NYMU Taipei/Primer List

From 2007.igem.org

(Difference between revisions)
 
(54 intermediate revisions not shown)
Line 1: Line 1:
-
{| style="color:green;background-color:#ffffcc;" cellpadding="20" cellspacing="0" border="1"
+
<p><font size="4">
 +
[[NYMU_Taipei/ProjectDescription| Project Description]] /
 +
[[NYMU_Taipei/Lab_Notes| Lab Notes]]  /
 +
[[NYMU_Taipei/Part_List| Part List]]  /
 +
[[NYMU_Taipei/Primer_List| Primer List]]
 +
</font><br /><hr></p>
 +
 
 +
{| style="color:green;background-color:#ffffcc;" cellpadding="20" cellspacing="0" border="1" width="100%"
!Name
!Name
!Sequence
!Sequence
!Length
!Length
-
!Tm
+
!Tm (C)
-
!Restriction site
+
!RE site
!Target length
!Target length
!Description
!Description
|-
|-
-
|M_INS_A 5'
+
|M_INS_A F
-
|<font color="green">GTTTCTTCGAATTCGCGGCCGCTTCTAGATG</font><font color="red">GTTGCAGTAGTTCTCCAGCT</font>
+
|<font color="green">GTTTCTTCTCTAGAaaagaggagaaaACTAGATG</font><font color="red">GGCATTGTAGATCAGTGCTG</font>
-
|51 bp
+
|54 bp
-
|
+
|56.85
-
|EcoRI, XbaI
+
|XbaI
-
|63 bp
+
|119 bp
-
|Potential dimer formation!
+
|Potential dimer formation! XbaI+RBS
|-
|-
|-
|-
-
|M_INS_A 3'
+
|M_INS_A R
|<font color="green">GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTA</font><font color="red">GTTGCAGTAGTTCTCCAGCT</font>
|<font color="green">GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTA</font><font color="red">GTTGCAGTAGTTCTCCAGCT</font>
-
|55 bp
+
|48 bp
-
|
+
|54.74
|SpeI, PstI
|SpeI, PstI
-
|63 bp
+
|119 bp
|Potential dimer formation!
|Potential dimer formation!
|-
|-
-
|M_INS_B 5'
+
|-
-
|<font color="green">GTTTCTTCGAATTCGCGGCCGCTTCTAGATG</font><font color="red">TTTGTCAAGCAGCACCTTTGT</font>
+
|M_INS_B F
-
|52 bp
+
|<font color="green">GTTTCTTCTCTAGAaaagaggagaaaACTAGATG</font><font color="red">TTTGTCAAGCAGCACCTTTGT</font>
 +
|55 bp
|60.85
|60.85
-
|EcoRI, XbaI
+
|XbaI
-
|90 bp
+
|149 bp
-
|
+
|Potential dimer formation!
|-
|-
|-
|-
-
|M_INS_B 3'
+
|M_INS_B R
|<font color="green">GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTA</font><font color="red">GGACATGGGTGTGTAGAAGA</font>
|<font color="green">GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTA</font><font color="red">GGACATGGGTGTGTAGAAGA</font>
-
|55 bp
+
|48 bp
|55.86
|55.86
|SpeI, PstI
|SpeI, PstI
-
|90 bp
+
|149 bp
 +
|Potential dimer formation!
 +
|-
 +
|TAT F
 +
|<font color="green">GTTTCTTCTCTAGAaaagaggagaaaACTAG</font><font color="red">ATGAACAATAACGATCTCTTTCAGG</font>
 +
|56 bp
 +
|59.92
 +
|XbaI
 +
| bp
 +
|XbaI+RBS
 +
|-
 +
|-
 +
|TAT F
 +
|<font color="green">GTTTCTTCTCTAGAaaagaggagaaaACTAG</font><font color="red">ATGAACAATAACGATCTCTTTCAGG</font>
 +
|108 bp
 +
|59.92
 +
|XbaI
 +
| bp
 +
|XbaI+RBS
 +
|-
 +
|H_INS_A F
 +
|<font color="green">GTTTCTTCTCTAGAaaagaggagaaaACTAGATG</font><font color="red">GGCATTGTGGAACAATGCTG</font>
 +
|54 bp
 +
|62.45
 +
|XbaI
 +
|122 bp
 +
|Potential dimer formation! XbaI+RBS
 +
|-
 +
|H_INS_A TAT F
 +
|<font color="green">CGCTTGCGCCGCAGTCGCAC</font><font color="red">GGCATTGTGGAACAATGCTG</font>
 +
|bp
 +
|
 +
|
 +
|bp
|
|
|-
|-
 +
|TAT H_INS_A R
 +
|<font color="green">CAGCATTGTTCCACAATGCC</font><font color="red">CGCTTGCGCCGC</font>
 +
|32 bp
 +
|59.26
 +
|
 +
|bp
 +
|Potential dimer formation!
|-
|-
-
|RcsC 5'
+
|H_INS_A R'
-
|<font color="green">GTTTCTTCGAATTCGCGGCCGCTTCTAGAT</font><font color="red">GAAATACCTTGCTTCTTTTCG</font>
+
|<font color="green">GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTA</font><font color="red">GTTGCAGTAGTTCTCCAGCTG</font>
-
|51 bp
+
|49 bp
-
|55.92
+
|57.77
-
|EcoRI, XbaI
+
|SpeI, PstI
-
|1396 bp
+
|122 bp
 +
|Potential dimer formation!
 +
|-
 +
|H_INS_B F
 +
|<font color="green">GTTTCTTCTCTAGAaaagaggagaaaACTAGATG</font><font color="red">TTTGTGAACCAACACCTGTG</font>
 +
|54 bp
 +
|57.98
 +
|XbaI
 +
|149 bp
 +
|Potential dimer formation! XbaI+RBS
 +
|-
 +
|H_INS_B TAT F
 +
|<font color="green">CGCTTGCGCCGCAGTCGCAC</font><font color="red">TTTGTGAACCAACACCTGTG</font>
 +
|bp
|
|
 +
|
 +
|bp
 +
|
 +
|-
 +
|TAT H_INS_B R
 +
|<font color="green">CACAGGTGTTGGTTCACAAA</font><font color="red">CGCTTGCGCCGC</font>
 +
|bp
 +
|
 +
|
 +
|bp
 +
|
 +
|-
 +
|-
 +
|-
 +
|H_INS_B R
 +
|<font color="green">GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTA</font><font color="red">GGTCTTGGGTGTGTAGAAGA</font>
 +
|48 bp
 +
|55.10
 +
|SpeI, PstI
 +
|149 bp
 +
|
 +
|-
 +
|-
 +
|RcsC F
 +
|<font color="green">GTTTCTTCTCTAGAaaagaggagaaaACTAGATG</font><font color="red">GAAATACCTTGCTTCTTTTCG</font>
 +
|54 bp
 +
|55.92
 +
|XbaI
 +
|1404 bp
 +
|XbaI+RBS
|-
|-
|-
|-
-
|RcsC 3'-2
+
|RcsC R
-
|<font color="green">AAGTATAC</font><font color="red">CAACGACTCTTCCATCTTCAC</font>
+
|<font color="green">GTTTCTTCCATATG</font><font color="red">CAACGACTCTTCCATCTTCAC</font>
-
|29 bp
+
|34 bp
|59.63
|59.63
|NdeI
|NdeI
-
|1396 bp
+
|1404 bp
-
|Two extra adenosine was added to the 5' side of the NdeI cutting site.
+
|BioBrick standard spacer was added to the 5' side of the NdeI cutting site.
|-
|-
|-
|-
Line 69: Line 160:
|Forward sequencing primer.
|Forward sequencing primer.
|-
|-
 +
|-
 +
|[http://partsregistry.org/Part:BBa_G00101 VR]
 +
|attaccgcctttgagtgagc
 +
|20 bp
 +
|59.34
 +
|
 +
|
 +
|Reverse sequencing primer.
 +
|-
 +
|M_IDE TAT F
 +
|<font color="green">CGCTTGCGCCGCAGTCGCAC</font><font color="red">CGGAACGGGCTCGTGTGGCT</font>
 +
|40 bp
 +
|
 +
|
 +
| bp
 +
|Potential dimer formation!
 +
|-
 +
|TAT M_IDE R
 +
|<font color="green">AGCCACACGAGCCCGTTCCG</font><font color="red">CGCTTGCGCCGC</font>
 +
|bp
 +
|
 +
|
 +
|bp
 +
|
 +
|-
 +
|-
 +
|-
 +
|M_IDE R
 +
|<font color="green">GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTA</font><font color="red">GAGTTTTGCAGCCATGAAGT</font>
 +
|48 bp
 +
|54.74
 +
|SpeI, PstI
 +
| bp
 +
|Potential dimer formation!
 +
|-
 +
|-
 +
|H_IGFBP3 F
 +
|<font color="green">GTTTCTTCTCTAGAaaagaggagaaaACTAGATG</font><font color="red">CAGCGGGCGCGACCCACGCT</font>
 +
|54 bp
 +
|
 +
|XbaI
 +
| bp
 +
|Potential dimer formation! XbaI+RBS
 +
|-
 +
|-
 +
|H_IGFBP3 R
 +
|<font color="green">GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTA</font><font color="red">CTTGCTCTGCATGCTGTAGC</font>
 +
|48 bp
 +
|54.74
 +
|SpeI, PstI
 +
| bp
 +
|Potential dimer formation!
 +
|-
 +
|H_IGFBP7 F
 +
|<font color="green">GTTTCTTCTCTAGAaaagaggagaaaACTAGATG</font><font color="red">GAGCGGCCGTCGCTGCGCGC</font>
 +
|54 bp
 +
|
 +
|XbaI
 +
| bp
 +
|Potential dimer formation! XbaI+RBS
 +
|-
 +
|-
 +
|H_IGFBP7 R
 +
|<font color="green">GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTA</font><font color="red">TAGCTCGGCACCTTCACCTT</font>
 +
|48 bp
 +
|54.74
 +
|SpeI, PstI
 +
| bp
 +
|Potential dimer formation!
 +
|-
 +
|-
 +
|OmpRBS F
 +
|<font color="green">GTTTCTTCGAATTCGCGGCCGCTTCTAGAG</font><font color="red">TACATTTTGAAACATCTATAGCG</font>
 +
|bp
 +
|
 +
|
 +
|bp
 +
|Primer dimer
 +
|-
 +
|OmpRBS R
 +
|<font color="green">GTTTCTTCCTGCAGCGGCCGCTACTAGTA</font><font color="red">ACGAATATGATACTAAAACTTTTAAGAT</font>
 +
|bp
 +
|
 +
|
 +
|bp
 +
|Primer dimer
 +
|-
 +
|TAT signal peptide
 +
|<font color="lightseagreen">ATG gacaaattcgacgct</font><font color="black">aatcgccgcaaattgctggcgcttggtggcgttgcactcggtgccgccatcctg</font><font color=purple>ccgacccctgcgtttgca</font>
 +
|90 bp
 +
|
 +
|
 +
|
 +
|TAT signal peptide for transport protein expressed in ''E.coli''
 +
|-
 +
|TAT_FP
 +
|<font color="black">AAG TCTAGA aaagaggagaaa ACTAG </font><font color="lightseagreen">ATG gacaaattcgacgc </font>
 +
|44 - 1 bp
 +
|55.26
 +
|XbaI
 +
|90 bp
 +
|TAT signal peptide forward primer
 +
|-
 +
|TAT_RP
 +
|<font color="orange">GCATTGTTCCACAATGCC </font><font color="purple">tgcaaacgcaggggt</font>
 +
|36 -3 bp
 +
|58.05
 +
|potential dimer (overlap 10)
 +
|90 bp
 +
|TAT signal peptide reverse primer
 +
|-
 +
|INS_A
 +
|<font color="orange">GGCATTGTGGAACAATGC </font><font color="black">TGTACCAGCATCTGCTCCCTCTACCAGCTGGAG </font><font color=greenyellow>AACTACTGCAAC <b>TAG</b></font>
 +
|63 + 3 bp
 +
|
 +
|
 +
|
 +
|human insulin A chain
 +
|-
 +
|TAT_INS_A_FP
 +
|<font color="purple">ccgacccctgcgtttgca </font><font color="orange">GGCATTGTGGAACAATGC </font>
 +
|36 bp
 +
|58.40
 +
|potential dimer (overlap 17)
 +
|63 bp
 +
|INS_A forward primer with TAT
 +
|-
 +
|TAT_INS_A_RP
 +
|<font color="black"><b>ctgcag</b> cggccgct <b>actagt</b> a <b>TTA TTA</b>  </font><font color="greenyellow">CTAGTTGCAGTAGTT </font><font color=black>CTCCAG</font>
 +
|42 + 6 bp
 +
|52.05
 +
|SpeI, PstI
 +
|63 bp
 +
|INS_A reverse primer with TAT
 +
|-
 +
|}
 +
* [http://www.mdbio.com.tw/pfu.htm pfu primer]
 +
* [http://partsregistry.org/Help:Contents Biobrick Help]
 +
* Tm is estimated by Amplify 3

Latest revision as of 10:03, 20 September 2007

Project Description / Lab Notes / Part List / Primer List

Name Sequence Length Tm (C) RE site Target length Description
M_INS_A F GTTTCTTCTCTAGAaaagaggagaaaACTAGATGGGCATTGTAGATCAGTGCTG 54 bp 56.85 XbaI 119 bp Potential dimer formation! XbaI+RBS
M_INS_A R GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTAGTTGCAGTAGTTCTCCAGCT 48 bp 54.74 SpeI, PstI 119 bp Potential dimer formation!
M_INS_B F GTTTCTTCTCTAGAaaagaggagaaaACTAGATGTTTGTCAAGCAGCACCTTTGT 55 bp 60.85 XbaI 149 bp Potential dimer formation!
M_INS_B R GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTAGGACATGGGTGTGTAGAAGA 48 bp 55.86 SpeI, PstI 149 bp Potential dimer formation!
TAT F GTTTCTTCTCTAGAaaagaggagaaaACTAGATGAACAATAACGATCTCTTTCAGG 56 bp 59.92 XbaI bp XbaI+RBS
TAT F GTTTCTTCTCTAGAaaagaggagaaaACTAGATGAACAATAACGATCTCTTTCAGG 108 bp 59.92 XbaI bp XbaI+RBS
H_INS_A F GTTTCTTCTCTAGAaaagaggagaaaACTAGATGGGCATTGTGGAACAATGCTG 54 bp 62.45 XbaI 122 bp Potential dimer formation! XbaI+RBS
H_INS_A TAT F CGCTTGCGCCGCAGTCGCACGGCATTGTGGAACAATGCTG bp bp
TAT H_INS_A R CAGCATTGTTCCACAATGCCCGCTTGCGCCGC 32 bp 59.26 bp Potential dimer formation!
H_INS_A R' GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTAGTTGCAGTAGTTCTCCAGCTG 49 bp 57.77 SpeI, PstI 122 bp Potential dimer formation!
H_INS_B F GTTTCTTCTCTAGAaaagaggagaaaACTAGATGTTTGTGAACCAACACCTGTG 54 bp 57.98 XbaI 149 bp Potential dimer formation! XbaI+RBS
H_INS_B TAT F CGCTTGCGCCGCAGTCGCACTTTGTGAACCAACACCTGTG bp bp
TAT H_INS_B R CACAGGTGTTGGTTCACAAACGCTTGCGCCGC bp bp
H_INS_B R GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTAGGTCTTGGGTGTGTAGAAGA 48 bp 55.10 SpeI, PstI 149 bp
RcsC F GTTTCTTCTCTAGAaaagaggagaaaACTAGATGGAAATACCTTGCTTCTTTTCG 54 bp 55.92 XbaI 1404 bp XbaI+RBS
RcsC R GTTTCTTCCATATGCAACGACTCTTCCATCTTCAC 34 bp 59.63 NdeI 1404 bp BioBrick standard spacer was added to the 5' side of the NdeI cutting site.
[http://partsregistry.org/Part:BBa_G00100 VF2] tgccacctgacgtctaagaa 20 bp 59.44 Forward sequencing primer.
[http://partsregistry.org/Part:BBa_G00101 VR] attaccgcctttgagtgagc 20 bp 59.34 Reverse sequencing primer.
M_IDE TAT F CGCTTGCGCCGCAGTCGCACCGGAACGGGCTCGTGTGGCT 40 bp bp Potential dimer formation!
TAT M_IDE R AGCCACACGAGCCCGTTCCGCGCTTGCGCCGC bp bp
M_IDE R GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTAGAGTTTTGCAGCCATGAAGT 48 bp 54.74 SpeI, PstI bp Potential dimer formation!
H_IGFBP3 F GTTTCTTCTCTAGAaaagaggagaaaACTAGATGCAGCGGGCGCGACCCACGCT 54 bp XbaI bp Potential dimer formation! XbaI+RBS
H_IGFBP3 R GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTACTTGCTCTGCATGCTGTAGC 48 bp 54.74 SpeI, PstI bp Potential dimer formation!
H_IGFBP7 F GTTTCTTCTCTAGAaaagaggagaaaACTAGATGGAGCGGCCGTCGCTGCGCGC 54 bp XbaI bp Potential dimer formation! XbaI+RBS
H_IGFBP7 R GTTTCTTCCTGCAGCGGCCGCTACTAGTATTATTATAGCTCGGCACCTTCACCTT 48 bp 54.74 SpeI, PstI bp Potential dimer formation!
OmpRBS F GTTTCTTCGAATTCGCGGCCGCTTCTAGAGTACATTTTGAAACATCTATAGCG bp bp Primer dimer
OmpRBS R GTTTCTTCCTGCAGCGGCCGCTACTAGTAACGAATATGATACTAAAACTTTTAAGAT bp bp Primer dimer
TAT signal peptide ATG gacaaattcgacgctaatcgccgcaaattgctggcgcttggtggcgttgcactcggtgccgccatcctgccgacccctgcgtttgca 90 bp TAT signal peptide for transport protein expressed in E.coli
TAT_FP AAG TCTAGA aaagaggagaaa ACTAG ATG gacaaattcgacgc 44 - 1 bp 55.26 XbaI 90 bp TAT signal peptide forward primer
TAT_RP GCATTGTTCCACAATGCC tgcaaacgcaggggt 36 -3 bp 58.05 potential dimer (overlap 10) 90 bp TAT signal peptide reverse primer
INS_A GGCATTGTGGAACAATGC TGTACCAGCATCTGCTCCCTCTACCAGCTGGAG AACTACTGCAAC TAG 63 + 3 bp human insulin A chain
TAT_INS_A_FP ccgacccctgcgtttgca GGCATTGTGGAACAATGC 36 bp 58.40 potential dimer (overlap 17) 63 bp INS_A forward primer with TAT
TAT_INS_A_RP ctgcag cggccgct actagt a TTA TTA CTAGTTGCAGTAGTT CTCCAG 42 + 6 bp 52.05 SpeI, PstI 63 bp INS_A reverse primer with TAT
  • [http://www.mdbio.com.tw/pfu.htm pfu primer]
  • [http://partsregistry.org/Help:Contents Biobrick Help]
  • Tm is estimated by Amplify 3
Retrieved from "http://2007.igem.org/wiki/index.php/NYMU_Taipei/Primer_List"