Several points should be noted to avoid DNA degradation: (1) DNA degradation occurs when the sample is not fresh or is stored improperly for a long time. Samples not used immediately should be flash frozen in liquid nitrogen and stored at -80°C. Genomic DNA in samples stored at room temperature, 4°C, or -20°C are subject to degradation. It is also not advised to keep samples in buffer or medium while storing at -80°C. (2) For whole blood samples, if they are stored at room temperature for more than 2 days or at 4°C or -20°C, isolated genomic DNA appears smeared at an extent proportional to the storage time. (3) Use fresh TAE or TBE running buffer for electrophoresis. Running buffer that is used repeatedly may be contaminated with DNase. (4) If isolated DNA needs to be stored for a long time, use 10 mM Tris-HCl (pH 9.0) or TE for elution. Using ddH2O is not advised in this case as DNA fragments in H2O suffer from gradual degradation through acid hydrolysis. (5) If DNA is to be used frequently, elute in 10 mM Tris-HCl (pH 9.0) or TE and store at 4°C. Keep DNA at -20°C only for long-term storage. Repeated freeze-thaw cycles can cause shearing of genomic DNA. (6) Genomic DNA extracted from paraffin-embedded tissue is usually degraded. This is because genomic DNA in paraffin-embedded tissue unavoidably suffers from degradation when samples are treated and stored for a long time. DNA in this case is not suitable for Southern blotting or restriction analysis due to smearing. However, it is applicable for PCR.
Why does the genomic DNA band appear smeared in agarose gel electrophoresis? "