Nanotech instruments allow first direct observations of RNA 'proofreading'

When Ralph Waldo Emerson said that nature pardons no mistakes, he wasn't thinking about RNA polymerase (RNAP) - the versatile enzyme that copies genes from DNA onto strands of RNA, which then serve as templates for all of the proteins that make life possible.

Emerson's comment notwithstanding, RNAP makes plenty of mistakes but also proofreads and corrects them before they have a chance to create abnormal proteins. The error-prone nature of RNAP is not surprising given the size of its task. In human cells, for example, the RNAP enzyme has to make precise genetic copies from a DNA double helix that consists of billions of chemical bases known as A, T, G and C. It works like this: After latching onto the double helix, RNAP pulls it apart and starts building new RNA molecules by copying one DNA base at a time.

With thousands of A's, T's, G's and C's to transcribe, RNAP sometimes gets confused and copies the wrong base. Such errors occur roughly once every 1,000 bases, but RNAP's remarkable self-correcting mechanism manages to catch most of them.

''If the error is allowed to propagate, it could result in a bad protein or a wrong protein, but RNAP is an incredibly smart enzyme,'' says Steven M. Block, a professor of biological sciences and of applied physics at Stanford University. ''When RNAP adds the wrong base, it backs up on the DNA helix a little bit, cleaves off the piece of RNA that has the bad base in it and starts up again. That's the hypothesis, at least.''

New experiments

In a new study in the journal Nature, Block and his colleagues present strong evidence to support this proofreading hypothesis. Their results - based on actual observations of individual molecules of RNAP - are posted on Nature's website: http://www.nature.com. In another set of experiments published in the Nov. 14 issue of Cell magazine, the researchers discovered that RNAP makes thousands of brief pause

Contact: Mark Shwartz
Stanford University

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