why did the nuclei enriched fraction appear in the centrifuge fraction spun at the slower speed? Why didn't this fraction contain only nuclei(Why wasn't it pure?)?

The reason the nuclei enriched fraction did not appear as pure nuclei in the centrifuge fraction spun at the slower speed is likely due to the relative density and size of the cellular components present in the sample.

During centrifugation, different components of a sample sediment at different rates based on their density and size. In this case, the centrifuge fraction spun at the slower speed likely contained not just nuclei, but also other cellular components that have similar density or size. These could include membrane fragments, organelles, and other cellular debris.

In order to achieve a pure nuclei fraction, a more rigorous purification process might be needed, such as using a higher centrifugation speed, density gradient centrifugation, or other methods of cellular fractionation.

To obtain a pure nuclei fraction, you could try the following steps:

1. Start with a cell culture or tissue sample and homogenize it to break open the cells and release their contents.
2. Centrifuge the homogenate at a low speed to remove larger cellular debris and unbroken cells. This will generate a supernatant, which is a mixture of smaller cellular components.
3. Transfer the supernatant to a new tube and centrifuge it at a higher speed. This will cause the nuclei, which are relatively denser, to sediment at the bottom of the tube.
4. Carefully remove the supernatant (containing other cellular components) without disturbing the pellet of nuclei.
5. Wash the nuclei pellet with a buffer solution to remove any contaminants.
6. Centrifuge the nuclei suspension again at a low speed to remove any remaining debris or contaminants.
7. Collect the final nuclei pellet, which should contain a purified fraction of nuclei.

By following these steps, you can increase the purity of the nuclei fraction and reduce the presence of other cellular components.