I want to check plasmid DNA and peptide binding quantitatively and to compare different peptide affinity to DNA. Except ITC which other technique can be used to do this study because I am facing aggregation problem in ITC
There are some spectroscopic studies you may try. If your peptide has Trp/Tyr you may go for fluorescence quenching study. If not you can monitor the absorption change of DNA upon addition of peptide. You may also use some fluorescent dyes (intercalating/groove binding) to saturate DNA and then perform a fluorescence quenching study.
In addition to spectroscopic methods, polyacrylamide gel electrophoresis would be another option that will give a clear view of the complex(ex) that are being formed in solution. If the plasmid itself is not relevant for your experiment, you can replace it with short oligonucleotides; this should help with the precipitation.
ITC usually requires higher concentrations than fluorescence measurements described by Uttam and William, so those can be a good option too.