Dataset Information

Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks.

ABSTRACT: Bending with high curvature is one of the major mechanical properties of double-stranded DNA (dsDNA) that is essential for its biological functions. The emergence of a kink arising from local melting in the middle of dsDNA has been suggested as a mechanism of releasing the energy cost of bending. Herein, we report that strong bending induces two types of short dsDNA deformations, induced by two types of local melting, namely, a kink in the middle and forks at the ends, which we demonstrate using D-shaped DNA nanostructures. The two types of deformed dsDNA structures dynamically interconvert on a millisecond timescale. The transition from a fork to a kink is dominated by entropic contribution (anti-Arrhenius behavior), while the transition from a kink to a fork is dominated by enthalpic contributions. The presence of mismatches in dsDNA accelerates kink formation, and the transition from a kink to a fork is removed when the mismatch size is three base pairs.

SUBMITTER: Kim C

PROVIDER: S-EPMC4744731 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks.

Kim Cheolhee C Lee O-chul OC Kim Jae-Yeol JY Sung Wokyung W Lee Nam Ki NK

Angewandte Chemie (International ed. in English) 20150605 31

Bending with high curvature is one of the major mechanical properties of double-stranded DNA (dsDNA) that is essential for its biological functions. The emergence of a kink arising from local melting in the middle of dsDNA has been suggested as a mechanism of releasing the energy cost of bending. Herein, we report that strong bending induces two types of short dsDNA deformations, induced by two types of local melting, namely, a kink in the middle and forks at the ends, which we demonstrate using ...[more]

PMID: 26046547

Similar Datasets

Project description:Mitochondrial dysfunction and oxidative stress-mediated inflammasome activation play critical roles in the pathogenesis of the non-alcoholic fatty liver disease (NAFLD). Non-steroidal anti-inflammatory drug (NSAID)-activated gene-1 (NAG-1), or growth differentiation factor-15 (GDF15), is associated with many biological processes and diseases, including NAFLD. However, the role of NAG-1/GDF15 in regulating oxidative stress and whether this process is associated with absent in melanoma 2 (AIM2) inflammasome activation in NAFLD are unknown. In this study, we revealed that NAG-1/GDF15 is significantly downregulated in liver tissues of patients with steatosis compared to normal livers using the Gene Expression Omnibus (GEO) database, and in free fatty acids (FFA, oleic acid/palmitic acid, 2:1)-induced HepG2 and Huh-7 cellular steatosis models. Overexpression of NAG-1/GDF15 in transgenic (Tg) mice significantly alleviated HFD-induced obesity and hepatic steatosis, improved lipid homeostasis, enhanced fatty acid β-oxidation and lipolysis, inhibited fatty acid synthesis and uptake, and inhibited AIM2 inflammasome activation and the secretion of IL-18 and IL-1β, as compared to their wild-type (WT) littermates without reducing food intake. Furthermore, NAG-1/GDF15 overexpression attenuated FFA-induced triglyceride (TG) accumulation, lipid metabolism deregulation, and AIM2 inflammasome activation in hepatic steatotic cells, while knockdown of NAG-1/GDF15 demonstrated opposite effects. Moreover, NAG-1/GDF15 overexpression inhibited HFD- and FFA-induced oxidative stress and mitochondrial damage which in turn reduced double-strand DNA (dsDNA) release into the cytosol, while NAG-1/GDF15 siRNA showed opposite effects. The reduced ROS production and dsDNA release may be responsible for attenuated AIM2 activation by NAG-1/GDF15 upon fatty acid overload. In conclusion, our results provide evidence that other than regulating lipid homeostasis, NAG-1/GDF15 protects against hepatic steatosis through a novel mechanism via suppressing oxidative stress, mitochondrial damage, dsDNA release, and AIM2 inflammasome activation.

Project description:Electromechanical coupling defines the ratio of electrical and mechanical energy exchanged during a flexure cycle of a piezoelectric actuator. This paper presents an analysis of the dynamic electromechanical coupling factor (dynamic EMCF) for cantilever based piezoelectric actuators and provides for the first time explicit expressions for calculation of dynamic EMCF based on arrangement of passive and active layers, layer geometry, and active and passive materials selection. Three main cantilever layer configurations are considered: unimorph, dual layer bimorph and triple layer bimorph. The actuator is modeled using standard constitutive dynamic equations that relate deflection and charge to force and voltage. A mode shape formulation is used for the cantilever dynamics that allows the generalized mass to be the actual mass at the first resonant frequency, removing the need for numerical integration in the design process. Results are presented in the form of physical insight from the model structure and also numerical evaluations of the model to provide trends in dynamic EMCF with actuator design parameters. For given material properties of the active and passive layers and given system overall damping ratio, the triple layer bimorph topology is the best in terms of theoretically achievable dynamic EMCF, followed by the dual layer bimorph. For a damping ratio of 0.035, the dynamic EMCF for an example dual layer bimorph configuration is 9% better than for a unimorph configuration. For configurations with a passive layer, the ratio of thicknesses for the passive and active layers is the primary geometric design variable. Choice of passive layer stiffness (Young's modulus) relative to the stiffness of the material in the active layer is an important materials related design choice. For unimorph configurations, it is beneficial to use the highest stiffness possible passive material, whereas for triple layer bimorph configurations, the passive material should have a low stiffness. In all cases, increasing the transverse electromechanical coupling coefficient of the active material improves the dynamic EMCF.

Dataset Information

Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks.

Publications

Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets