Satellite Banner
Genomics
Scientific Community
 
Become a Member | Sign in
Home>News>This Article
  News
Return

Stanford Biologists Watch RNA Fold in Real Time

Published: Monday, October 22, 2012
Last Updated: Monday, October 22, 2012
Bookmark and Share
Using optical tweezers and sub-nanoscale precision, Steven Block and Kirsten Frieda follow the process – and the consequences – of RNA folding.

In a soundproofed, vibration-stabilized, temperature-controlled room, Stanford biophysicist Steven Block was watching a very small origami project.

"The apparatus is so sensitive that, if you talk in the room, the vibrations in the air disturb the movement you're trying to measure," he said quietly. On a black-and-white monitor, two microscopic plastic beads were being slowly drawn apart.

Although we couldn't see it even at this high level of magnification, between the beads was stretched a single strand of RNA, folding up in real time.

Because RNA nucleotides are so small – each is only nanometers long – these effects had never been directly observed before. The Block Lab apparatus is so precise, it can measure distances to within the diameter of a hydrogen atom.

But Block's feat isn't remarkable only for its sensitivity. How RNA molecules fold is a longstanding biological problem. It's crucial for the molecules' function, and different RNA configurations play a fundamental regulatory role during the transcription of those very RNA molecules.

"Issues of gene control are arguably more important than the genes themselves," Block said. "What differentiates organisms are not the genes per se, it's which genes get expressed where and when."
Block, a professor of applied physics and of biology, and graduate student Kirsten Frieda published their findings today in the journal Science.

Laser traps

The key to the "tour-de-force of instrumentation," as Block punned, was the use of "optical tweezers." When placed in the path of a highly focused laser, the team's tiny beads were attracted to the center of the beam, where the electric field produced by the light is strongest. The researchers were thereby able to position and immobilize the beads with extreme consistency and accuracy.

In Block's elegant setup, a single molecule of RNA polymerase – the enzyme that transcribes DNA strands into RNA – was attached to one bead, while the emerging RNA transcript was linked to the other.

By keeping the tension between the two beads constant and measuring the distance between them as they moved apart, Block was able to gauge the changing length of the new RNA strand.

"What we got was a blow-by-blow readout of how RNA folds as it is processed by RNA polymerase," said Block.

Switching the riboswitch

In the case of the RNA transcript studied by Block and Frieda, there were two conformation options, which led to two very different functional results.

The "favored" option – about 10 billion times more likely to form, all things being equal – was a terminator structure that would stop transcription if it formed.

The other structure was an anti-terminator formed by an RNA element known as a riboswitch located a little upstream of the terminator. Riboswitches are a common but poorly understood method of gene regulation, found in all kingdoms of life. These stretches of RNA transcripts change conformation after binding certain small target molecules, with consequences for gene control.

The anti-terminator was less thermodynamically stable than the terminator, and therefore much less likely to form. Because it formed slightly more quickly than the terminator, however, "it got its foot in the door," said Block.

"It's a bit like the old joke about escaping a bear in the woods," he said. "You don't actually have to run more quickly than the bear, you just have to run faster than your friend who's with you."

When the riboswitch's target molecule was present, the researchers found, the anti-terminator would consistently form, preventing the terminator from folding and allowing transcription to continue onward. The anti-terminator would only hold its shape for a second or so, but a second is just long enough.
"We were the first to actually see a riboswitch switch," Block said.

The team hopes to extend its techniques to other structured RNAs, including more riboswitches, as well as ribozymes – RNAs that can catalyze chemical reactions – and the tRNAs crucial to protein translation.


Further Information
Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,400+ scientific posters on ePosters
  • More than 3,700+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

DNA Damage Seen in Patients Undergoing CT Scanning
Along with the burgeoning use of advanced medical imaging tests over the past decade have come rising public health concerns about possible links between low-dose radiation and cancer.
Monday, July 27, 2015
Genetic Signature Enables Early, Accurate Sepsis Diagnosis
Systemic inflammation after injuries or surgery can dramatically alter the activity of thousands of genes, but a new study shows that changes in just 11 of them are enough to detect the presence or absence of accompanying infection.
Monday, May 18, 2015
Existing Drug May Treat Deadliest Childhood Brain Tumor
For the first time, scientists have identified an existing drug that slows the growth of the deadliest childhood brain tumor.
Friday, May 08, 2015
Foreign Antibodies Mobilize Immune System to Fight Cancer
A mouse’s T cells can be primed to attack and eliminate a malignant tumor by injecting antibodies from another mouse with resistance to the tumor, as well as by activating certain signaling cells, a study has found.
Thursday, May 07, 2015
Tiny Fish Makes Big Splash In Aging Research At Stanford
Researchers disabled aging-associated genes in the short-lived African killifish, including one for an enzyme called telomerase, whose absence caused humanlike disease in the animal.
Friday, February 13, 2015
Tumor Suppressor Also Inhibits Key Property Of Stem Cells
The retinoblastoma protein inhibits cancer by controlling cell division. Now, researchers have shown that it also binds to and inhibits genes necessary for pluripotency.
Friday, November 14, 2014
Scientists Discern Signatures of Old Versus Young Stem Cells
A chemical code scrawled on histones determines which genes in that cell are turned on and which are turned off.
Wednesday, July 03, 2013
Protein Complex May Play Role in Preventing Many Forms of Cancer, Study Shows
Researchers at the Stanford University School of Medicine have identified a group of proteins that are mutated in about one-fifth of all human cancers.
Tuesday, May 07, 2013
Antibody Hinders Growth of Gleevec-Resistant Gastrointestinal Tumors in Lab Test
An antibody that binds to a molecule on the surface of a rare but deadly tumor of the gastrointestinal tract inhibits the growth of the cancer cells in mice.
Thursday, February 07, 2013
Stanford Launches New Center to Advance 'Information Age of Genomics'
With a new research center, Stanford scientists from across campus will join a new "information age of genomics." The goal is nothing short of improving human well-being.
Tuesday, December 04, 2012
Where Chromosomes Agree, Stanford researchers Trace Human History
Examining shared stretches of genome from dozens of world populations, Stanford biologists have found a new way, not only to find signatures of human migrations and marriage practices, but to help find hidden disease genes.
Monday, August 20, 2012
New Method Enables Sequencing of Fetal Genomes using only Maternal Blood Sample
The findings from the new approach, published July 4 in Nature, are related to research that was reported a month ago from the University of Washington.
Friday, July 06, 2012
New Genetic Regions Linked to Bone-Weakening Disease and Fractures, Researcher Says
Thirty-two previously unidentified genetic regions associated with osteoporosis and fracture have been identified by a large, worldwide consortium of researchers, including Stanford Prevention Research Center chief John Ioannidis, MD, DSc.
Friday, April 20, 2012
Stanford Scientist Omics Profile used to Discover, Track his Diabetes Onset
Researchers also spied on Dr Snyder's immune system and watched it battle viral infections.
Monday, March 19, 2012
New Method Allows Human Embryonic Stem Cells to Avoid Immune System Rejection, Study Finds
According to Stanford University researchers, a short-term treatment with three immune-dampening drugs allowed human embryonic stem cells to survive and thrive in mice.
Wednesday, March 09, 2011
Scientific News
Long Telomeres Associated with Increased Lung Cancer Risk
Genetic predisposition for long telomeres predicts increased lung adenocarcinoma risk.
Expanding the Brain
A team of researchers has identified more than 40 new “imprinted” genes, in which either the maternal or paternal copy of a gene is expressed while the other is silenced.
Identifying a Key Growth Factor in Cell Proliferation
Researchers discover that aspartate is a limiter of cell proliferation.
Study Uncovers Target for Preventing Huntington’s Disease
Scientists from Cardiff University believe that a treatment to prevent or delay the symptoms of Huntington’s disease could now be much closer, following a major breakthrough.
The Genetic Roots of Adolescent Scoliosis
Scientists at the RIKEN Center for Integrative Medical Sciences in collaboration with Keio University in Japan have discovered a gene that is linked to susceptibility of Scoliosis.
A Gene-Sequence Swap Using CRISPR to Cure Haemophilia
For the first time chromosomal defects responsible for hemophilia have been corrected in patient-specific iPSCs using CRISPR-Cas9 nucleases
New Tool Uses 'Drug Spillover' to Match Cancer Patients with Treatments
Researchers have developed a new tool that improves the ability to match drugs to disease: the Kinase Addiction Ranker (KAR) predicts what genetics are truly driving the cancer in any population of cells and chooses the best "kinase inhibitor" to silence these dangerous genetic causes of disease.
Understanding the Molecular Origin of Epigenetic Markers
Researchers at IRB Barcelona discover the molecular mechanism that determines how epigenetic markers influence gene expression.
New Tech Enables Epigenomic Analysis with a Mere 100 Cells
A new technology that will dramatically enhance investigations of epigenomes, the machinery that turns on and off genes and a very prominent field of study in diseases such as stem cell differentiation, inflammation and cancer has been developed by researchers at Virginia Tech.
Access Denied: Leukemia Thwarted by Cutting Off Link to Environmental Support
A new study reveals a protein’s critical – and previously unknown -- role in the development and progression of acute myeloid leukemia (AML), a fast-growing and extremely difficult-to-treat blood cancer.
Skyscraper Banner

Skyscraper Banner
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,400+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
3,700+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FREE!