NanoBio: Oligonucleotide Inserts: Difference between revisions
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Arthur K Yu (talk | contribs) (Reworded the ordering thingy, added link to oligocalc) |
Arthur K Yu (talk | contribs) m (reminder to mix oligos to 100 µM) |
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== Hybridize ssDNA to form ds insert (start here if you ordered phosphorylated oligos(right move!))== | == Hybridize ssDNA to form ds insert (start here if you ordered phosphorylated oligos(right move!))== | ||
*Make oligos 100 µM | |||
*Mix: | *Mix: | ||
**3 uL 100 µM sense oligo | **3 uL 100 µM sense oligo |
Revision as of 12:38, 10 June 2008
Design of oligonucleotide inserts
- The sense oligo should be of the form:
5' CTAGA(coding sequence)ACTAGTAGCGGCCGCTGCA 3'
The bolded sequences will be the overhanging "sticky" ends. - The anti-sense oligo should be of the form:
5' GCGGCCGCTACTAGT(reverse complement of coding sequence)T 3' - Design considerations. Make sure that:
- either primer will not form a stable internal hairpin structure, ΔG < -3 kcal/mole. You can use OligoCalc
- either primer does not contain a EcoRI, PstI, SpeI, XbaI, NotI, or BstEII site outside of the flanking regions
- the insert for the forward primer does not begin with TC (or else a DAM I site (GATC) is formed, the A is methylated and XbaI cannot cut at its site)
- Order 25 nmol DNA oligo with 5' phosphorylated ends (click 5' Mods at the bottom) from IDT.
Note: if your oligo insert is large 40+ bp, use PAGE purification (it's a little slower and more expensive).
Hybridize ssDNA to form ds insert (start here if you ordered phosphorylated oligos(right move!))
- Make oligos 100 µM
- Mix:
- 3 uL 100 µM sense oligo
- 3 uL 100 µM anti-sense oligo
- 3 uL 10 x PNK (polynucleotide kinase) buffer (in common buffer stocks)
- 3 uL 0.5 M NaCl
- 18 uL distilled water
to give 30 µL total volume
- Place in boiling water bath for 2 min., then remove water bath from the heat source and allow the DNA (still in the water bath) to cool to room temperature.
- 1x PNK buffer (NEB catalog # B0201S) contains: 70 mM Tris-HCl, 10 mM MgCl2, 5 mM Dithiothreitol, pH 7.6.
Phosphorylation of 5' ends & hybridization (only if you didn't order 5'phosphorylated oligos)
- Note: it is really just better in terms of time & efficiency to order 5' phosphorylated oligos. Really.
- Mix:
- 3 uL 100 µM sense oligo
- 3 uL 100 µM anti-sense oligo
- 3 uL 10 x PNK (polynucleotide kinase) buffer
- 2 uL 10mM ATP
- 2 uL T4 polynucleotide kinase (PNK)
- 17 uL distilled water
to give 30 uL total volume
- Incubate at 37C for 1.5 hours.
- Add 4 uL 0.5 M NaCl.
- Place in boiling water bath for 2 min., then remove water bath from the heat source and allow the reaction (still in the water bath) to cool to room temperature.