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Reflections on a DNA mutation scanning tool

Nature Biotechnology volume 19, pages 18–19 (2001)Cite this article

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Although some 1.6 million human single-nucleotide polymorphisms have been found in the human genome and deposited to public databases, as of November 20001, there is still a great need for identifying unknown DNA sequence variations. This is particularly important in positional cloning studies in which genes in candidate regions identified by genetic mapping must be scanned for mutations. Add to this the requirement for ways of finding DNA sequence variants in pathogens, crops, and domesticated animals, and it becomes evident that efficient and cost-effective DNA scanning methods are in great demand. In this issue, Nakatani et al.2 describe a promising new method for DNA mismatch scanning.

Although the gold standard of mutation scanning is still Sanger DNA sequencing, the expense and labor involved makes it difficult for most groups to scan more than a handful of genes in any given candidate region. To speed up the process and reduce the cost of finding DNA sequence variations, several scanning methods have been developed. DNA sequence variation scanning methods can be divided into three groups: those based on detecting the presence of heteroduplex mismatches, those based on physical differences of single-stranded DNA molecules between the variants, and those based on simplified DNA sequencing approaches3. By far the most widely used scanning methods are those involving the detection of mismatched DNA molecules. Regardless of the mechanism of variation scanning, a separation step by gel (or capillary) electrophoresis or high-performance liquid chromatography is required in most methods.

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Figure 1: Diagram of surface plasmon resonance assay using a sensor chip with immobilized dimeric naphthyridine ligands (shown in green) that specifically bind to G-G mismatches (indicated by asterisks).

©Bob Crimi

References

  1. http://www.ncbi.nlm.nih.gov/SNP/

  2. Nakatani, K. et al. Nat. Biotechnol. 19, 51– 55 (2000).

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  3. Kwok, P.-Y. & Chen, X. In Genetic engineering, principles and methods, Vol. 20. (ed. Setlow, J.K.) 125– 134 (Plenum Press, New York, NY; 1998).

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  1. associate professor of dermatology and genetics at Washington University, School of Medicine, St. Louis, 63110, MO

    Pui-Yan Kwok

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  1. Pui-Yan Kwok
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Kwok, PY. Reflections on a DNA mutation scanning tool. Nat Biotechnol 19, 18–19 (2001). https://doi.org/10.1038/83454

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