Organización Supramolecular de ADN en Solución Bajo Condiciones de Cizallamiento

Abstract

DNA is a long, semi-flexible natural polyelectrolyte that carries the genetic information of all living organisms. Despite decades of intense study, the capacity of DNA in solutions to align and organize under flow conditions remains relatively underexplored. Although more than 70 years have passed since the discovery of the DNA double helix, an event that marked the beginning of extensive research into one of the most essential biopolymers in the development of life, there is still much to uncover about DNA’s structural and dynamic behavior. From a mechanical and physicochemical perspective, studying the dynamics of nucleic acids in solution, together with their flow behavior and viscoelastic properties, is essential for understanding their biological functions. DNA displays unique behaviors such as flow-induced birefringence and the ability to form liquid crystalline phases. These properties are modulated by parameters such as DNA concentration, molecular weight (Mw) and ionic strength, which impact the electrostatic interactions between DNA chains in a solution. The objective of this PhD thesis is to elucidate how these key parameters influence the supramolecular organization of DNA solutions under flow conditions. Three DNA samples with different Mw (in the range from 3.9 x 105 to 6.5 x 106 g/mol) were studied over a broad concentration range, from the dilute to entangled semi-dilute regimes (0.1 - 200 mg/mL), in solvents with varying ionic strengths. SAXS confirmed interchain correlations and the characteristic form-factor peak of DNA. At a constant concentration of 16 mg/mL, shear-induced birefringent textures strongly depended on DNA MW: High MW-DNA formed well-defined textures at low shear rates, Medium MW-DNA showed weak birefringence at higher shear, and Low MW-DNA exhibited none, highlighting the key role of chain length. Birefringence also revealed that HMW-DNA (Mw ~6.5 x 106 g/mol) develops orientational ordering at lower concentrations than shorter chains. Ionic strength influenced DNA conformation and shear-induced ordering. Transient rheo-birefringence and rheo-SAXS of HMW-DNA revealed a stress plateau (~1–1000 s⁻¹) and two relaxation processes: a rapid, an orientational relaxation at ~20 nm scales, scaling inversely with shear rate, and a slower, diffusion governed process corresponding to texture disappearance. These findings provide a basis for future research on DNA’s ability to form well-organized domains that supports its essential biological functions within cells.