Alkaline denatured bacterial chromosomal DNA and most of RNA,since they are much much bigger than plasmid DNA.Plasmid is still soluble and is in the solution under the same condition.Proteins also get denatured,also,chromosomal DNA is linked to the bacterial proteins,therefore they all are precipitated when you include the 3 M potassium acetate.
The principal is that alkaline denatures proteins,chromosomal DNA and most of RNA,but leave plasmid in the solution,then potassium acetate precipitates those denatured materials.Finally,alcohol (usually isopropanol ) is used to precipitate plasmid DNA.Plasmid DNA is obtained.
