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When it comes to gene transcription, random pauses aren’t quite so random, study finds

protein that causes a serious disease or birth defect.

Transcription, the first step in protein synthesis, begins when an RNAP enzyme unzips a small section of the DNA double helix where a gene is located. The enzyme then builds a new complementary strand of RNA by chemically copying ("transcribing") the gene one base at a time. RNAP will continue moving along the DNA strand until the entire gene sequence is transcribed onto the encoded RNA, which then serves as a template for building the actual protein.

Nanotechnology

To observe RNAP in action, Block and his colleagues use a custom-built "optical trap" housed in his Stanford lab. This sensitive instrument allows researchers to observe transcription in real time by trapping individual molecules of DNA and RNAP in minute beams of infrared light.

"Our measurements are accurate to one-tenth of a nanometer--the width of a single hydrogen atom," Block explained. "When you study an RNAP enzyme at that scale, you discover that it moves along the DNA for a while, and then for no apparent reason it appears to stop. Some pauses we've already figured out. The really long ones, which happen every 1,000 bases or so and last up to 30 minutes, often occur when the enzyme makes a mistake. Then, it's got to back up and correct the mistake. But for every one of those, there are roughly 10 ubiquitous pauses that only last about 1 second and occur every 100 bases or so--and their role is really something of a mystery."

Sequence dependent

To find the answer, Kristina M. Herbert, a graduate student in Block's lab and lead author of the Cell study, created experimental DNA templates using a special 240-base pair sequence that triggers one of two types of long pauses in RNAP--a "backtracking pause" associated with gene regulation in which the enzyme reverses direction briefly; or a "hairpin pause, " named for tiny hairpin-shaped structures that sometimes form when an RNA stra
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Source:Stanford University


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