Enzymatic Sculptors: The Proteins that Shape siRNA and microRNA

Enzymatic Sculptors
Reported by
Beth Schachter

Posted January 24, 2007


The process of generating single-stranded small inhibitory RNAs (siRNAs) from larger, double-stranded (duplexed) precursors involves a sort of molecular sculpting. The starting material—either long double-stranded RNAs or long single-stranded RNAs with regions of duplex—is cleaved to a discretely sized short, double-stranded intermediate, typically between 22 and 27 bases long, and then one of the two strands is selectively retained as the RNA component of the mature RNA inhibitory (RNAi) complex while the other is discarded.

Researchers are getting increasingly clearer pictures of machinery involved in each stage of this sculpting process, through a combination of structural and functional studies. Two scientists who have made significant recent contributions to this understanding described their work at the April 11, 2006, meeting of the RNAi Discussion Group.

Use the tabs above to find a meeting report and multimedia from this event.

Web Sites

RNAi resources
"The latest techniques, hot papers, new products & events near you for this exciting research"; from Abcam, producers of monoclonal antibodies.

Journal of RNAi and Gene Silencing
An open-access journal launched in 2005, from Library Publishing Media of Oxford, UK.

ExPASy Proteomics Server
The Expert Protein Analysis System (ExPASy) proteomics server of the Swiss Institute of Bioinformatics (SIB), dedicated to the analysis of protein sequences and structures as well as the protein analysis technique of two-dimensional polyacrylamide gel electrophoresis (2D PAGE).

Analysis of flexibility in biomolecules and networks, from Arizona State University.


From RNase H to RNAi: Substrate Recognition and Two-metal Ion Catalysis

Ji, X. 2006. Structural basis for non-catalytic and catalytic activities of ribonuclease III. Acta Crystallogr. D Biol. Crystallogr. 62(Pt 8): 933-940.

Nowotny, M., S. A. Gaidamakov, R. J. Crouch & W. Yang. 2005. Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell 121: 1005-1016.

Yang, W., J. Y. Lee & M. Nowotny. 2006. Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity. Mol. Cell 22: 5-13.

Structural Studies of Dicer

Cook, A. & E. Conti. 2006. Dicer measures up. Nat. Struct. Mol. Biol. 13: 190-192.

Gan, J., J. E. Tropea, B. P. Austin, et al. 2006. Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III. Cell 124: 355-366.

MacRae, I. J., K. Zhou, F. Li, et al. 2006. Structural basis for double-stranded RNA processing by Dicer. Science 311: 195-198.


Wei Yang, PhD

National Institute of Diabetes and Digestive and Kidney Diseases
email | web site | publications

Wei Yang is chief of the Structural Biology and Cell Signaling Section at the Laboratory of Molecular Biology of the National Institute of Diabetes and Digestive and Kidney Diseases. Her group studies DNA recombination, repair, and replication, in particular V(D)J recombination, methyl-directed mismatch repair and translesion DNA synthesis. They use X-ray crystallography, molecular biology and various biochemical and biophysical approaches to find out the molecular mechanisms in these biological processes. Yang completed her PhD at Columbia University.

Ian MacRae, PhD

University of California, Berkeley
email | web site | publications

Ian MacRae is a postdoctoral scientist working in the laboratory of Jennifer Doudna at the University of California, Berkeley. The Doudna lab studies RNA-mediated initiation of protein synthesis, RNA-protein complexes involved in targeting proteins for export out of cells, and the early steps in gene regulation by RNA interference.

Beth Schachter, PhD

web site

Beth Schachter, PhD, writes about life science, medicine and biotechnology. She is also a partner in Still Point Coaching & Consulting, a firm that helps life scientists with communications and career development skills.

Schachter has published in Nature Biotechnology, The New York Times, The Scientist, Bio IT-World, and the HMS Beagle, and has written for the Howard Hughes Medical Institute, The Society for Women's Health Research and The Institute of Medicine. She entered science communications as HMS Beagle's first scientific editor.

Schachter's benchtop-to-laptop transition took place in 1997. Before that she was a biomedical researcher. She had been an associate professor at Mount Sinai Medical School, and also had taught at Cold Spring Harbor Laboratories. She received her PhD in cell and molecular biology from University of Southern California, and received postdoctoral training at the University of California, San Francisco and Columbia University. She serves on the board of Science Writers in New York (SWINY), the local affiliate of National Association of Science Writers.