an enhanced method for sequence walking and paralog mining topo？ vector-ligation pcr一个增强的方法序列步行和假字矿业威尼斯平底渔船 vector-ligation pcr.pdfVIP

Orcheski and Davis BMC Research Notes 2010, 3:61 /1756-0500/3/61 TECHNICAL NOTE Open Access An enhanced method for sequence walking and paralog mining: TOPO® Vector-Ligation PCR 1 2* Benjamin B Orcheski , Thomas M Davis Abstract Background: Although technological advances allow for the economical acquisition of whole genome sequences, many organisms’ genomes remain unsequenced, and fully sequenced genomes may contain gaps. Researchers reliant upon partial genomic or heterologous sequence information require methods for obtaining unknown sequences from loci of interest. Various PCR based techniques are available for sequence walking - i.e., the acquisition of unknown DNA sequence adjacent to known sequence. Many such methods require rigid, elaborate protocols and/or impose narrowly confined options in the choice of restriction enzymes for necessary genomic ® digests. We describe a new method, TOPO Vector-Ligation PCR (or TVL-PCR) that innovatively integrates available tools and familiar concepts to offer advantages as a means of both targeted sequence walking and paralog mining. ® ® Findings: TVL-PCR exploits the ligation efficiency of the pCR 4-TOPO (Invitrogen, Carlsbad, California) vector system to capture fragments of unknown sequence by creating chimeric molecules containing defined priming sites at both ends. Initially, restriction enzyme-digested genomic DNA is end-repaired to create 3’ adenosine overhangs and is then ligated to pCR4-TOPO vectors. The ligation product pool is used directly as a template for nested PCR, using specific primers to target orthologous sequences, or degenerate primers to enable