DNA Analysis by Structure

Applied Genetics News,  August, 2001  

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Scientists at Third Wave Technologies, Inc. (502 Rosa Rd., Madison, WI, 5371-1256; Tel: 608/273-8933; Website: www.twt.com) have demonstrated the ability to analyze genetic sequences based on their structure, a departure from conventional methods that only involve the linear sequence. Their results published in the current issue of Nucleic Acids Research.

"Third Wave's structure-specific sequence analysis technology has the potential to radically reshape the landscape of nucleic acid analysis by allowing the detection of genetic variations more easily, efficiently and inexpensively than current, linear analysis methods," says Lance Fors, chairman and CEO of Third Wave.

Because nucleic acids have a natural tendency to fold on themselves, traditional hybridization assays and arrays use a variety of methods to overcome the interference created when they do, adding multiple steps and additional cost to the analysis. Third Wave's structure-specific hybridization approach eliminates those steps by using the structure of the nucleic acid to detect variations anywhere in the molecule of interest.

The number of probes needed for structure-specific analysis is reduced because the probes bridge the unique, 3-D structure of a single, folded strand of DNA or RNA rather than targeting its linear sequence. In addition, structure-specific analysis can be performed on the bench top at room temperature on simple instruments that are now widely used in hospitals, clinics and physicians' offices because the method targets the nucleic acid's natural structural fingerprint.

The ability to genotype variations by structure may facilitate the diagnosis of disease, particularly viral disease. In the case of the hepatitis C virus (HCV), for example, there are numerous changes in the RNA sequence of the virus that do not determine genotype. Some of these changes either do not affect the structure or are offset by other changes that permit functionally important structural features in the genome to be conserved. However, sequence changes associated with specific viral genotypes (HCV 1a, 1b, 2a/c, 3a, etc.) are associated with changes in the genome structure that allow different genotypes to be easily distinguished by structure-specific probing.

In addition, genotyping HCV isolates using structure-specific analysis; for example, it used half as many probes as would be needed for conventional, linear analysis methods, according to Third Wave.

Other potentially valuable features of structure-specific analysis include the ability to identify secondary and tertiary structures of a particular sequence and the detection of long-range DNA interactions.

"The power of structure-specific sequence analysis is in its combination of flexible test conditions with powerful discrimination capability," says Fors. "This technology is ideal for the high-volume analysis needed for pathogen genotyping and mutation discovery research."

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COPYRIGHT 2001 Gale Group