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These methods are usually based on restriction digestion: genomic DNA is digested using one or several restriction enzymes, with simultaneous ligation of appropriate adaptors to the restriction fragments and subsequent amplification of fragments by PCR using the adapter and the restriction site as targets for primer annealing [ 6].
About 250 ng of genomic DNA is digested with one of two restriction enzymes and ligated to adaptors recognizing the cohesive four base overhangs.
If chromosomal DNA is digested with a restriction enzyme that cuts in the DNA flanking the tandem array, or if polymerase chain reaction (PCR) amplification is performed using primers designed to recognize sites in the flanking DNA, products will be produced whose length is proportional to the number of repeats in the array.
In this technique, genomic DNA is digested to yield overhanging sticky ends (Figure 1B).
In this assay, genomic DNA is digested (chopped) with HaeIII and PCR primers flanking the three HaeIII restriction enzyme sites are then used to amplify the intervening region.
In the RAD protocol, genomic DNA is digested with a six to eight base-cutter RE and a barcoded adapter is ligated to compatible sticky ends.
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DNA was digested using standard digestion protocols for restriction enzymes.
Chromatin (equivalent to 1 μg DNA) was digested using 0.0020 U MNase in the digestion buffer.
Chromatin (equivalent to 1 μg DNA) was digested using 0.0014 U MNase in the Atlantis MN Digestion buffer.
Briefly, the genomic DNA was digested by restriction enzyme MspI.
Decrosslinked DNA were digested with proteinase K and purified using PCR purification kit (Qiagen).
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