Protocol - Circularization of DNA fragments for the molecular characterization of new deletions
During the molecular characterization of new deletions (to define the breakpoints) can occur that one extreme is known, but not the second one. In these cases it is very useful and suitable to perform the circulatization by ligase of DNA fragments containing the beakpoints of the deletion, followed by the inverse-PCR. Using these methods we were able to define the breakpoints of two new beta-Thalassemia deletions.
Category:
Molecular Biology
Creation date: Jan 13, 1997
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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Select the restriction enzyme giving rise to an anomalous pattern through restriction mapping analysis
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1) Digestion of DNA from a carrier of the new deletion with the selected restriction enzyme following the protocol reported below
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over night
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Prepare 1.5 ml tube for each reaction and the reaction mix as reported below
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2) Prepare a 1.2% GTG Nu-Sieve agarose gel in 1X TBE
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Choose a beaker that is 2-4 times the volume of the solution
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Add the cold 1X TBE solution and a stir bar, than slowly spill the agarose powder while the solution is stirred. Cover the beaker with aluminum sheet
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Place on heated plate and boil while stirring until the agarose is dissolved
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10 minutes
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Add an intercalant of the DNA (ethidium bromide or other). Allow to cool on cold plate while stirring
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10 minutes
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Pour the agarose into the tray with comb. Allow to cool, and cover with foil or plastic wrap and hold
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cold room
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over night
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3) Electroforesis of digested DNA on agarore gel (1.2% NuSieve GTG agarose gel)
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Load the samples of DNA between two DNA ladders, chosen in according to the length of the fragment to be recovered. Migrate to 22mA
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9 hours
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4) Excision of DNA band from gel
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Cut out the region of the gel in correspondence to the band of interest, using as reference the DNA ladders bands
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Put the recovered band in a 1.5 ml tube
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Melt the gel
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65° C
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10 minutes
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Define the volume of the liquid agarose. Add 1X TE so that the final concentration of agarose is <0.5%
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65° C
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10 minutes
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5) Extraction and precipitation of DNA from agarose gel
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Add one volume of phenol saturated with TE
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Shake and centrifuge at 10.000g
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RT
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10 minutes
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Transfer the upper aqueous phase to a clean tube
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Add one volume of chloroform-isoamyl alcohol 24:1, shake and centrifuge at 10.000g
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RT
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10 minutes
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Recover the upper phase and determine the volume
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Add sodium acetate 3.3M, coming to a final concentration of 0.33M, and two volumes of 95% cold ethanol
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Centrifuge at 12.000g
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4° C
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30 minutes
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Remove the supernatant paying attention to the pellet
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Wash the DNA pellet with 500μl of 80% cold ethanol
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-20° C
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Centrifuge at 12.000g
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4° C
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30 minutes
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Discard the supernatant and dry the DNA pellet in a vacuum concentrator (Savant) or at RT
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Suspend the DNA pellet in 50μl TE
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Prepare a 1% agarose (normal) gel
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Load 5μl of the recovered DNA and DNA ladders for a quantitative and qualitative analysis
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Determine the amount of the recovered DNA
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6) Circularization of DNA fragment by DNA ligase
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For each ligase prepare a 1.5ml tube as follows:
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-DNA digested with R.E. in TE 100ng
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-H2O bd up to 150μl
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To facilitate the distension of the digested DNA fragments incubate
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65° C
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10 minutes
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after incubate put in ice with H2O
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Add into each tube the 50 μl of the Ligase mix
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Centrifuge and incubate
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16° C
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over night
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To inactivate theT4 DNA Ligase incubate
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65° C
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10 minutes
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7) Purification of DNA circularized
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Add one volume of phenol-chloroform, shake and centrifuge at 12.000g
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RT
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10 minutes
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Transfer the upper aqueous phase to a fresh tube and precipitate with the addition of 20μl of 3.3M sodium acetate and 2 volumes (400μl) of 95% ethanol
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Incubate
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-80° C
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30 minutes
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Centrifuge at 12.000g
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4° C
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10 minutes
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Wash with 80% ethanol
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Centrifuge as above and drying in a vacuum concentrator(Savant)
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Re-suspend in 20μl TE 1X
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Proceed with the Inverse-PCR protocol
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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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Restriction Enzyme reaction mix (40μl)
Reagents F-concentration Quantity I-concentration DNA15 μgRestriction enzyme1 μl20U/μlBuffer 10X4 μl10XH2Oup to 40 μl -
Ligase mix (50 μl)
Reagents F-concentration Quantity I-concentration Buffer20 μl10XT4 DNA Ligase1 μl400.000 U/mlH2O bd29 μl