNPs become closed to the DNA molecule and phosphate groups of the DNA molecule guided the nanoparticles toward its major groove. At the end of the DNA molecule chain, the terminal nucleotide of the chain was laid flat on the surface of the GNPs due to excessive exposure to solvent molecules and occurrence of peeling and untwisting states. According to the results, proximity of the GNPs and functionalized GNPs to the DNA molecule led to increased configuration entropy. While conformational energy and van der Waals energy of the DNA molecule increased in the presence of the GNPs and functionalized GNPs, there was a reduction and an increase in the number of hydrogen bonds between complementary bases in the presence of the GNPs and functionalized GNPs, respectively. Radial distribution function was estimated for water molecules and sodium cations, compared to oxygen atoms of the phosphate group of the DNA molecule. Results were indicative of the release of water molecules from around the DNA molecule in the presence of the GNPs. In addition, the distance between sodium cations and the GNPs decreased. Nevertheless, no such phenomenon occurred in the presence of the functionalized GNPs. Therefore, according to results, it seems that GNPs decreased the stability of the DNA molecule and the functionalized GNPs with partial negative charge caused structural changes and created compression, but did not destroy the double-strand structure of the DNA molecule.

83 Application of differential scanning calorimetry to measure the differential binding of ions, water, and protons in the unfolding of DNA molecules

The overall stability of DNA molecules globally depends on base-pair stacking, base pairing, polyelectrolyte effect, and hydration contributions. In order to improve our understanding of the role of ions, water, and protons in the stability and melting behavior of DNA structures, we report an experimental approach to determine the differential binding of ions (Δn ion), water (Δn W), and protons (Δn H+) in the helix-coil transition of DNA molecules. A combination of differential scanning calorimetry (DSC) and temperature-dependent UV and CD spectroscopic techniques to investigate the unfolding of a variety of DNA molecules: S.T. DNA, two dodecamers, one undecamer, nine short hairpins as a function of the GC content of their stem, and two triplexes. We determine complete thermodynamic profiles, including all the three linking numbers, for the unfolding of each molecule. The CD spectra indicated that all molecules adopted the B-conformation at low temperatures. Thermodynamic profiles obtained from the DSC curves indicate that the favorable folding of each molecule results from the typical compensation of favorable enthalpy and unfavorable entropy contributions, and negligible heat capacity effects. UV and DSC melting curves as a function of salt, osmolyte, and proton concentrations yielded releases of ions, water, and protons (for the triplex with C+GC base triplets). Therefore, the favorable folding of each DNA molecule results from the formation of base-pair stacks and uptake of water and counterions. The thermodynamic data will be discussed in terms of the effects of DNA length, loop contributions and type of water molecules.