User:Torsten Waldminghaus/Primer: Difference between revisions
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|AGTGGGATTCCGCATGCTAGT | |AGTGGGATTCCGCATGCTAGT | ||
| | | | ||
| | |14 | ||
|- | |- | ||
! MseIshortnewNo | ! MseIshortnewNo | ||
|TAACTAGCATGC | |TAACTAGCATGC | ||
|Not phosphorilated | |Not phosphorilated | ||
| | |15 | ||
|- | |- | ||
! MseIshortnew | ! MseIshortnew | ||
|TAACTAGCATGC | |TAACTAGCATGC | ||
|5'modified with phosphate | |5'modified with phosphate | ||
| | |16 | ||
|- | |- | ||
! bet-fw | ! bet-fw | ||
| GTCGACCCACAGGAACTGAT | | GTCGACCCACAGGAACTGAT | ||
|To distinguish DY330 (with lambda phage) from other E. coli strains use primers for bet as part of the recombination machinery of lambda | |To distinguish DY330 (with lambda phage) from other E. coli strains use primers for bet as part of the recombination machinery of lambda | ||
| | |17 | ||
|- | |- | ||
! bet-rev | ! bet-rev | ||
| GGCTGACGTTCTGCAGTGTA | | GGCTGACGTTCTGCAGTGTA | ||
|To distinguish DY330 (with lambda phage) from other E. coli strains use primers for bet as part of the recombination machinery of lambda | |To distinguish DY330 (with lambda phage) from other E. coli strains use primers for bet as part of the recombination machinery of lambda | ||
| | |18 | ||
|- | |- | ||
! Cut-test_fw | ! Cut-test_fw | ||
| TAATAGGCATGCTAGCAGCTG AGCGTAGCTAGCGATGCAACGAC GGTGATCAGCGTCGATGCAGCCG AAACGATGACTGTCACATAGCTG ATGCTTTGCT | | TAATAGGCATGCTAGCAGCTG AGCGTAGCTAGCGATGCAACGAC GGTGATCAGCGTCGATGCAGCCG AAACGATGACTGTCACATAGCTG ATGCTTTGCT | ||
| | | | ||
| | |19 | ||
|- | |- | ||
! Cut_test_rv | ! Cut_test_rv | ||
| TAAGCAAAGCATCAGCTATGT GACAGTCATCGTTTCGGCTGCAT CGACGAAGATCACCGTCGTTGCA TCGCTAGCTACGCTCAGCTGCTA GCATGCCTAT | | TAAGCAAAGCATCAGCTATGT GACAGTCATCGTTTCGGCTGCAT CGACGAAGATCACCGTCGTTGCA TCGCTAGCTACGCTCAGCTGCTA GCATGCCTAT | ||
| | | | ||
| | |20 | ||
|- | |- | ||
! Cut-test-meth_fw | ! Cut-test-meth_fw | ||
| TAATAGGCATGCTAGCAGCTG AGCGTAGCTAGCGATGCAACGAC GGTG'''A'''TCAGCGTCGATGCAGCCG AAACGATGACTGTCACATAGCTG ATGCTTTGCT | | TAATAGGCATGCTAGCAGCTG AGCGTAGCTAGCGATGCAACGAC GGTG'''A'''TCAGCGTCGATGCAGCCG AAACGATGACTGTCACATAGCTG ATGCTTTGCT | ||
|modified at position 49 with N6-methyl-dA | |modified at position 49 with N6-methyl-dA | ||
| | |21 | ||
|- | |- | ||
! Cut_test-meth_rv | ! Cut_test-meth_rv | ||
| TAAGCAAAGCATCAGCTATGT GACAGTCATCGTTTCGGCTGCAT CGACGAAG'''A'''TCACCGTCGTTGCA TCGCTAGCTACGCTCAGCTGCTA GCATGCCTAT | | TAAGCAAAGCATCAGCTATGT GACAGTCATCGTTTCGGCTGCAT CGACGAAG'''A'''TCACCGTCGTTGCA TCGCTAGCTACGCTCAGCTGCTA GCATGCCTAT | ||
|modified at position 53 with N6-methyl-dA | |modified at position 53 with N6-methyl-dA | ||
| | |22 | ||
|- | |- | ||
! gatRfw | ! gatRfw | ||
|cgctttctcgaacaaaaagg | |cgctttctcgaacaaaaagg | ||
| | | | ||
| | |23 | ||
|- | |- | ||
! gatRrv | ! gatRrv | ||
|atgaatcgagaacggcaatc | |atgaatcgagaacggcaatc | ||
| | | | ||
| | |24 | ||
|- | |- | ||
! yoeAfw | ! yoeAfw | ||
|actgcaaccgcaacttcttc | |actgcaaccgcaacttcttc | ||
| | | | ||
| | |25 | ||
|- | |- | ||
! yoeArv | ! yoeArv | ||
|cactacctcaacacgctcca | |cactacctcaacacgctcca | ||
| | | | ||
| | |26 | ||
|- | |- | ||
! ter-check-fw | ! ter-check-fw | ||
|tcgtactggtgatggaacga | |tcgtactggtgatggaacga | ||
|For checking the insertion of GATC cluster near terC with outside primers | |For checking the insertion of GATC cluster near terC with outside primers | ||
| | |27 | ||
|- | |- | ||
! ter-check-rv | ! ter-check-rv | ||
|aggattcacgcgataagtgg | |aggattcacgcgataagtgg | ||
| | | | ||
| | |28 | ||
|- | |- | ||
! T7fw | ! T7fw | ||
|GAAATTAATACGACTCACTATAGGG | |GAAATTAATACGACTCACTATAGGG | ||
| | | | ||
| | |29 | ||
|- | |- | ||
!ORIrvT7 | !ORIrvT7 | ||
|CACCGATCATTCACAGTTAATGATCC TTTCCAGGTTGTTGATCTTA AAAGCCGGATCCTTGCCC TATAGTGAGTCGTATTAATTTC | |CACCGATCATTCACAGTTAATGATCC TTTCCAGGTTGTTGATCTTA AAAGCCGGATCCTTGCCC TATAGTGAGTCGTATTAATTTC | ||
| | | | ||
| | |30 | ||
|- | |- | ||
! ORIfwT7 | ! ORIfwT7 | ||
|CAAGGATCCGGCTTTTAAGATCAACA ACCTGGAAAGGATCATTAAC TGTGAATGATCGGTGCCC TATAGTGAGTCGTATTAATTTC | |CAAGGATCCGGCTTTTAAGATCAACA ACCTGGAAAGGATCATTAAC TGTGAATGATCGGTGCCC TATAGTGAGTCGTATTAATTTC | ||
| | | | ||
| | |31 | ||
|- | |- | ||
!ORIfwBIO | !ORIfwBIO | ||
|CAAGGATCCGGCTTTTAAGATCAACA ACCTGGAAAGGATCATTAAC TGTGAATGATCGGTG | |CAAGGATCCGGCTTTTAAGATCAACA ACCTGGAAAGGATCATTAAC TGTGAATGATCGGTG | ||
|5'-biotin labeled | |5'-biotin labeled | ||
| | |32 | ||
|- | |- | ||
!ORIrv | !ORIrv | ||
|CACCGATCATTCACAGTTAATGATCC TTTCCAGGTTGTTGATCTTA AAAGCCGGATCCTTG | |CACCGATCATTCACAGTTAATGATCC TTTCCAGGTTGTTGATCTTA AAAGCCGGATCCTTG | ||
| | | | ||
| | |33 | ||
|- | |- | ||
} | } |
Revision as of 02:11, 15 August 2011
- All primers are in concentrations of 100pmol/μL
Name | Sequence | Characteristics | Primer number |
---|---|---|---|
GFPrv | ctgatttaatctgtatcaggc | The following primers are for the mutagenesis of GFP to introduce GATC sites as silent mutation (GFPrv, GFPfw, GFPmut1fw, GFPmut2rv, GFPmut3fw, GFPmut4rv, GFPmut5fw, GFPmut6fw, GFPmut7fw, GFPmut8fw, GFPmut9fw) Tm 55 (salt adjusted)[1] | 1 |
GFPfw | CTCTCTACTGTTTCTCCATAC | Tm 57 | 2 |
GFPmut1fw | caaacaaaagaatggGatcaaagctaac | 5’-phosph. HPLC Tm 62 [without mutated nucleotide] | 3 |
GFPmut2rv | caatgttgtggcgGatCttgaagttag | 5’-phosph. HPLC Tm 63 [without mutated nucleotide] | 4 |
GFPmut3fw | caactagcagaTcattatcaacaaaatac | 5’-phosph. HPLC Tm 63 [without mutated nucleotide] | 5 |
GFPmut4rv | gccatcgccGatCggagtattttg | 5’-phosph. HPLC Tm 62 [without mutated nucleotide] | 6 |
GFPmut5fw | cgaaaagcgtgaTcacatggtcc | 5’-phosph. HPLC Tm 64 [without mutated nucleotide] | 7 |
GFPmut6fw | ctgctgctgggatCacacatggc | 5’-phosph. HPLC Tm 66 [without mutated nucleotide] | 8 |
GFPmut7fw | GTTATCCGGACCATATGAAACGGC | 5’-phosph. HPLC | 9 |
GFPmut8fw | CATTGAAGATGGGTCCGTTCAACTAG | 5’-phosph. HPLC | 10 |
GFPmut9fw | CCTTTCGAAAGACCCCAACGAAAAG | 5’-phosph. HPLC | 11 |
GATC19DNAfw | GCCCGCGGATCCGCCCGCC | oligo for methylation experiment from A. Humeny et al. 2003 | 12 |
GATC19DNArv | GGCGGGCGGATCCGCGGGC | oligo for methylation experiment from A. Humeny et al. 2003 | 13 |
MseIlong | AGTGGGATTCCGCATGCTAGT | 14 | |
MseIshortnewNo | TAACTAGCATGC | Not phosphorilated | 15 |
MseIshortnew | TAACTAGCATGC | 5'modified with phosphate | 16 |
bet-fw | GTCGACCCACAGGAACTGAT | To distinguish DY330 (with lambda phage) from other E. coli strains use primers for bet as part of the recombination machinery of lambda | 17 |
bet-rev | GGCTGACGTTCTGCAGTGTA | To distinguish DY330 (with lambda phage) from other E. coli strains use primers for bet as part of the recombination machinery of lambda | 18 |
Cut-test_fw | TAATAGGCATGCTAGCAGCTG AGCGTAGCTAGCGATGCAACGAC GGTGATCAGCGTCGATGCAGCCG AAACGATGACTGTCACATAGCTG ATGCTTTGCT | 19 | |
Cut_test_rv | TAAGCAAAGCATCAGCTATGT GACAGTCATCGTTTCGGCTGCAT CGACGAAGATCACCGTCGTTGCA TCGCTAGCTACGCTCAGCTGCTA GCATGCCTAT | 20 | |
Cut-test-meth_fw | TAATAGGCATGCTAGCAGCTG AGCGTAGCTAGCGATGCAACGAC GGTGATCAGCGTCGATGCAGCCG AAACGATGACTGTCACATAGCTG ATGCTTTGCT | modified at position 49 with N6-methyl-dA | 21 |
Cut_test-meth_rv | TAAGCAAAGCATCAGCTATGT GACAGTCATCGTTTCGGCTGCAT CGACGAAGATCACCGTCGTTGCA TCGCTAGCTACGCTCAGCTGCTA GCATGCCTAT | modified at position 53 with N6-methyl-dA | 22 |
gatRfw | cgctttctcgaacaaaaagg | 23 | |
gatRrv | atgaatcgagaacggcaatc | 24 | |
yoeAfw | actgcaaccgcaacttcttc | 25 | |
yoeArv | cactacctcaacacgctcca | 26 | |
ter-check-fw | tcgtactggtgatggaacga | For checking the insertion of GATC cluster near terC with outside primers | 27 |
ter-check-rv | aggattcacgcgataagtgg | 28 | |
T7fw | GAAATTAATACGACTCACTATAGGG | 29 | |
ORIrvT7 | CACCGATCATTCACAGTTAATGATCC TTTCCAGGTTGTTGATCTTA AAAGCCGGATCCTTGCCC TATAGTGAGTCGTATTAATTTC | 30 | |
ORIfwT7 | CAAGGATCCGGCTTTTAAGATCAACA ACCTGGAAAGGATCATTAAC TGTGAATGATCGGTGCCC TATAGTGAGTCGTATTAATTTC | 31 | |
ORIfwBIO | CAAGGATCCGGCTTTTAAGATCAACA ACCTGGAAAGGATCATTAAC TGTGAATGATCGGTG | 5'-biotin labeled | 32 |
ORIrv | CACCGATCATTCACAGTTAATGATCC TTTCCAGGTTGTTGATCTTA AAAGCCGGATCCTTG | 33 |