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A genomic walking method for screening sequence length polymorphism
Article first published online: 28 APR 2006
DOI: 10.1111/j.1471-8286.2006.01276.x
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How to Cite
WALSER, J.-C., EVGEN’EV, M. B. and FEDER, M. E. (2006), A genomic walking method for screening sequence length polymorphism. Molecular Ecology Notes, 6: 563–567. doi: 10.1111/j.1471-8286.2006.01276.x
Publication History
- Issue published online: 28 APR 2006
- Article first published online: 28 APR 2006
- Received 31 October 2005; revision received 21 November 2005; accepted 8 December 2005
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Keywords:
- heat-shock genes;
- high-throughput screening;
- insertion;
- promoter regulation;
- transposable elements;
- universal fast walking
Abstract
We adapted a recently developed nonrestrictional, nonligational genome walking method, Universal Fast Walking (UFW), for detection of length polymorphism in the proximal promoter region of genes. We demonstrate its efficacy at discovering naturally occurring transposition into heat-shock genes of wild Drosophila and show that it surmounts limitations of simple polymerase chain reaction (PCR) approaches. We further present modifications to the standard UFW protocol and provide some guidelines to improve specificity. Although the resultant banding pattern of a standard UFW can be regarded as a DNA fingerprint, many amplicons result from false priming and not real polymorphisms. We describe ways to distinguish between UFW amplicons and false priming products in a high-throughput assay.