Smaller, Better, Faster Transfection Assays; Really Ready Redivue; Visualizing RNA with RnaViz 2

PATENT WATCH | Smaller, Better, Faster Transfection Assays Courtesy of Akceli Cambridge, Mass.-based Akceli has been awarded a US patent for a reverse-transfection assay method (US patent 6,544,790, issued April 8, 2003). Akceli says the method condenses more than 6,000 data points on a single microtiter plate, which can be imaged in about 20 minutes. "Our technology allows us to do very rapid compound profiling and target ID and validation," says David Chao, president and cofounder of Akceli. The process is "much faster and more scaleable" because of the throughput advantages possible with microarrays of transfected mammalian cells, he adds. The method, based on work by David Sabatini at Massachusetts Institute of Technology, can be used to make living protein arrays or multiplexed cell-based assays. Nucleic acids are encapsulated in a hydrogel and printed in spots on a 96-well microtiter plate. A transfection reagent is then added, and cells directly above each printed spot take up the nucleic acids and either overexpress or underexpress the gene being studied. Akceli is now using the method internally for collaborations with pharmaceutical companies, and it is discussing licensing with instrument and reagent companies. The method, says Chao, can fit a microarray of 64 transfected cell clusters in each well of a microtiter plate. It can be integrated into off-the-shelf microarraying robots, imaging platforms, and image analysis software: "It's very scalable within the existing infrastructure of cell biology labs." --Ivan Oransky GADGET WATCH | Really Ready Redivue Courtesy of Amersham Biosciences Over the years, Amersham Biosciences of Piscataway, NJ, has tried to make radioactivity handling as painless as possible. Redivue, the company's first offering, includes both a compound to stabilize the materials at 4°C (normally, radioactive materials must be frozen) and a dye that makes them easier to see. Now Amersham is making radioactivity handling even easier with its newly released Redivue Tips™, in which reaction-sized aliquots of the nucleotides are reversibly adhered to the inside walls of pipette tips; to use, simply elute into an appropriate buffer or reaction mix. Because the inside of each tip is coated with an anion-exchange film, only solutions of sufficiently high ionic strength can elute the nucleotides. Currently, Redivue Tips are available loaded with [a-32P] dCTP. Each pack includes five tips, with 20, 30, or 50 µCi per tip. The tips contain no chemical stabilizers, yet like other Redivue reagents, can still be stored at 4°C. Amersham's Web site (www.radiochemicals.com) includes protocols for using the tips in random priming, 3'-end labeling, first-strand (cDNA) DNA synthesis, and sequencing reactions. --Jeffrey M. Perkel SOFTWARE WATCH | Visualizing RNA with RnaViz 2 Courtesy of Peter De Rijk Click for larger version (51K) Peter De Rijk, a postdoc at the University of Antwerp, Belgium, has upgraded RnaViz, his venerable RNA secondary-structure drawing software (rrna.uia.ac.be/rnaviz). De Rijk says he designed RnaViz, originally written in 1997, to bypass the shortcomings of existing software. These programs relied heavily on de novo structural prediction, making it difficult for the user to alter the computed configuration. They also could not be made to emphasize the similarities in certain molecules, such as tRNAs, were limited in the size of the molecules they could model, and could not handle structural elements called pseudoknots. RnaViz does not attempt to compute a structure; instead, it employs user-supplied information. Originally, such data could be specified in DCSE or CT files (produced by DCSE and MFOLD, respectively); new version 2.0 adds support for RNAML, an XML-based format (www-lbit.iro.umontreal.ca/rnaml). Also updated: the user interface and annotation tools, plus the usual bug fixes. Each base, helix, and loop on the page can be edited, moved, or modified (e.g., font, color, and size) to produce the clearest possible image. In addition, labels, polygons, and arrows can be added and edited. The user can then create a skeleton from the desired structure, producing a template on which to overlay similar molecules. Several common skeletons are included in the distribution. RnaViz 2 is written in C and Tcl/Tk. Binaries are supplied for Windows and Linux, but source code is also available, which can be compiled on any Tcl/Tk-compatible platform. With the exception of maintenance updates, says De Rijk, this new overhaul is the last for RnaViz. --Jeffrey M. Perkel function sendData() { document.frm.pathName.value = location.pathname; result = false if (document.frm.score[0].checked) result = true; if (document.frm.score[1].checked) result = true; if (document.frm.score[2].checked) result = true; if (document.frm.score[3].checked) result = true; if (document.frm.score[4].checked) result = true; if (!result) alert("Please select") return result; } .myradio{background-color : #94bee5} Please indicate on a 1 - 5 scale how strongly you would recommend this article to your colleagues? Not recommended 1 2 3 4 5 Highly recommended Please register your vote

Smaller, Better, Faster Transfection Assays; Really Ready Redivue; Visualizing RNA with RnaViz 2

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