Statistics of Time-Dependent Rupture of Single ds-DNA

• Published in: The journal of physical chemistry. B Vol. 117; no. 29; pp. 8875 - 8879
• Main Authors: Liang, Hua, Severin, Nikolai, Fugmann, Simon, Sokolov, Igor M, Rabe, Jürgen P
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 25.07.2013
• Subjects: Analytical, structural and metabolic biochemistry; Backbone; Biological and medical sciences; Constants; Deoxyribonucleic acid; DNA - chemistry; DNA Sequence, Unstable; Dna, deoxyribonucleoproteins; Fundamental and applied biological sciences. Psychology; Microscopy, Electron, Scanning; Molecular Conformation; Nonlinearity; Nucleic acids; Rate constants; Statistics; Statistics as Topic; Stress-strain relationships; Surface chemistry; Time Factors; Mechanical properties; Time dependence; Phase transformation; Chemical bond; Activation energy; DNA
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp400872k

Double-stranded (ds-) DNA molecules were stretched and ruptured on molecularly modified graphite surfaces with a scanning force microscope (SFM) exerting a force parallel to the surface. The stretching force was either large enough to break the molecule immediately or compensated by the elastic restoring force of the DNA backbone, which stabilized the molecular length. However, the size-stabilized molecules broke gradually from longer molecules to shorter ones with time. The breakage of different lengths of stabilized molecules was recorded in order to study time-dependent mechanical properties of the molecules under constant forces. From these data, a relatively high rate constant, k 0 = (2.2 ± 0.1) × 10–7 s–1, was calculated. Moreover, we found a nonlinear stress–strain dependence of DNA on the surface which we attributed to DNA conformational transition. Assuming that the structural transition on the surface is similar to that in solution we estimated the forces needed to stretch the molecules and thereby verify the estimation of the activation energy barrier.