Protocol - Inverse-PCR (I-PCR) for the identification of the breakpoints of deletions
The Inverse-PCR is a method that allows to amplify unknown regions of DNA, starting from the flanking known region on which are positioned the primers, in inverse direction compared to a normal PCR. It is necessary circularizing the DNA fragments, using ligase, then perform the I-PCR.
Category:
Molecular Biology
Creation date: Mar 10, 2009
Last revision: Feb 08, 2016
Author(s):
Maria De Angioletti, Clementina Carestia, Giuseppina Lacerra
Contact
Name: Giuseppina Lacerra
Address: Institute of Genetics and Biophysics - CNR Via Pietro Castellino, 111 Naples 80131 ITALY
Phone: +39-081-6132602
Figure legend:
Steps
Description | Temperature | Time | Note |
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Prepare tubes for I-PCR and add 10 ng of the circularized DNA (2 μl)
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Prepare the I-PCR mix and dispense 23 μl in each tube with DNA sample
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Prepare a 2% Nu Sieve GTG agarose gel (small) and load 12μl of PCR reaction. Also load a DNA ladder to check that the length of the amplicomer band
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Recover the band and electro elute
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Sequencing by dsDNA or by cloning
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Other informations
I-PCR program
33 cycles:
1) T°: 94° 1 min
2) T°: 55° 1 min
3) T°: 72° 1.5 min
Quality validation:
Yes
Validation info
The protocol has been used to define the breakpoints of two new deletions: the South-Italy β°-thalassemia and the Italian (G)γ((A)γδβ)°-thalassemia. The data has been published in peer-reviewed journals.
Related Protocols:
Related Oligos:
Solutions
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Inverse-PCR mix
Reagents F-concentration Quantity I-concentration Buffer1X2.5 μl10XPrimer For0.4 μM10-12 pmolPrimer Rev0.4 μM10-12 pmoldNTP0.2 mM4 μl1.25 mMTaq Polimerasi0.125 μl5 U/μlH2O bdup to 25 μlNote
The primers used are in inverse direction