What is the effect of nucleic acids in the sample?
High nucleic acid content can cause gel smearing in the second dimension due to the clogging of pores in the gel. This can be reduced by sufficient sonication to shear the DNA. DNA can also be removed by treating the sample with DNAseI, or using Ettan™ 2-D Clean-Up Kit (Code no. 80-6484-51). Using DNase or RNase as part of the sample preparation may result in the enzymes appearing on the gel depending on the molecular weight and type of gel. Significant amounts of DNA in the sample can aggregate and cause the sample to become viscous and awkward to pipette. We recommend that magnesium acetate be added to the lysis buffer to prevent this aggregation.
