title: IRE-bubble PCR: a rapid method for efficient and representative amplification of human genomic DNA sequences from complex sources.
abstract: A significant issue in the analysis of any genomic DNA segment is the generation of a unique set of short single-copy sequences that are representative of that region. In this report we describe a novel technique, IRE-bubble PCR, which was designed to amplify the human DNA content of somatic cell hybrids, YACs, cosmids, and lambda phage and result in greater complexity and representation than standard inter-IRE PCR. Here we demonstrate that IRE-bubble PCR is species specific and that it results in the generation of a product that is at least 10-fold more complex and representative than that produced by standard inter-IRE PCR. In addition, we have addressed the factors that contribute to the representation of the IRE-bubble PCR product and show how they may be used to further increase the complexity of this reaction. Finally, we have illustrated how the complexity and distribution of products generated by IRE-bubble PCR can be exploited and applied to FISH mapping and "chromosome painting" as well as to the generation of STSs targeted to specific chromosomal or subchromosomal regions.
authors.affiliation: Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.
authors.forename: D J
authors.initials: DJ
authors.lastname: Munroe
authors.forename: M
authors.initials: M
authors.lastname: Haas
authors.forename: E
authors.initials: E
authors.lastname: Bric
authors.forename: T
authors.initials: T
authors.lastname: Whitton
authors.forename: H
authors.initials: H
authors.lastname: Aburatani
authors.forename: K
authors.initials: K
authors.lastname: Hunter
authors.forename: D
authors.initials: D
authors.lastname: Ward
authors.forename: D E
authors.initials: DE
authors.lastname: Housman
mesh_terms: D000818:Animals; D001483:Base Sequence; D006224:Cricetinae; D004247:DNA / Q000235:genetics*; D017931:DNA Primers; D015894:Genome, Human; D006801:Humans; D006822:Hybrid Cells; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods*; D012091:Repetitive Sequences, Nucleic Acid; D013698:Templates, Genetic
chemical_list: D017931:DNA Primers; D004247:DNA