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ATG
Stop
ATG rrs
Stop
ATG
Stop
B1
rrs
B2
B1
B2
B1
rrs
B2
Native
N-terminal Fusion
C-terminal Fusion
Figure 1. Structures of Expression Clones for native, N-terminal and C-terminal fusion expression. Note the position of start codons, rrs, and stop codons with respect to the recombination sites.
Table 1 provides examples of primer pairs (attB1 and attB2) which can be used to amplify genes for specific protein expression formats. Shine-Dalgarno (E. coli ribosome binding sequence) and Kozak (eukaryotic ribosome recognition sequence) show are typical sequences. Other sequences than those depicted may also function well for protein expression. Choose the primer pair that will allow for the appropriate expression format.
5' GGGG ACA AGT TTG TAC AAA AAA GCA GGC TTC* GAA GGA GAT AGA ACC ATG (18-24 gsp) 3' A. 5' GGGG ACA AGT TTG TAC AAA AAA GCA GGC TTC GAA GGA GAT AGA ACC ATG (18-24 gsp) 3' B. 5' GGGG ACA AGT TTG TAC AAA AAA GCA GGC TTC - - - - - - - - - - - - - - - ACC ATG (18-24 gsp) 3' C. 5' GGGG ACA AGT TTG TAC AAA AAA GCA GGC TTC (ATG) - - - - - - - - - - - - - - - - - - - (18-24 gsp) 3'
K. 5' GGGG AC CAC TTT GTA CAA GAA AGC TGG GTT TTA** (18-24 gsp) L. 5' GGGG AC CAC TTT GTA CAA GAA AGC TGG GTG*** (18-24 gsp)
A & B. To leave the possibility open for N-terminal fusion, keep the ATG in-frame with the reading frame of attB1. C. For N-terminal fusion only primer, including the ATG of the open reading frame is optional. The reading frame of the gene must match the reading frame through attB1. L. The reading frame of the gsp must match the reading frame of the attB2 sequence.
* The following combinations are NOT possible because they form a STOP codon: TTA, TAG, TGA. ** CTA and TCA may also be used here for stop codon. *** One base must be added here to complete this codon.
B. Adapter PCR Protocol----To save cost and avoid possible primer dimers
5' AA AAA GCA GGC TTC* GAA GGA GAT AGA ACC ATG (18-24 gsp) 3' A. B. C. 5' AA AAA GCA GGC TTC GAA GGA GAT AGA ACC ATG (18-24 gsp) 3' 5' AA AAA GCA GGC TTC - - - - - - - - - - - - - - - ACC ATG (18-24 gsp) 3' 5' AA AAA GCA GGC TTC (ATG) - - - - - - - - - - - - - - - - - - - (18-24 gsp) 3'
K. 5' A GAA AGC TGG GTG TTA** (18-24 gsp) L. 5' A GAA AGC TGG GTG
G GGG ACA AGT TTG TAC AAA AAA GCA GGC T GGG GAC CAC TTT GTA CAA GAA AGC TGG GT
If you with to insert a TEV protease cleavage site after the N-terminal tag for removal of the tag the following forward primer is recommended: 5' GGGG ACA AGT TTG TAC AAA AAA GCA GGC TTC GAA-AAC-CTG-TAT-TTT-CAG-GGC-ATG-forward gene specific sequence-3' TEV will cleave between the 6th and 7th amino acid residues in the recognition site. Therefore, your protein will contain a single glycine residue on the N-terminus of the protein. If this is undesirable, the ATG in your protein can be replaced by the GGC (encoding a glycine residue) codon. Following cleavage with TEV, your protein will contain a single Met -> Gly substitution. The primer sequences for sequencing your entry vectors are: Clones derived from pDONR201 (kanR) and pDONR207 (genR) SeqL-A (proximal to attL1) (106 nt from cloned ORFs) SeqL-B (proximal to attL2) (123 nt from cloned ORFs) GTAACATCAGAGATTTTGAGACAC TCGCGTTAACGCTAGCATGGATCTC