IGEM:Harvard/2006/Adaptamers/Oligos: Difference between revisions

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<div class="tabs">
<div class="tabs">
<ul>
<ul>
<li>[[IGEM:Harvard/2006/Adaptamers|1. Lab Notebook]]</li>
<li>[[IGEM:Harvard/2006/Adaptamers|News and Updates]]</li>
<li>[[IGEM:Harvard/2006/Adaptamers/Overview|2. Overview]]</li>
<li>[[IGEM:Harvard/2006/Adaptamers/Notebook|Notebook]]</li>
<li>[[IGEM:Harvard/2006/Adaptamers/Literature|3. Literature]]</li>
<li id="current">[[IGEM:Harvard/2006/Adaptamers/Oligos|Oligos]]</li>
<li id="current">[[IGEM:Harvard/2006/Adaptamers/Oligos|4. Oligos]]</li>
<li>[[IGEM:Harvard/2006/Adaptamers/Code|Code]]</li>
<li>[[IGEM:Harvard/2006/Adaptamers/Code|5. Code]]</li>
<li>[[IGEM:Harvard/2006/Adaptamers/Plans|Plans]]</li>
<li>[[IGEM:Harvard/2006/Adaptamers/Plans|6. Plans]]</li>
<li>[[IGEM:Harvard/2006/Adaptamers/Overview|Overview (for site visitors)]]</li>
<li>[[IGEM:Harvard/2006/Adaptamers/Literature|Literature]]</li>
</ul>
</ul>
</div>
</div>
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GGTTGGTGTGGTTGGAAGTAGTATGGAAAGGATTA
GGTTGGTGTGGTTGGAAGTAGTATGGAAAGGATTA
    CATACCTTTCCTAATCGTTTGACACTCTGTTTTGGACGCTGGCCACGCAGCAGAGTGTCT
    CATACCTTTCCTAATCGTTTGACACTCTGTTTTGGACGCTGGCCACGCAGCAGAGTGTCT
</pre>
==Biotinylated oligos==
Biotinylated oligos as positive control in viscosity experiment:
5' and 3' biotinylated:
B35.0
5' GAGTTATGATTAGGCGGACGGTCTGAACAAGGTTT 3'
5' biotinylated:
B35.1
5' TGAGTTATGATTAGGCGGACGGTCTGAACAAGGTTT 3'
B35.2
5' TAAACCTTGTTCAGACCGTCCGCCTAATCATAACTC 3'
==Strand Displacement Oligos==
R20.20
5' TAATCCTTTCCATACTACTT 3'
R20.35
5' TAATCCTTTCCATACTACTTCCAACCACACCAACC 3'
T20-R20.20
<pre>
5' GGTTGGTGTGGTTGGAAGTAGTATGGAAAGGATTA 3'
3'           TTCATCATACCTTTCCTAAT 5'
</pre>
T20-R20.35
<pre>
5' GGTTGGTGTGGTTGGAAGTAGTATGGAAAGGATTA 3'
3' CCAACCACACCAACCTTCATCATACCTTTCCTAAT 5'
</pre>
</pre>

Latest revision as of 12:03, 21 August 2006


v.1

  • Oligos (8 ssDNA sequences):

SN = streptavidin aptamer + N bp 3' tail

TN = thrombin aptamer + N bp 3' tail

S5

5' TCTGTGAGACGACGCACCGGTCGCAGGTTTTGTCTCACAGCATAG 3'

S20:

5' TCTGTGAGACGACGCACCGGTCGCAGGTTTTGTCTCACAGCATAGAGCATCTAGAGGTTC 3'

S35:

5' TCTGTGAGACGACGCACCGGTCGCAGGTTTTGTCTCACAGCATAGAGCATCTAGAGGTTCACTTCTGCAGCAATA 3'

S50:

5' TCTGTGAGACGACGCACCGGTCGCAGGTTTTGTCTCACAGCATAGAGCATCTAGAGGTTCACTTCTGCAGCAATAGAATTAAGCTTGTCC 3'

T5:

5' GGTTGGTGTGGTTGGACACT 3'

T20:

5' GGTTGGTGTGGTTGGACACTGAACCTCTAGATGCT 3'

T35:

5' GGTTGGTGTGGTTGGACACTTATTGCTGCAGAAGTGAACCTCTAGATGCT 3'

T50:

5' GGTTGGTGTGGTTGGACACTGGACAAGCTTAATTCTATTGCTGCAGAAGTGAACCTCTAGATGCT 3'


  • Alignment

+20: 

5' TCTGTGAGACGACGCACCGGTCGCAGGTTTTGTCTCACAGCATAGAGCATCTAGAGGTTC                        3'
3'                                              TCGTAGATCTCCAAGTCACAGGTTGGTGTGGTTGG    5'

+35: 

5' TCTGTGAGACGACGCACCGGTCGCAGGTTTTGTCTCACAGCATAGAGCATCTAGAGGTTCACTTCTGCAGCAATA 				3'
3'                                              TCGTAGATCTCCAAGTGAAGACGTCGTTATTCACAGGTTGGTGTGGTTGG      5'

+50: 

5' TCTGTGAGACGACGCACCGGTCGCAGGTTTTGTCTCACAGCATAGAGCATCTAGAGGTTCACTTCTGCAGCAATAGAATTAAGCTTGTCC			  3'
3'                                              TCGTAGATCTCCAAGTGAAGACGTCGTTATCTTAATTCGAACAGGTCACAGGTTGGTGTGGTTGG 5'

v.2

T50.2

5' GGTTGGTGTGGTTGGAAGTAGTATGGAAAGGATTAGCAATGATAGGCATATTTATACGGCTCGGA 3'

T35.2

5' GGTTGGTGTGGTTGGAAGTAGTATGGAAAGGATTAGCAATGATAGGCATA 3'

T20.2

5' GGTTGGTGTGGTTGGAAGTAGTATGGAAAGGATTA 3'

S50.2

5' TCTGTGAGACGACGCACCGGTCGCAGGTTTTGTCTCACAGTTCTTTCCGAGCCGTATAAATATGCCTATCATTGCTAATCCTTTCCATAC 3'

S35.2

5' TCTGTGAGACGACGCACCGGTCGCAGGTTTTGTCTCACAGTTAAATATGCCTATCATTGCTAATCCTTTCCATAC 3'

S20.2

5' TCTGTGAGACGACGCACCGGTCGCAGGTTTTGTCTCACAGTTTGCTAATCCTTTCCATAC 3'

A15

5' TCTGTGAGACGACGCACCGGTCGCAGGTTTTGTCTCACAGTTGCTTTCCATTCTACATATGAAGGTTGGTGTGGTTGGAAGTAATGTAGAATGGAAAG 3'


  • Alignment

A50.2 

GGTTGGTGTGGTTGGAAGTAGTATGGAAAGGATTAGCAATGATAGGCATATTTATACGGCTCGGA
   		    CATACCTTTCCTAATCGTTACTATCCGTATAAATATGCCGAGCCTTTCTTGACACTCTGTTTTGGACGCTGGCCACGCAGCAGAGTGTCT

A35.2 

GGTTGGTGTGGTTGGAAGTAGTATGGAAAGGATTAGCAATGATAGGCATA
		    CATACCTTTCCTAATCGTTACTATCCGTATAAATTGACACTCTGTTTTGGACGCTGGCCACGCAGCAGAGTGTCT

A20.2 

GGTTGGTGTGGTTGGAAGTAGTATGGAAAGGATTA
		    CATACCTTTCCTAATCGTTTGACACTCTGTTTTGGACGCTGGCCACGCAGCAGAGTGTCT

Biotinylated oligos

Biotinylated oligos as positive control in viscosity experiment:

5' and 3' biotinylated:

B35.0

5' GAGTTATGATTAGGCGGACGGTCTGAACAAGGTTT 3'

5' biotinylated:

B35.1

5' TGAGTTATGATTAGGCGGACGGTCTGAACAAGGTTT 3'

B35.2

5' TAAACCTTGTTCAGACCGTCCGCCTAATCATAACTC 3'

Strand Displacement Oligos

R20.20

5' TAATCCTTTCCATACTACTT 3'

R20.35

5' TAATCCTTTCCATACTACTTCCAACCACACCAACC 3'


T20-R20.20 


5' GGTTGGTGTGGTTGGAAGTAGTATGGAAAGGATTA 3'
3' 	          TTCATCATACCTTTCCTAAT 5'

T20-R20.35 


5' GGTTGGTGTGGTTGGAAGTAGTATGGAAAGGATTA 3'
3' CCAACCACACCAACCTTCATCATACCTTTCCTAAT 5'
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