The long term goal of Sfold development is to provide the scientific community with the best possible tools for the rational and efficient design of RNA-targeting nucleic acids. With support from both NSF and NIH, this objective is expected to be achieved by collaborating with experimental labs to conduct large scale experiments both in vitro and in vivo (in cultured cells), for improving the design methods and tools through analyzing experimental feedback data.
We have on-going collaborations with three "wet" labs at the Wadsworth Center to test our prediction of target accessibility and methods for the rational design of siRNAs, antisense oligos, and hammerhead ribozymes. We are currently seeking additional collaborative opportunities for validating and improving siRNA design. Information on the "wet" labs and collaborative projects is summarized below.
Validation of siRNA design
| PI | Brian Pentecost, Ph.D.; Michael Fasco, Ph.D. |
| Web Site | http://www.wadsworth.org/resnres/bios/pentecst.htm http://www.wadsworth.org/resnres/bios/fascomj.htm |
| Project | Target accessibility prediction and rational design of siRNAs for silencing human estrogen receptor (ER) and green fluorescence protein (GFP) in cultured cells |
Validation and improvement of antisense oligo design
| PI | Kathleen McDonough, Ph.D. |
| Web Site | http://www.wadsworth.org/resnres/bios/mcdongh.htm |
| Project | Target accessibility prediction and rational design of antisense oligos for inhibition of E. coli lacZ in vitro and bacterial targets in cultured cells |
| Source of Support | Large-scale testing for validation and design improvement is funded by NSF (grant 0200970) |
Validation and improvement of trans-cleaving ribozyme design
| PI | Erasmus Schneider, Ph.D. |
| Web Site | http://www.wadsworth.org/resnres/bios/schnder.htm |
| Project | Target accessibility prediction and rational design of hammerhead ribozymes for RNA target cleavage in vitro and gene down regulation of breast cancer resistance protein (BCRP) in cultured cells |
| Source of Support | Large-scale testing for validation and design improvement will be funded by NIH (grant 1 R01 GM068726-01) |
Experimental results
Preliminary testing results are highly encouraging. For a summary of the results presented at RNAi03-Boston, please click here for a PDF file.
Updated by Ye Ding, April 25, 2003