Automated design of genomic Southern blot probes.

BMC Genomics
Mike D R CroningSeth G N Grant

Abstract

Sothern blotting is a DNA analysis technique that has found widespread application in molecular biology. It has been used for gene discovery and mapping and has diagnostic and forensic applications, including mutation detection in patient samples and DNA fingerprinting in criminal investigations. Southern blotting has been employed as the definitive method for detecting transgene integration, and successful homologous recombination in gene targeting experiments.The technique employs a labeled DNA probe to detect a specific DNA sequence in a complex DNA sample that has been separated by restriction-digest and gel electrophoresis. Critically for the technique to succeed the probe must be unique to the target locus so as not to cross-hybridize to other endogenous DNA within the sample.Investigators routinely employ a manual approach to probe design. A genome browser is used to extract DNA sequence from the locus of interest, which is searched against the target genome using a BLAST-like tool. Ideally a single perfect match is obtained to the target, with little cross-reactivity caused by homologous DNA sequence present in the genome and/or repetitive and low-complexity elements in the candidate probe. This is a labor intensive pro...Continue Reading

References

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Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Nov 29, 2001·Bioinformatics·F Li, G D Stormo
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Feb 17, 2005·BMC Bioinformatics·Guy St C Slater, Ewan Birney
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Nov 27, 2008·Nucleic Acids Research·T J P HubbardP Flicek

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Citations

Jun 25, 2013·Biotechnology Letters·Li-Yeh ChuangCheng-Hong Yang
Jul 3, 2021·Cold Spring Harbor Protocols·Michael R Green, Joseph Sambrook

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Methods Mentioned

BETA
electrophoresis
PCR

Software Mentioned

Config
BLAST
Run
MySQL
Ensembl
SQL
Primer3
BioPerl
Perl
Linux

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