Synopsis: Double, Double…Bubble

DNA flexibility depends on how strands separate, which, in turn, depends on temperature.

Many biological processes, such as how DNA is packed in a virus or combines with proteins to form nuclei in cells, depend on the flexibility of DNA strands. A single strand of DNA is understandably highly flexible, as it can rotate freely around chemical bonds. The double helix, with its hydrogen-bonded base pairs, is considerably more rigid. But how rigid?

One measure of flexibility of such a molecule is its persistence length, which is the distance beyond which correlations arising from thermal fluctuations die out. Experimentalists have studied the effect of temperature on DNA using multiple approaches. From these experiments one feature is clear: the persistence length quickly decreases with rising temperature.

To understand these thermal effects, theorists initially modeled DNA as homogeneous flexible rods, and subsequently as rods that have rigid sections interspersed with “flexible joints.” A possible origin of such joints is the so-called DNA bubble, a region where the double helix separates locally. Now, in a paper in Physical Review Letters, Nikos Theodorakopoulos at the National Hellenic Research Foundation, Greece, and Michel Peyrard at Ecole Normale Supérieure de Lyon, France, calculate in detail how two particular base sequences develop bubbles as they are heated, and how these bubbles in turn increase local flexibility. This quantitative link between bubbles and the temperature dependence of the persistence length turns out to be stronger than previously thought. Relatively few bubbles, or base-pair openings, suffice to change the persistence length significantly. A better knowledge of the persistence length should, in turn, provide a sensitive probe of how DNA strands separate. – Sami Mitra


Announcements

More Announcements »

Subject Areas

Biological Physics

Previous Synopsis

Nanophysics

Nanoparticle Sifting

Read More »

Next Synopsis

Atomic and Molecular Physics

Fermionic Switch

Read More »

Related Articles

Synopsis: Runaway Brain
Biological Physics

Synopsis: Runaway Brain

Ultralight wirelessly powered devices can stimulate the neurons of a mouse as it moves freely over a large area. Read More »

Synopsis: Bacterial Superfluids
Fluid Dynamics

Synopsis: Bacterial Superfluids

Self-propelling bacteria can reduce the viscosity of a fluid to zero through a collective organization of their swimming. Read More »

Synopsis: Magnetic Carpet Ride
Magnetism

Synopsis: Magnetic Carpet Ride

Magnetic particles self-assemble into a sheet that can carry cells and other tiny cargo to a specific location. Read More »

More Articles