Abstract:DNA elongation induced by fluidic stress was investigated on a microfluidic chip composed of a large inlet pool and a narrow channel. Through single-DNA observation with fluorescence microscopy, the manner of stretching of individual T4 DNA molecules (166 kbp) was monitored near the area of accelerating flow with narrowing streamlines. The results showed that the DNA long-axis length increased in a sigmoidal manner depending on the magnitude of flow acceleration, or shear, along the DNA chain. To elucidate the… Show more
“…The fact that no polymers were observed in the presence of pentasaccharide suggests that heparinoid length plays a role, with a heparin molecule having to be able to bind multiple nucleosomes/DNA fragments in order to form these polymers. Nonetheless, the striking similarities of the polymers with DNA are difficult to overlook: they bind SYTOX, contain histones, and show shear-dependent elongation 25–27 .Figure 7Proposed mechanism for the formation of polymers between heparin and histones/DNA on the surface of platelet aggregates. Negatively charged heparin molecules (in orange) sequester circulating nucleosomes in plasma (in blue) by binding to protruding positively charged N-termini of histones.…”
Heparin is a widely used anticoagulant which inhibits factor Xa and thrombin through potentiation of antithrombin. We recently identified that the nucleic acid stain SYTOX reacts with platelet polyphosphate due to molecular similarities, some of which are shared by heparin. We attempted to study heparin in flowing blood by live-cell fluorescence microscopy, using SYTOX for heparin visualisation. Immunostaining was performed with monoclonal antibodies directed against various heparin-binding proteins. In addition, we studied modulation of heparin activity in coagulation assays, as well its effects on fibrin formation under flow in recalcified whole blood. We found that SYTOX-positive polymers appear in heparinised blood under flow. These polymers typically associate with platelet aggregates and their length (reversibly) increases with shear rate. Immunostaining revealed that of the heparin-binding proteins assessed, they only contain histones. In coagulation assays and flow studies on fibrin formation, we found that addition of exogenous histones reverses the anticoagulant effects of heparin. Furthermore, the polymers do not appear in the presence of DNase I, heparinase I/III, or the heparin antidote protamine. These findings suggest that heparin forms polymeric complexes with cell-free DNA in whole blood through a currently unidentified mechanism.
“…The fact that no polymers were observed in the presence of pentasaccharide suggests that heparinoid length plays a role, with a heparin molecule having to be able to bind multiple nucleosomes/DNA fragments in order to form these polymers. Nonetheless, the striking similarities of the polymers with DNA are difficult to overlook: they bind SYTOX, contain histones, and show shear-dependent elongation 25–27 .Figure 7Proposed mechanism for the formation of polymers between heparin and histones/DNA on the surface of platelet aggregates. Negatively charged heparin molecules (in orange) sequester circulating nucleosomes in plasma (in blue) by binding to protruding positively charged N-termini of histones.…”
Heparin is a widely used anticoagulant which inhibits factor Xa and thrombin through potentiation of antithrombin. We recently identified that the nucleic acid stain SYTOX reacts with platelet polyphosphate due to molecular similarities, some of which are shared by heparin. We attempted to study heparin in flowing blood by live-cell fluorescence microscopy, using SYTOX for heparin visualisation. Immunostaining was performed with monoclonal antibodies directed against various heparin-binding proteins. In addition, we studied modulation of heparin activity in coagulation assays, as well its effects on fibrin formation under flow in recalcified whole blood. We found that SYTOX-positive polymers appear in heparinised blood under flow. These polymers typically associate with platelet aggregates and their length (reversibly) increases with shear rate. Immunostaining revealed that of the heparin-binding proteins assessed, they only contain histones. In coagulation assays and flow studies on fibrin formation, we found that addition of exogenous histones reverses the anticoagulant effects of heparin. Furthermore, the polymers do not appear in the presence of DNase I, heparinase I/III, or the heparin antidote protamine. These findings suggest that heparin forms polymeric complexes with cell-free DNA in whole blood through a currently unidentified mechanism.
“…Deformation of DNA nanostructures may also be induced by external loadings. External forces are applied by multiple methods including optical tweezers, [117][118][119] magnetic tweezers, 78,120,121 electric elds, [122][123][124] ow elds, [125][126][127] and direct contact forces such as AFM. 74,128,129 These devices can add forces or torques precisely and be used for studying deformation mechanisms as well as mechanical properties.…”
In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations....
“…Such slip, which has been hypothesized for cases of other types of PE (e.g. DNA molecules in a background fluid flow (Galla et al 2014;Hirano et al 2018)), is expected to be present on the PE brush surfaces and ensures that the brushes do not behave as rigid cylinders that stagnate the flow on their surfaces. It is to be noted that the contribution of H + ions is very significant at very low salt concentrations, whereas this contribution is very small at very high concentrations.…”
Section: Variation Of the Thermo-osmotically Induced Electric Fieldmentioning
confidence: 98%
“…Nanofluidic transport involves the flow of liquids and flow-driven transport of ions, solutes, bioanalytes and other species in nanochannels and nanopores (Eijkel & Van Den Berg 2005;Sparreboom et al 2009;Das et al 2012;Ziemys et al 2012;Koltonow & Huang 2016;Gao et al 2017;Zhu et al 2019). Such transport has received immense attention over the past few decades motivated by its applications in fabricating sensors that require very little sample volumes (Venkatesan & Bashir 2011;Miles et al 2013), devices capable of ionic gating (Liu et al 2015;Fang et al 2016), and platforms capable of a variety of biomedical applications (Hood et al 2017;Weerakoon-Ratnayake et al 2017), water filtration and desalination (Chen et al 2017;Anand et al 2018), oil recovery (Zhang et al 2019), etc. The significantly large interfacial effects in such nanofluidic systems have enabled the utilization of novel and unconventional flow-driving mechanisms such as electro-osmotic (EOS) transport (Eijkel & Van Den Berg 2005).…”
Section: Introductionmentioning
confidence: 99%
“…This, in a way, supports the idea of a possible absence of a no-slip condition along the surface of the brushes. Also, there are several studies probing the interaction of a DNA molecule in a background fluid flow: these studies point out that there might be a slip condition on the DNA surface (Galla et al 2014;Hirano et al 2018). The DNA is a charged polymer (or a PE) molecule and along that argument it is not too unreasonable an assumption that there will be a finite slip along the surface of the PE brushes.…”
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