Squeezing New Information out of DNA

Abstract:

In a human cell, DNA strands totaling two meters in length are spooled up and compacted into a nucleus only 10 microns—about a tenth the thickness of a sheet of paper—in diameter. This is comparable to taking a piece of linguini that is long as the distance from Halifax to Vancouver, and fitting it inside a sphere less than the width of a football field across. The behavior of DNA under such confinement is of immense interest to both basic and applied research. It’s of interest to biology, since that’s the state in which DNA is encountered by all the other cellular components, and it’s of interest to physics, as DNA is a polymer, like the material making up the screen on which you’re watching this or the clothes you’re wearing. The physical properties of confined DNA are of particular importance in efforts to read the sequence of a single piece of DNA. Typical schemes for single-DNA sequencing generally involve forcing small segments of DNA into a groove such that it adopts a linear conformation, or threading it through a pore. If we could develop whole-genome sequencing, it would let us detect dangerous mutations present in only a small part of a tumour.

In this talk, I’ll present the capabilities of a novel platform to manipulate and visualize single pieces of DNA, called “Convex Lens-induced Confinement” (CLiC). CLiC treats molecules gently, keeping the long DNA strands intact, rather than breaking them up into smaller pieces, which is how typical sequencing currently works. We precisely explore the polymer physics underlying the DNA polymers’ behaviour as a function of applied nanoscale confinement.

We also study the behavior of supercoiled DNA. Just from the arrangement of bonds between atoms in DNA, the polymer consists of two spirals that wind around each other even when no external twisting is applied, like the outer rim of a piece of fusilli. But supercoiled DNA is twisted additionally, either making the pair of spirals wind more tightly or more loosely about each other. When they’re wound more tightly, they are harder to pull apart from each other. When they’re wound more loosely, they’re easier to separate. A number of biological processes, such as transferring the information in DNA to protein-making factories (called transcription), rely on pulling apart the two strands of DNA, and, furthermore, as these processes proceed, they in turn affect the supercoiling state of the DNA they’re interacting with. Our lab has developed a model supercoiling system that would be difficult to study using techniques other than CLiC, to learn about how supercoiling affects the ease of DNA unwinding and the interaction of unwound DNA with other biomolecules.

The overarching vision of this talk is that by “getting into that room at the bottom” of nanobiophysics by innovative technologies, we open doors to complementary biophysical discovery and biomedical diagnostics which can act hand in hand.