Does NPA is nanoparticles here?

No, but if you want to avoid fake phenotypes keep DMSO concentration below 0.5%

I would go even lower with DMSO, and keep it below 0.1% of the final volume.

NPA interferes with polar auxin transport, so you should observe at least the inhibition of lateral root growth.

http://www.plantcell.org/content/13/4/843.short

DMSO is a very good solvent for all plant hormones (NPA as well). BUT you must keep DMSO concentration less than 1 µl/ml (less than 0.1%). You can also use a control medium with same amount of DMSO like in the treated roots. 

when I have been observing shoot phenotypes up to 0.4% was fine. As Taras wrote always compare with DMSO grown plants.

Dear Daniel,

I germinated wildtype Col-0 Arabidopsis seeds on agar plates with medium that contained NPA (dissolved in DMSO) and kept them on this medium for four weeks. They exhibited a phenotype similar to aux-1 mutants. Their roots grow agravitropic and they are smaller than controls on normal medium. Hope that helps.

All the best.

Thanks for the suggestions everyone. I do see the phenotype in a dose-dependent manner and now I know my NPA is working.