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News Release 08-184

More Spring in the Double Helix's Step

DNA proven softer than previously thought

strands of DNA showing variation in compression of base pairs.

DNA may compress and extend more than previously thought possible.

October 16, 2008

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The DNA's double helix--the sub-microscopic core of our life--has been the subject of intense study and scrutiny for decades.

Observations and measurements at the scale of DNA are tricky. The distance between the rungs in DNA's ladder (or base pairs), for example, was thought to be barely over 3 millionths of a millimeter, or 3.4 Å (angstroms). And this ladder has been typically assumed to be very rigid.

But now a team of Stanford scientists, supported in part by the National Science Foundation, have used a novel molecular ruler to cast doubts on this picture. Using this molecular ruler, they marked each end of a snippet of DNA with electron-dense gold nanocrystals. These markers scattered X-rays directed at the sample differently than the rest of the molecules, and allowed for a more precise calculation.

The observations led the Stanford team to discover that DNA is much softer than previously thought. Variation--both compression and stretching--was observed.

Most surprisingly, the team found that if a base pair had compressed, the base pairs in at least the next two turns of the double helix were more likely to be compressed as well.

These observations have important ramifications for biologists looking at proteins binding to DNA, such as transcription factors regulating gene expression. Because this study has shown regions of DNA affecting the behavior of neighboring regions, it could mean that proteins binding to the DNA could communicate across greater molecular distances than previously thought.


Media Contacts
Lily Whiteman, National Science Foundation, (703) 292-8310, email:
Michelle Brandt, Stanford University School of Medicine, (650) 723-0272, email:

Program Contacts
William J. Hahn, National Science Foundation, (703) 292-8545, email:

Principal Investigators
Pehr Harbury, Stanford University School of Medicine, (650) 723-6161, email:

The National Science Foundation (NSF) is an independent federal agency that supports fundamental research and education across all fields of science and engineering. In fiscal year (FY) 2019, its budget is $8.1 billion. NSF funds reach all 50 states through grants to nearly 2,000 colleges, universities and other institutions. Each year, NSF receives more than 50,000 competitive proposals for funding and makes about 12,000 new funding awards.

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