AbstractsBiology & Animal Science

Computational study of DNA in non-canonical environment

by Annalisa Arcella

Institution: Universitat de Barcelona
Year: 2014
Keywords: Bioquímica física; Physical biochemistry; Dinàmica molecular; Dinámica molecular; Molecular dynamics; ADN; DNA; Simulació per ordinador; Simulación por ordenador; Computer simulation; Ciències Experimentals i Matemàtiques
Record ID: 1124396
Full text PDF: http://hdl.handle.net/10803/279220


During my PhD thesis used theoretical techniques, in particular Molecular Dynamics to study the structural properties of nucleie acids in non-canonical environment, especially in the gas phase and apolar conditions. The highly charged nature of the nucleic acids backbone clearly suggests that the environrnent plays a key role in the behavior of these molecules. As the DNA is found in aqueous solution under physiological conditían, the vast majority of published works on nudeic acids naturally investigates its behavior under these conditions. Water is excellent to stabilize DNA, but it is not the ideal solvent for favoring specific recognition, certain reactions or physical processes such as charge transfer. Interest exists then to explore the nature of nucleic acids, particularly DNA, in non-•aqueous solvents, where the universe of nucleic acids applications will expand even more. In the first part of this thesis I used atomistic molecular dynamics simulations to investiga te the structural and thermodynamics changes of a DNA hairpin when transferred from an aqueous solution to a low dielectric media, carbon tetrachloride (CTC), under different DNA charge states. I simulated the pulling of a short DNA hairpin from a water compartment through a CTC slap and estimated the free energy related to the transfer of the DNA from water to CTC through atomistic Umbrella Sampling simulation. The second part of my thesis is centered in the challenge af the mast recent experimental techniques, such as Mass Spectrometry and X-Ray Free Electron Laser (XFEL) which use gas phase ions to provide structural information of macromolecules. They are fast and require low sample consumption but the question is to what extent does gas phase structural information renect the most populated conformation in solution. A series of both experimental and theoretical studies with proteins have demonstrated that gas phase ensembles can be used to accurately madel the solution structure. The question is then, whether or not these findings also stand for a highly flexible and charged non-globular molecule as DNA, depends on the solvent environment. An analysis of the energetics oE DNA suggests that in the absence of solvent screening DNA should unfold, but experimental studies clearly points in the opposite. I used MD simulations to characterize the conformational ensemble of non- canonical structure of DNA, such as triple-stands and hairpins DNA, in the gas phase, validating the results by means of state of the art mass spectroscopy experiments. My results suggest that the ensemble of DNA triplex-strand structures in the gas phase is well defined over the experimental time scale, with the three strands tightly bound. Triplex DNA in the gas phase maintains memory of the solution structure, well-preserved helicity, and a significant number of native contacts. As a breakthrough I considered a very small model of a DNA hairpin containing 2 duplex steps, and combined extended Replica Exchange MD simulations, quantum mechanical Car-Parrinello MD…