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This Week in Nucleic Acids Research: Jul 18, 2012

A public-private team including investigators from SomaGenics, the University of California, San Francisco, Integrated DNA Technologies, and Stanford University School of Medicine shows in a paper published online in advance in Nucleic Acids Research this week that certain short shRNAs — or sshRNAs, which are "designated as L-type or R-type according to whether the loop is positioned 3′ or 5′ to the guide sequence, respectively" — require loop cleavage for optimum activity. Using nucleotide modifications that inhibit RNA cleavage, the team shows that such is the case for R- but not L-sshRNAs. "We conclude that active L-sshRNAs depend on slicing of the passenger arm to facilitate opening of the duplex, whereas R-sshRNAs primarily act via loop cleavage to generate a 5′-phosphate at the 5′-end of the guide strand," the authors write.

Researchers at the California Institute of Technology and Stanford University describe a "high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity" in another Nucleic Acids Research advance online publication posted this week. This approach, based on a quantitative two-color fluorescence-activated cell sorting-based screening strategy, enables the "rapid generation of ribozyme-based control devices with user-specified regulatory activities," the researchers write. "We demonstrated the versatility of our approach by screening large libraries generated from randomizing individual components within the ribozyme device platform to efficiently isolate new device sequences that exhibit increased in vitro cleavage rates up to 10.5-fold and increased in vivo activation ratios up to two-fold," they add.

The Scan

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Science Papers Examine Feedback Mechanism Affecting Xist, Continuous Health Monitoring for Precision Medicine

In Science this week: analysis of cis confinement of the X-inactive specific transcript, and more.