Presentation of Large DNA Molecules for Analysis as
Nanoconfined Dumbbells
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Abstract
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 propertiesbuttressed by
molecular simulationswe 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