Abstract Background and objectives: Paraffin-embedded tissues and clinical samples are a valuable resource for molecular genetic studies, but the extraction of high-quality genomic DNA from this tissues is still a problematic issue. In the Present study, the efficiency of two DNA extraction protocols, a commercial kit and a traditional method based on heating and K Proteinase was compared. Material and Methods: Fifty paraffin-embedded blocks of colon cancer tissues (more than 5 years old) were used to compare two methods of DNA extraction. DNA was extracted by traditional method using heat and commercial DNA extraction (Qiagen kit) method. Then the purity and concentration of extracted DNA were measured by Spectrophotometer. Two sequences of TLR4 “The most important receptors in innate immunity” were amplified by polymerase chain reaction. SH-1 ‘188bp’ and SH-2 ‘124bp’ were amplified and then the products were separated on a 2% agarose gel. Results: The results show that the yield of DNA by traditional method (297 mg/ml) is significantly (p
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