Registry of standard biological parts/PCR-based assembly
- Automated PCR primer design for worm genes - This is a good example of a simple CAD tool to encourage assembly. You could imagine something similar to auto-generate the primers necessary for PCR-based assembly of standard parts.
- Sauer:Stitching Genes by PCR
- patent on some of this stuff
Going to get a better feel for this by doing a few biobrick constructions using PCR-assembly
- <bbpart>J04500</bbpart>+<bbpart>I13501</bbpart> = <bbpart>J04450</bbpart>
- <bbpart>R0010</bbpart>+<bbpart>I13504</bbpart> = <bbpart>J04430</bbpart>
- will try this one as a 3-way
Can use UDG (NEB USER enzyme) to replace all restriction digests and could also eliminate secondary PCRs also. You would just need to design your oligos to contain a U in the right location, assuming that there'll be a T somewhere in the vacinity of the ends of the parts you are trying to combine.
- Clontech In-Fusion PCR cloning -- this could be used for the last step so that we don't need to do a digest/ligation at any point in the process.
- Seamless cloning and gene fusion review 
- Useful forum discussion
- Patents: 1, 2 (might be same as 1, title same though filing date is later), 3
- This reference describes a system similar to In-Fusion using the vaccinia virus DNA polymerase 
- Lu Q. Seamless cloning and gene fusion. Trends Biotechnol. 2005 Apr;23(4):199-207. DOI:10.1016/j.tibtech.2005.02.008 |
- Hamilton MD, Nuara AA, Gammon DB, Buller RM, and Evans DH. Duplex strand joining reactions catalyzed by vaccinia virus DNA polymerase. Nucleic Acids Res. 2007;35(1):143-51. DOI:10.1093/nar/gkl1015 |
- Horton RM, Cai ZL, Ho SN, and Pease LR. Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction. Biotechniques. 1990 May;8(5):528-35.
- Yon J and Fried M. Precise gene fusion by PCR. Nucleic Acids Res. 1989 Jun 26;17(12):4895.
- Karreman C. Fusion PCR, a one-step variant of the "megaprimer" method of mutagenesis. Biotechniques. 1998 May;24(5):736, 740, 742.
- Wang HL, Postier BL, and Burnap RL. Optimization of fusion PCR for in vitro construction of gene knockout fragments. Biotechniques. 2002 Jul;33(1):26, 28, 30 passim.
- Geu-Flores F, Nour-Eldin HH, Nielsen MT, and Halkier BA. USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products. Nucleic Acids Res. 2007;35(7):e55. DOI:10.1093/nar/gkm106 |
- Donahue WF, Turczyk BM, and Jarrell KA. Rapid gene cloning using terminator primers and modular vectors. Nucleic Acids Res. 2002 Sep 15;30(18):e95.
- Shevchuk NA, Bryksin AV, Nusinovich YA, Cabello FC, Sutherland M, and Ladisch S. Construction of long DNA molecules using long PCR-based fusion of several fragments simultaneously. Nucleic Acids Res. 2004 Jan 22;32(2):e19. DOI:10.1093/nar/gnh014 |
- McDonald WF and Traktman P. Overexpression and purification of the vaccinia virus DNA polymerase. Protein Expr Purif. 1994 Aug;5(4):409-21. DOI:10.1006/prep.1994.1059 |