Nanoslit Confined DNA at Low Ionic Strengths

We present nanoslit confined DNA conformations at very low ionic strengths and a theory to explain most measurements for single DNA molecule size under strong nanoslit confinement. Very low ionic strength conditions not only increase the DNA persistence length dramatically, but also cause DNA molecules to swell to the extent that the effective diameter of DNA becomes larger than the nanoslit height. By accounting for these effects, our results and theory provide a reasonable clue for a current controversy regarding the dependence of the DNA conformation on slit height (<i>h</i>), persistence length (<i>p</i>), and effective diameter (<i>w</i>)

Presentation of Large DNA Molecules for Analysis as Nanoconfined Dumbbells

The analysis of very large DNA molecules intrinsically supports long-range, phased sequence information, but requires new approaches for their effective presentation as part of any genome analysis platform. Using a multipronged approach that marshaled molecular confinement, ionic environment, and DNA elastic propertiesbuttressed by molecular simulationswe have developed an efficient and scalable approach for presentation of large DNA molecules within nanoscale slits. Our approach relies on the formation of DNA dumbbells, where large segments of the molecules remain outside the nanoslits used to confine them. The low ionic environment, synergizing other features of our approach, enables DNA molecules to adopt a fully stretched conformation, comparable to the contour length, thereby facilitating analysis by optical microscopy. Accordingly, a molecular model is proposed to describe the conformation and dynamics of the DNA molecules within the nanoslits; a Langevin description of the polymer dynamics is adopted in which hydrodynamic effects are included through a Green’s function formalism. Our simulations reveal that a delicate balance between electrostatic and hydrodynamic interactions is responsible for the observed molecular conformations. We demonstrate and further confirm that the “Odijk regime” does indeed start when the confinement dimensions are of the same order of magnitude as the persistence length of the molecule. We also summarize current theories concerning dumbbell dynamics

Presentation of Large DNA Molecules for Analysis as Nanoconfined Dumbbells

The analysis of very large DNA molecules intrinsically supports long-range, phased sequence information, but requires new approaches for their effective presentation as part of any genome analysis platform. Using a multipronged approach that marshaled molecular confinement, ionic environment, and DNA elastic propertiesbuttressed by molecular simulationswe have developed an efficient and scalable approach for presentation of large DNA molecules within nanoscale slits. Our approach relies on the formation of DNA dumbbells, where large segments of the molecules remain outside the nanoslits used to confine them. The low ionic environment, synergizing other features of our approach, enables DNA molecules to adopt a fully stretched conformation, comparable to the contour length, thereby facilitating analysis by optical microscopy. Accordingly, a molecular model is proposed to describe the conformation and dynamics of the DNA molecules within the nanoslits; a Langevin description of the polymer dynamics is adopted in which hydrodynamic effects are included through a Green’s function formalism. Our simulations reveal that a delicate balance between electrostatic and hydrodynamic interactions is responsible for the observed molecular conformations. We demonstrate and further confirm that the “Odijk regime” does indeed start when the confinement dimensions are of the same order of magnitude as the persistence length of the molecule. We also summarize current theories concerning dumbbell dynamics

Presentation of Large DNA Molecules for Analysis as Nanoconfined Dumbbells

The analysis of very large DNA molecules intrinsically supports long-range, phased sequence information, but requires new approaches for their effective presentation as part of any genome analysis platform. Using a multipronged approach that marshaled molecular confinement, ionic environment, and DNA elastic propertiesbuttressed by molecular simulationswe have developed an efficient and scalable approach for presentation of large DNA molecules within nanoscale slits. Our approach relies on the formation of DNA dumbbells, where large segments of the molecules remain outside the nanoslits used to confine them. The low ionic environment, synergizing other features of our approach, enables DNA molecules to adopt a fully stretched conformation, comparable to the contour length, thereby facilitating analysis by optical microscopy. Accordingly, a molecular model is proposed to describe the conformation and dynamics of the DNA molecules within the nanoslits; a Langevin description of the polymer dynamics is adopted in which hydrodynamic effects are included through a Green’s function formalism. Our simulations reveal that a delicate balance between electrostatic and hydrodynamic interactions is responsible for the observed molecular conformations. We demonstrate and further confirm that the “Odijk regime” does indeed start when the confinement dimensions are of the same order of magnitude as the persistence length of the molecule. We also summarize current theories concerning dumbbell dynamics