Nuclear matrices from White bush (Cucurbita pepo var. patisoniana) cell nuclei were isolated. Three different preparation methods were used. The methods were: I- the method of Berezney and Coffey [1] involving extraction of cell nuclei with 2M NaCl and Triton X-100 (called the “High Salt” method); II- the same with pre-treatment of cell nuclei with 0.5 mM CuSO4 (stabilisation step); III- the method of Mirkovitch et al. [2] involving lithium diiodosalicylate (LIS) extraction (called the “LIS” method). Each of the three methods was used in three variants of nucleic acid removal: restriction enzymes, endogenous nucleases and DN-ase I with RN-ase A digestion. Nuclear matrices were analysed for protein and DNA content, residual RNA and DNA synthesis activity, endonucleolytic activity and specific SAR DNA binding properties. The lowest protein and DNA content and endonucleolytic activity was found in nuclear matrices isolated by the “High Salt” method. It also had the lowest RNA and DNA synthesis and endonucleolytic activity. The highest protein and DNA content, and RNA and DNA synthesis and endonucleolytic activity was found in nuclear matrices isolated by the “LIS” method. When exogenous SAR DNA binding activity was compared, the highest was found in nuclear matrices isolated by the “High Salt” method while the lowest was in the “LIS” method preparation. Nuclear matrices isolated by the “High Salt” method with a stabilisation step always displayed average values of assayed parameters. These data indicate that the biological residual properties of a nuclear matrix preparation strongly depend on the method used.
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