Stanford Synchrotron Radiation Lightsource
Date Published: December 17, 2008

A Golden Ruler Used to Measure the Stretching Rigidity of Short-length Scale DNA
summary written by Brad Plummer, SLAC Communication Office

DNA is softer and stretchier than previously believed, at least on the short length scales of up to 20 base pairs. This finding is the result of a recent study conducted in part at SSRL's biological small-angle x-ray scattering Beam Line 4-2 by a team of researchers from Stanford University. The results were published in the October 17 edition of the journal Science.

In a cell nucleus, enzymes constantly pull, twist and bend DNA molecules in order to transmit and express genetic information. Therefore, the bending, twisting and stretching rigidity of DNA affect how it wraps around histones to form chromosomes, supercoils during replication, bends and stretches upon interactions with proteins and packs into the confined space within a virus particle. Understanding these mechanical properties could deepen our understanding of how it functions in cells. Until now, however, measuring the stretching rigidity of DNA has been difficult on short length scales.

The team of Stanford researchers, led by Pehr Harbury, solved the problem using specially prepared nanocrystals that contain 75 gold atoms. The nanocrystals were attached to modified sections of DNA of various lengths—from 3 to 35 base pairs—and used as reference points. Using small-angle x-ray scattering interference between the nanocrystals for this series of DNA double helices in solution, the team found that, for short duplexes up to 20 base pairs in length, DNA is far "softer" and more elastic than previously thought by an order of magnitude. Although the research is ongoing, the team believes this cooperative stretching behavior could underlie a mechanism of molecular communication between neighboring strands of DNA during transcription and other key processes.

To learn more about this research see the full Scientific Highlight

R.S. Mathew-Fenn, R. Das, J.A. Silverman, P.A. Walker, P.A.B. Harbury, "A Molecular Ruler for Measuring Quantitative Distance Distributions." PLoS ONE 3, e3229 (2008).

R.S. Mathew-Fenn, R. Das, P.A.B. Harbury, "Remeasuring the Double Helix." Science 322, 446 (2008).

SLAC National Accelerator Laboratory
Stanford University