Difference between revisions of "HPP New Start and Finish"
(Created page with 'July 23, 2011 New Oligos to Order START_TOP (67 nt) AATTCGGTCTCAGACGTTGACGGCTAGCTCAGTCCTAGGTACAGTGCTAGCGTGGAGAGACGCTGCA START_Bot (59 nt) GCGTCTCTCCACGCTAGCACTGTACCTAGGACTGAGC…') |
|||
| Line 1: | Line 1: | ||
July 23, 2011 | July 23, 2011 | ||
| − | New Oligos to Order | + | New Oligos to Order <br> |
START_TOP (67 nt) | START_TOP (67 nt) | ||
| Line 16: | Line 16: | ||
GGGTCTCTCTCGACTGATGCCCACTGAGACGG | GGGTCTCTCTCGACTGATGCCCACTGAGACGG | ||
| + | |||
NewHPPVec_Top (36 nt) | NewHPPVec_Top (36 nt) | ||
AATTCGTCCAGAGACCGCTAGCGGTCTCACGAGCTGCA | AATTCGTCCAGAGACCGCTAGCGGTCTCACGAGCTGCA | ||
NewHPPVec_Bot (32 nt) | NewHPPVec_Bot (32 nt) | ||
| − | GCTCGTGAGACCGCTAGCGGTCTCTGGACG | + | GCTCGTGAGACCGCTAGCGGTCTCTGGACG<br> |
| − | New START Half Edge | + | '''New START Half Edge''' |
1. Use BsaI to free up new START word (GTCC) on 5’ end that allows ligation to new HPP vector. | 1. Use BsaI to free up new START word (GTCC) on 5’ end that allows ligation to new HPP vector. | ||
2. Use BsmBI to free up half-edge word (GTGG) on 3’ end that allows ligation to any Gene1 half-edge. | 2. Use BsmBI to free up half-edge word (GTGG) on 3’ end that allows ligation to any Gene1 half-edge. | ||
3. In between these is a J23100 promoter. | 3. In between these is a J23100 promoter. | ||
| − | 4. Flanked by EcoRI and PstI sticky ends for cloning. | + | 4. Flanked by EcoRI and PstI sticky ends for cloning.<br><br> |
| + | |||
RI BsaI> /START J23100 /Half <BsmBI PstI | RI BsaI> /START J23100 /Half <BsmBI PstI | ||
AATTC GGTCTC A GTCC TTGACGGCTAGCTCAGTCCTAGGTACAGTGCTAGC GTGG A GAGACG CTGCA | AATTC GGTCTC A GTCC TTGACGGCTAGCTCAGTCCTAGGTACAGTGCTAGC GTGG A GAGACG CTGCA | ||
G CCAGAG T CAGG AACTGCCGATCGAGTCAGGATCCATGTCACGATCG CACC T CTCTGC G | G CCAGAG T CAGG AACTGCCGATCGAGTCAGGATCCATGTCACGATCG CACC T CTCTGC G | ||
/ / | / / | ||
| − | + | <br><br> | |
| − | |||
| − | |||
| − | New FINISH Half Edge | + | '''New FINISH Half Edge''' |
1. Use BsmBI to free up half-edge word (GTGG) on 5’ end that allows ligation to any Gene2 half-edge. | 1. Use BsmBI to free up half-edge word (GTGG) on 5’ end that allows ligation to any Gene2 half-edge. | ||
2. Use BsaI to free up new FINISH word (CGAG) on 3’ end that allows ligation to new tr5f4HPP vector. | 2. Use BsaI to free up new FINISH word (CGAG) on 3’ end that allows ligation to new tr5f4HPP vector. | ||
3. In between these is a 8 nt spacer. | 3. In between these is a 8 nt spacer. | ||
| − | 4. Flanked by EcoRI and PstI sticky ends for cloning. | + | 4. Flanked by EcoRI and PstI sticky ends for cloning.<br><br> |
| + | |||
RI BsmBI> /Half Spacer /FINISH <BsaI PstI | RI BsmBI> /Half Spacer /FINISH <BsaI PstI | ||
AATTC CGTCTC A GTGG GCATCAGT CGAG A GAGACC CTGCA | AATTC CGTCTC A GTGG GCATCAGT CGAG A GAGACC CTGCA | ||
G GCAGAG T CACC CGTAGTCA GCTC T CTCTGG G | G GCAGAG T CACC CGTAGTCA GCTC T CTCTGG G | ||
/ / | / / | ||
| − | New HPP Vector | + | '''New HPP Vector''' |
1. Use BsaI to free up a new START word and a new FINISH word that are different from any of the Gene words (listed below). | 1. Use BsaI to free up a new START word and a new FINISH word that are different from any of the Gene words (listed below). | ||
2. NheI site in the middle for cloning in any XbaI/SpeI BioBrick fragment, such as the ccdB Death Gene or a reporter expression cassette. | 2. NheI site in the middle for cloning in any XbaI/SpeI BioBrick fragment, such as the ccdB Death Gene or a reporter expression cassette. | ||
3. Flanked by EcoRI and PstI sticky ends. | 3. Flanked by EcoRI and PstI sticky ends. | ||
| + | |||
| + | '''Specific Words Used So Far''' | ||
START GTCC GGAC | START GTCC GGAC | ||
FINISH CGAG CTCG | FINISH CGAG CTCG | ||
| Line 58: | Line 61: | ||
ilvE GGGG CCCC | ilvE GGGG CCCC | ||
CAT CGGT ACCG | CAT CGGT ACCG | ||
| − | TyrB CGCA TGCG | + | TyrB CGCA TGCG<br> |
| + | |||
RI / START <BsaI NheI BsaI> / FINISH PstI | RI / START <BsaI NheI BsaI> / FINISH PstI | ||
AATTC GTCC A GAGACC GCTAGC GGTCTC A CGAG CTGCA | AATTC GTCC A GAGACC GCTAGC GGTCTC A CGAG CTGCA | ||
G CAGG T CTCTGG CGATCG CCAGAG T GCTC G | G CAGG T CTCTGG CGATCG CCAGAG T GCTC G | ||
/ / | / / | ||
Revision as of 20:10, 27 July 2011
July 23, 2011
New Oligos to Order
START_TOP (67 nt)
AATTCGGTCTCAGACGTTGACGGCTAGCTCAGTCCTAGGTACAGTGCTAGCGTGGAGAGACGCTGCA
START_Bot (59 nt)
GCGTCTCTCCACGCTAGCACTGTACCTAGGACTGAGCTAGCCGTCAACGTCTGAGACCG
FINISH_Top (40 nt)
AATTCCGTCTCAGTGGGCATCAGTCGAGAGAGACCCTGCA
FINISH_Bot (32 nt)
GGGTCTCTCTCGACTGATGCCCACTGAGACGG
NewHPPVec_Top (36 nt) AATTCGTCCAGAGACCGCTAGCGGTCTCACGAGCTGCA
NewHPPVec_Bot (32 nt)
GCTCGTGAGACCGCTAGCGGTCTCTGGACG
New START Half Edge
1. Use BsaI to free up new START word (GTCC) on 5’ end that allows ligation to new HPP vector.
2. Use BsmBI to free up half-edge word (GTGG) on 3’ end that allows ligation to any Gene1 half-edge.
3. In between these is a J23100 promoter.
4. Flanked by EcoRI and PstI sticky ends for cloning.
RI BsaI> /START J23100 /Half <BsmBI PstI
AATTC GGTCTC A GTCC TTGACGGCTAGCTCAGTCCTAGGTACAGTGCTAGC GTGG A GAGACG CTGCA
G CCAGAG T CAGG AACTGCCGATCGAGTCAGGATCCATGTCACGATCG CACC T CTCTGC G
/ /
New FINISH Half Edge
1. Use BsmBI to free up half-edge word (GTGG) on 5’ end that allows ligation to any Gene2 half-edge.
2. Use BsaI to free up new FINISH word (CGAG) on 3’ end that allows ligation to new tr5f4HPP vector.
3. In between these is a 8 nt spacer.
4. Flanked by EcoRI and PstI sticky ends for cloning.
RI BsmBI> /Half Spacer /FINISH <BsaI PstI
AATTC CGTCTC A GTGG GCATCAGT CGAG A GAGACC CTGCA
G GCAGAG T CACC CGTAGTCA GCTC T CTCTGG G
/ /
New HPP Vector 1. Use BsaI to free up a new START word and a new FINISH word that are different from any of the Gene words (listed below). 2. NheI site in the middle for cloning in any XbaI/SpeI BioBrick fragment, such as the ccdB Death Gene or a reporter expression cassette. 3. Flanked by EcoRI and PstI sticky ends.
Specific Words Used So Far
START GTCC GGAC
FINISH CGAG CTCG
Half-Edge GTGG CCAC
GFP GGGT ACCC
RFP CTGC GCAG
LacZ CCTG CAGG
AspC CGTC GACG
PyrE GGCG CGCC
ilvE GGGG CCCC
CAT CGGT ACCG
TyrB CGCA TGCG
RI / START <BsaI NheI BsaI> / FINISH PstI
AATTC GTCC A GAGACC GCTAGC GGTCTC A CGAG CTGCA
G CAGG T CTCTGG CGATCG CCAGAG T GCTC G
/ /
