We normalized our SGAG levels to dry weight of the cartilage explant, and got reproducible results. Due to the low cellular content and high ECM content in cartilage, normalizing to total protein (rather than DNA), makes sense. Along these lines, one could argue that normalizing to total collagen level in the cartilage piece should work! In the end, its best to choose a method that is reproducible in your lab.

I agree with you Dr. Venil that normalizing to dry weight is a good option. Have you also tried normalizing to wet weight of the tissue? Could this be a better option rather than dry weight as cartilage may lose its water content with age/time.

Charan, Wet weight can be inaccurate because of the gel like nature of cartilage and its variable absorptive capacity (once it is dissected out-it is partly dessicated anyway!). True, cartilage looses water but the molecular contents, relative amounts of HA, sGAGS etc remain as they were. So, we stuck to dry weight. Hope this helps!

I routinely do a papain digest on connective tissues such as cartilage (60 degrees C overnight) which will dissolve the majority of the cartilage and result in a solution that is suitable for both sGAG assay (by the DMMB assay) and DNA assay (I usually use the Hoechst assay as its cheap and easy). It really depends whether you want to know the proportion of your proteoglycan in the tissue or how it relates to the cell number in the tissue. In agreement with previous answers, its usual with cartilage to relate to total protein (although the DNA content is valid data in its own right) and its always more accurate to start with a freeze-dried tissue but not absolutely necessary.