For research use only!
Shipping: shipped on blue ice
Storage Conditions: store at -20 °C
avoid freeze/thaw cycles
Shelf Life: 12 months
gDNA Fragmentation Kit (AluI/RsaI-based) contains all reagents for sequence-specific enzymatic fragmentation of genomic DNA (gDNA) either purified or directly derived from WGA reactions (see #APP-004).
Both AluI and RsaI possess a four base-pair recognitions sequence (AluI: AG↓CT, RsaI: GT↓AC).
The resulting fragmented gDNA can subsequently be used for downstream applications such as preparation of hybridization probes via Klenow fragment-based DNA labeling.[1-3]
2x 600 units (10 U/μl) in 10 mM Tris-HCl pH 7.4, 100 mM KCl, 0.1 mM EDTA, 1 mM DTT, 200 μg/ml BSA and 50 % [v/v] glycerol
RsaI (10 U/μl)
1000 units (10 U/μl) in 10 mM Tris-HCl pH 7.4, 50 mM KCl, 0.1 mM EDTA, 200 μg/ml BSA and 50 % [v/v] glycerol
10x Universal Buffer (UB)
1 ml (10 mg/ml) in PCR-grade H2O
20 μl, 100 mM in PCR-grade H2O
General protocol for gDNA fragmentation
The protocol below is intended as a general guideline to generate gDNA fragments ranging from 250-1000 bp however, individual optimization might be required e.g. in terms of template amount, incubation time or AluI/RsaI concentration.
|Component||Final conc./amount||1 reaction|
|Genomic DNA||1-4 μg purified gDNA or up to 18 μl WGA Mix||X μl|
|10x Universal Buffer||1x||5 μl|
|AluI (10U/μl)||50U||5 μl|
|RsaI (10U/μl||50U||5 μl|
|BSA (10 mg/ml)||5 μg||0.5 μl|
|DTT (100 mM)||1 mM||0.5 μl|
|PCR-grade H2O||-||ad 50 μl|
1.2 Evaluation of gDNA fragmentation
 Hostetter et al. (2010) Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples. Nucleic Acid Res. 38 (2): e9.
 Kawachi et al. (2013) Deletion polymorphism at chromosome 3q26.1 and oral squamous cell carcinoma. International Journal of Oncology 42:384.
 Uda et al. (2007) Comparison of Whole Genome Amplification Methods for Detection of Pathogenic Bacterial Genomic DNA Using Microarray. Jpn. J. Infect. Dis. 60:355.