Mimicking DNA stretching with the Static Mode method: Shear stress versus transverse pulling stress

• Published in: The European physical journal. E, Soft matter and biological physics Soft matter and biological physics, 2012-08, Vol.35 (8), p.75, Article 75
• Main Authors: Brut, M., Estève, A., Landa, G., Djafari Rouhani, M.
• Format: Article
• Language: English
• Subjects: Analytical, structural and metabolic biochemistry; Base Pairing; Base Sequence; Biochemistry, Molecular Biology; Biological and Medical Physics; Biological and medical sciences; Biomechanical Phenomena; Biomechanics; Biophysics; Chemical Sciences; Complex Fluids and Microfluidics; Complex Systems; DNA - chemistry; DNA - genetics; Dna, deoxyribonucleoproteins; Fundamental and applied biological sciences. Psychology; Life Sciences; Mechanics; Models, Molecular; Nanopores; Nanotechnology; Nucleic acids; or physical chemistry; Phosphates - chemistry; Physics; Physics and Astronomy; Polymer Sciences; Regular Article; Soft and Granular Matter; Stress, Mechanical; Structural Biology; Surfaces and Interfaces; Theoretical and; Thin Films
• ISSN: 1292-8941; 1292-895X
• DOI: 10.1140/epje/i2012-12075-0

DNA sequencing using nanopores is closer than ever to become a reality, but further research and development still need to be done, especially to unravel the atomic-scale mechanisms of induced DNA stretching. At this level, molecular modeling and simulation are essential to investigate DNA conformational flexibility and its response to the forces involved. In this work, through a “Static Mode” approach, we present a directed exploration of the deformations of a 27-mer subjected to externally imposed forces, as it could be in a nanopore. We show how the DNA sugar-phosphate backbone undergoes the majority of the induced deformation, before the base pairing is affected, and to what extent unzipping initiation depends on the force direction.