SDM-Assist software to design site-directed mutagenesis primers introducing " silent" restriction sites

BMC Bioinformatics

Volumn 14, Issue , 2013, Pages

  Karnik, Abhijit ^a   Karnik, Rucha ^b   Grefen, Christopher ^b  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

Cloning; Oligonucleotides; PCR; Restriction endonucleases; SDM; Site directed mutagenesis; Software

Indexed keywords

DIRECT IDENTIFICATIONS; INDISPENSABLE TOOLS; PCR; RESTRICTION ENDONUCLEASES; SDM; SECONDARY STRUCTURES; SITE DIRECTED MUTAGENESIS; STRUCTURE-FUNCTION STUDIES;

COMPUTER SOFTWARE; ESCHERICHIA COLI; OLIGONUCLEOTIDES;

CLONING;

ESCHERICHIA COLI;

AKT1 PROTEIN, ARABIDOPSIS; ARABIDOPSIS PROTEIN; POTASSIUM CHANNEL; PRIMER DNA; RESTRICTION ENDONUCLEASE;

ALGORITHM; ARTICLE; CHEMISTRY; COMPUTER PROGRAM; ESCHERICHIA COLI; GENETICS; METHODOLOGY; POLYMERASE CHAIN REACTION; SITE DIRECTED MUTAGENESIS;

ALGORITHMS; ARABIDOPSIS PROTEINS; DNA PRIMERS; DNA RESTRICTION ENZYMES; ESCHERICHIA COLI; MUTAGENESIS, SITE-DIRECTED; POLYMERASE CHAIN REACTION; POTASSIUM CHANNELS; SOFTWARE;

EID: 84875138855     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-105     Document Type: Article

References (23)

1. Ling MM, Robinson BH. Approaches to DNA mutagenesis: an overview. Anal Biochem 1997, 254:157-178. 10.1006/abio.1997.2428, 9417773.
2. Braman J, Papworth C, Greener A. Site-directed mutagenesis using double-stranded plasmid DNA templates. Methods Mol Biol 1996, 57:31-44.
3. Wang W, Malcolm BA. Two-stage PCR protocol allowing introduction of multiple mutations, deletions and insertions using QuikChange site-directed mutagenesis. Biotechniques 1999, 26:680-682.
4. Lu L, Patel H, Bissler JJ. Optimizing DpnI digestion conditions to detect replicated DNA. Biotechniques 2002, 33:316-318.
5. Evans PM, Liu C. SiteFind: a software tool for introducing a restriction site as a marker for successful site-directed mutagenesis. BMC Mol Biol 2005, 6:22. 10.1186/1471-2199-6-22, 1314889, 16321147.
6. Grefen C, Chen Z, Honsbein A, Donald N, Hills A, Blatt MR. A novel motif essential for SNARE interaction with the K(+) channel KC1 and channel gating in Arabidopsis. Plant Cell 2010, 22:3076-3092. 10.1105/tpc.110.077768, 2965544, 20884800.
7. Horak J, Grefen C, Berendzen KW, Hahn A, Stierhof YD, Stadelhofer B. The Arabidopsis thaliana response regulator ARR22 is a putative AHP phospho-histidine phosphatase expressed in the chalaza of developing seeds. BMC Plant Biol 2008, 8:77. 10.1186/1471-2229-8-77, 2478664, 18625081.
8. Rashtchian A, Thornton CG, Heidecker G. A novel method for site-directed mutagenesis using PCR and uracil DNA glycosylase. PCR Methods Appl 1992, 2:124-130. 10.1101/gr.2.2.124, 1477668.
9. Little JW, Mount DW. Creating new restriction sites by silent changes in coding sequences. Gene 1984, 32:67-73. 10.1016/0378-1119(84)90033-7, 6099315.
10. Zhang BZ, Zhang X, An XP, Ran DL, Zhou YS, Lu J. An easy-to-use site-directed mutagenesis method with a designed restriction site for convenient and reliable mutant screening. J Zhejiang Univ Sci B 2009, 10:479-482. 10.1631/jzus.B0820367, 2689561, 19489114.
11. Zheng L, Baumann U, Reymond JL. An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res 2004, 32:e115. 10.1093/nar/gnh110, 514394, 15304544.
12. Liu H, Naismith JH. An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol. BMC Biotechnol 2008, 8:91. 10.1186/1472-6750-8-91, 2629768, 19055817.
13. Qi D, Scholthof KB. A one-step PCR-based method for rapid and efficient site-directed fragment deletion, insertion, and substitution mutagenesis. J Virol Methods 2008, 149:85-90. 10.1016/j.jviromet.2008.01.002, 18314204.
14. Park J, Labaer J. Recombinational cloning. Curr Protoc Mol Biol 2006, Chapter 3:Unit 3.20.
15. Shankarappa B, Vijayananda K, Ehrlich GD. SILMUT: a computer program for the identification of regions suitable for silent mutagenesis to introduce restriction enzyme recognition sequences. Biotechniques 1992, 12:882-884.
16. Turchin A, Lawler JF. The primer generator: a program that facilitates the selection of oligonucleotides for site-directed mutagenesis. Biotechniques 1999, 26:672-676.
17. Breslauer KJ, Frank R, Blocker H, Marky LA. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 1986, 83:3746-3750. 10.1073/pnas.83.11.3746, 323600, 3459152.
18. Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci USA 1986, 83:9373-9377. 10.1073/pnas.83.24.9373, 387140, 2432595.
19. Sentenac H, Bonneaud N, Minet M, Lacroute F, Salmon JM, Gaymard F. Cloning and expression in yeast of a plant potassium ion transport system. Science 1992, 256:663-665. 10.1126/science.1585180, 1585180.
20. Dreyer I, Blatt MR. What makes a gate? The ins and outs of Kv-like K+ channels in plants. Trends Plant Sci 2009, 14:383-390. 10.1016/j.tplants.2009.04.001, 19540150.
21. Grefen C, Obrdlik P, Harter K. The determination of protein-protein interactions by the mating-based split-ubiquitin system (mbSUS). Methods Mol Biol 2009, 479:217-233.
22. Tang W, Ruknudin A, Yang WP, Shaw SY, Knickerbocker A, Kurtz S. Functional expression of a vertebrate inwardly rectifying K+ channel in yeast. Mol Biol Cell 1995, 6:1231-1240. 301279, 8534918.
23. Grefen C, Lalonde S, Obrdlik P. Split-ubiquitin system for identifying protein-protein interactions in membrane and full-length proteins. Curr Protoc Neurosci 2007, Chapter 5:Unit 5.27.