Article

A “Double Adaptor” Method for Improved Shotgun Library Construction

Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030, USA.
Analytical Biochemistry (Impact Factor: 2.31). 04/1996; 236(1):107-13. DOI: 10.1006/abio.1996.0138
Source: PubMed

ABSTRACT The efficiency of shotgun DNA sequencing depends to a great extent on the quality of the random-subclone libraries used. We here describe a novel "double adaptor" strategy for efficient construction of high-quality shotgun libraries. In this method, randomly sheared and end-repaired fragments are ligated to oligonucleotide adaptors creating 12-base overhangs. Nonphosphorylated oligonucleotides are used, which prevents formation of adaptor dimers and ensures efficient ligation of insert to adaptor. The vector is prepared from a modified M13 vector, by KpnI/PstI digestion followed by ligation to oligonucleotides with ends complementary to the overhangs created in the digest. These adaptors create 5'-overhangs complementary to those on the inserts. Following annealing of insert to vector, the DNA is directly used for transformation without a ligation step. This protocol is robust and shows three- to fivefold higher yield of clones compared to previous protocols. No chimeric clones can be detected and the background of clones without an insert is <1%. The procedure is rapid and shows potential for automation.

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    • "In order to evaluate our approach on real data, we used as a test set reads from the Drosophila pseudoobscura genome sequencing project (Richards et al., 2005). We chose these particular data because the sequencing adapters used in the project are known (Andersson et al., 1996). "
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    • "purified bacterial cells (Charles and Ishikawa 1999) or gelpurified from a chromosomal fragment resolved through Pulsed Field Gel Electrophoresis (PFGE) (Wernegreen et al. 2002). Short (1.5–2.5 kb) insert libraries were generated from hydrosheared DNA using a double adaptor kit (SeqWright Inc.) (Andersson et al. 1996). Plasmid clones were purified and bidirectionally sequenced using BigDye v3.0 chemistry on either an ABI3700 or an ABI3730xl (Applied Biosystems). "
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    • "The M13 shotgun library from concatenated and sheared DNA fragments was constructed using the double adaptor method as described previously (Andersson et al. 1996). "
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