We are working with small ssDNA and making nanomaterials with them. We are using DNA in serum with 1% SDS in it (w/v).
We see that stability of DNA increases in SDS mixed serum.
My question what does SDS do to DNA? I know that SDS breaks protein structure, but the serum is already heat-killed etc.
So my question is what is the interaction of SDS with DNA? Does SDS forms micelles and interact with DNA?
Thanks.

The first thing I can think of is that SDS denatures olignucleotide degrading enzymes. Some of these can be very heat resistant and may even refold after heating. RNAses are particularly bad for this and I understand that some RNAses do have activity on ssDNA.

I agree with John re. SDS suppressing nuclease activity. SDS is a highly effective surfactant (good in hair shampoo!!) that lowers the surface tension of aqueous solutions (which depends on the micelle concentration) and alters the kinetics of nucleic acid interactions, and is particularly useful in reducing non-specificity (background) in nucleic acid hybridization reactions. There is a brief mention of the effects of SDS on the stability of plasmid DNA/peptide (serum) condensates at:
http://onlinelibrary.wiley.com/doi/10.1 … 800477/pdf

Two more relevant articles are: “Kinetics of DNA and RNA Hybridization in serum and serum-SDS” by  Graugnard E et al. (IEEE Transactions on Nanotechnology 9: 603-609, 2010) with which you are probably already familiar, and “Interfacial stabilization or organic-aqueous two-phase microflows for a miniaturized DNA extraction module” by Reddy V. & Zahn JD. J Colloid Interface Science 286: 158-165, 2005) which, despite the title, talks about DNA extractions, SDS micelle formation and surface tensions in a flow system.

Last edited by Steve Lolait (15th Oct 2010 09:50:41)