Avoiding adsorption of DNA to polypropylene tubes and denaturation of short DNA fragments.

Abstract

Two problems can arise when working with small quantities of DNA in polypropylene tubes: first, significant amounts of DNA can become lost by sticking to the tube walls; second, short DNA fragments tend to denature when binding to polypropylene. In addition, DNA also tends to denature upon dehydration. We have found that a simple way to solve these problems is by using polyallomer tubes instead of polypropylene and by avoiding certain salts, such as sodium acetate, when drying DNA. DNA is usually stored in polypropylene tubes, which have become widely used for their resistance to solvents, their strength, their ease of use and their low price. Polypropylene is a very hydrophobic material, whereas DNA is a highly charged macromolecule, two characteristics that minimize the interactions of DNA with tube walls and tend to avoid the adsorption problems often found with other macromolecules, especially proteins. But DNA can, in fact, bind to polypropylene tubes. This is particularly striking at high ionic strength: (Fig. 1) shows that DNA fragments bind quickly to polypropylene tube walls in 2.5 M NaCl, with 75\% of the material adsorbed after 1 h and 90% after 3 h in this experiment. Under such conditions, the amount of adsorbed DNA can be as high as 5 ng /mm 2 of tube wall. Tests performed at ionic conditions varying from TE (10 mM Tris-HCl, 1 mM EDTA, pH 7.5) to TE plus 0.5 M NaCl, showed that DNA also sticks to tube walls at lower ionic strength, but with important variations between different batches of tubes. Tests were performed with 1 ng of radioactively labelled DNA per tube in 10 µl. With some batches of tubes, the percentage of adsorption was always high (between 80\% and 95\%; such tubes actually had a binding capacity as high as >10 ng for a volume of 10 µl). With other tube batches from the same manufacturer (Eppendorf) the percentage of adsorption varied apparently at random between 5% to 95%, all conditions being kept identical. Finally, other batches always presented little adsorption (<10\%) at low ionic strength. In all those tests, using single-stranded instead of double-stranded DNA made no significant difference.