Targeted cloning of a subfamily of LINE-1 elements by subfamily-specific LINE-1-PCR

N. Carol Casavant, Stephen C. Hardies

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

Subfamily-specific LINE-1 PCR (SSL1-PCR) is the targeted amplification and cloning of defined subfamilies of LINE-1 elements and their flanking sequences. The targeting is accomplished by incorporating a subfamily-specific sequence difference at the 3′ end of a LINE-1 PCR primer and pairing it with a primer to an anchor ligated within the flanking region. SSL1-PCR was demonstrated by targeting amplification of a Mus spretus-specific LINE-1 subfamily. The amplified fragments were cloned to make an SSL1-PCR library, which was found to be 100-fold enriched for the targeted elements. PCR primers were synthesized based on the sequence flanking the LINE-1 element of four different clones. Three of the clones were recovered from Mus spretus DNA. A fourth clone was recovered from a congenic mouse containing both Mus spretus and Mus domesticus DNA. Amplification between these flanking primers and LINE-1 PCR primers produced a product in Mus spretus and not in Mus domesticus. These dimorphisms were further verified to be due to insertion of Mus spretus-specific LINE-1 elements into Mus spretus DNA and not into Mus domesticus DNA.

Original languageEnglish (US)
Pages (from-to)193-201
Number of pages9
JournalMammalian Genome
Volume4
Issue number4
DOIs
StatePublished - Apr 1 1993

ASJC Scopus subject areas

  • Genetics

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