title: A colony multiplex quantitative PCR-Based 3S3DBC method and variations of it for screening DNA libraries.
abstract: A DNA library is a collection of DNA fragments cloned into vectors and stored individually in host cells, and is a valuable resource for molecular cloning, gene physical mapping, and genome sequencing projects. To take the best advantage of a DNA library, a good screening method is needed. After describing pooling strategies and issues that should be considered in DNA library screening, here we report an efficient colony multiplex quantitative PCR-based 3-step, 3-dimension, and binary-code (3S3DBC) method we used to screen genes from a planarian genomic DNA fosmid library. This method requires only 3 rounds of PCR reactions and only around 6 hours to distinguish one or more desired clones from a large DNA library. According to the particular situations in different research labs, this method can be further modified and simplified to suit their requirements.
authors: Department of Biophysics, Kyoto University, Kyoto, Kyoto, Japan.
authors: Yang
authors: Y
authors: An
authors: Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors: Atsushi
authors: A
authors: Toyoda
authors: School of Pharmacy, Fudan University, Shanghai, China.
authors: Chen
authors: C
authors: Zhao
authors: Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors: Asao
authors: A
authors: Fujiyama
authors: Department of Biophysics, Kyoto University, Kyoto, Kyoto, Japan.
authors: Kiyokazu
authors: K
authors: Agata
mesh_terms: D000818:Animals; D015723:Gene Library; D060885:Multiplex Polymerase Chain Reaction / Q000191:economics / Q000379:methods*; D010932:Planarians / Q000235:genetics; D013997:Time Factors
references: Nature. 1992 Oct 1;359(6394):380-7
references: 1406950
references: Nucleic Acids Res. 1991 Nov 25;19(22):6241-7
references: 1956784
references: Genomics. 1993 Nov;18(2):270-6
references: 8288229
references: PCR Methods Appl. 1994 Feb;3(4):S65-75
references: 8173510
references: Genomics. 1995 Mar 20;26(2):178-91
references: 7601441
references: Biotechniques. 1997 Sep;23(3):504-11
references: 9298224
references: Genomics. 1998 Apr 15;49(2):209-17
references: 9598308
references: Nat Methods. 2006 Mar;3(3):183-9
references: 16489335
references: Theor Appl Genet. 2006 Jun;113(1):81-9
references: 16783592
references: Nat Protoc. 2007;2(7):1661-74
references: 17641631
references: Genome. 2009 Dec;52(12):993-1000
references: 19953127
references: BMC Genomics. 2010;11:301
references: 20462427
references: PLoS One. 2011;6(9):e24978
references: 21949817
references: Nature. 2012 Oct 4;490(7418):49-54
references: 22992520
references: Nat Genet. 2013 Feb;45(2):220-5
references: 23313953
references: Mamm Genome. 2000 May;11(5):360-3
references: 10790534
references: Genome Res. 2000 May;10(5):714-21
references: 10810094
references: Genome Res. 2000 Jun;10(6):789-807
references: 10854411
references: Clin Microbiol Rev. 2000 Oct;13(4):559-70
references: 11023957
references: J Mol Microbiol Biotechnol. 2002 Nov;4(6):551-4
references: 12432955
references: Genomics. 2003 Nov;82(5):571-4
references: 14559214
references: Anim Biotechnol. 2003 Nov;14(2):145-53
references: 14703073
references: Proc Natl Acad Sci U S A. 1975 Oct;72(10):3961-5
references: 1105573
references: Proc Natl Acad Sci U S A. 1976 Oct;73(10):3394-7
references: 1068453
references: Science. 1977 Apr 8;196(4286):180-2
references: 322279
references: Proc Natl Acad Sci U S A. 1981 Nov;78(11):6613-7
references: 6171820
references: Methods Enzymol. 1983;100:333-42
references: 6194407
references: Nucleic Acids Res. 1989 May 25;17(10):4000
references: 2734114
references: Proc Natl Acad Sci U S A. 1989 Aug;86(15):5898-902
references: 2668948
references: Proc Natl Acad Sci U S A. 1990 Feb;87(3):1213-7
references: 2405397
references: Nucleic Acids Res. 1990 May 11;18(9):2830
references: 2339075
references: Nucleic Acids Res. 1990 Dec 11;18(23):7191-2
references: 2263507
references: Nucleic Acids Res. 1993 Jun 11;21(11):2627-31
references: 8332459