DNA Detection Without PCR; Sequence-Analysis Beerware; Shuffling the Genome Deck

Front Page | DNA Detection Without PCR; Sequence-Analysis Beerware; Shuffling the Genome Deck Courtesy of AcaClone Software SOFTWARE WATCH | Sequence-Analysis Beerware DNA sequence analysis software needn't be expensive. For a decade, molecular biologist Kjeld Olesen has spent much of his spare time developing pDRAW32, a free sequence-analysis software package for Windows PCs. Researchers can perform restriction enzyme analyses, edit sequences, create plasmid maps, cut and ligate "in silico," analyze GC content, make homology plots, and select primer sites from a user-specified database. Now in version 1.1.60, pDRAW32 (www.acaclone.com) even has a feature that creates a virtual gel. "It's designed to assist the molecular biologist in what he does when he's working in the laboratory." Olesen says he started developing pDRAW32 because 10 years ago, the only available applications had to be accessed through remote servers using UNIX. Though he's unsure how many researchers use the software, Olesen says his Web site and its mirrors have logged more than 100,000 visitors. He continues to update the program based on user comments--often, he says, at the expense of additions he wants to include. The program remains freeware--or as Olesen puts it, beerware: Users are encouraged to buy him a pint if they find him at a meeting. "I wish Microsoft would do the same thing," he quips. --Brendan A. Maher GADGET WATCH | DNA Detection Without PCR Courtesy of Reza Ghadiri US researchers have developed a technique that bypasses the polymerase chain reaction for DNA-detection applications.1 Designed by Reza Ghadiri's team at the Scripps Research Institute in La Jolla, Calif., the system consists of a single DNA strand bound at one end to an enzyme, cereus neutral protease, and at the other end to its small-molecule inhibitor (reporter strand); a fluorescent substrate for the enzyme; and the test sample. While the reporter strand is unpaired, the inhibitor sits in the enzyme's active site, preventing it from functioning. If the desired sequence is present in the sample, however, it binds the reporter, releasing the inhibitor. With its hands untied, the enzyme activates the substrate, announcing the DNA's presence like a stranded mariner setting off flares. "The technology holds considerable promise as a future point-of-care diagnostic and in emergency settings where accuracy, ease of use, portability, and analysis speed are of paramount importance," Ghadiri says. "The method could do away with PCR for many analytical applications," adds Eric Anslyn of the University of Texas, "but PCR is also used simply to increase the amount of DNA present, and it would not replace these kinds of uses." --David Bradley 1. A. Saghatelian et al., "DNA detection and signal amplification via an engineered allosteric enzyme," J Am Chem Soc, 125:344-5, January 2003. PATENT WATCH | Shuffling the Genome Deck Erica P. Johnson Just as evolution by "biparental mating" (read: dating and sex) can be a messy, hit-or-miss process, rational polynucleotide design can be quite expensive, and take years. On Feb. 11, Redwood City, Calif.-based Maxygen was awarded US patent 6,518,065 for an accelerated method of recombining and selecting polynucleotides based on particular characteristics. "The technology we have mimics natural evolution," explains Willem Stemmer, Maxygen's vice president for research and development. The procedure involves partial, randomized fragmentation of the DNA followed by a PCR recombination step to regenerate full-length, but recombined, sequences. Such genome shuffling has already been used to "make large improvements," according to Stemmer, in genes encoding CO2-fixation enzymes in Streptomyces.1 Maxygen has collaborated with Eli Lilly and Co., and would welcome other large companies willing to work on a contract basis, but outlicensing to smaller labs is not feasible, Stemmer says, unless a targeted compound has clear promise of commercial viability: "It's not worth the up-front investment." So match.com OK, but neighborhood matchmakers need not apply. --Ivan Oransky 1. Y.X. Zhang et al., "Genome shuffling leads to rapid phenotypic improvement in bacteria," Nature, 415:644-6, 2002.

DNA Detection Without PCR; Sequence-Analysis Beerware; Shuffling the Genome Deck

Front Page | DNA Detection Without PCR; Sequence-Analysis Beerware; Shuffling the Genome Deck

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