It all depend on the nanoparticle's size. There are arguments that NPs that are much below 100nm can be harmful by crossing certain biological barriers that are not mean for them to penetrate, and also may trigger immune response. In pharmaceutical context, NPs above 100nm are more desirable.
Interaction of the nanoparticles with the living organisms due to their size, lower than 100nm, is very clear just noticing that:
The single molecules have around 1 nm in size, but there are some biological molecules with similar size such as proteins and nucleic acids which consist of long macromolecular chains which are folded and shaped by cooperative and weak interaction between side groups, H-bridges and salt bridges. Thus the interaction is possible. Evidence for such interactions is seen from the experience with immunolabelling and related surface functionalisation techniques to target nanoparticles to biomolecules as markers for high resolution Transmission Electron Microscopy and optical imaging systems.
In all that I know there are not proves that the damage is very important although I don't know if can be considered negligable. I attach you a link where you can find more information on this issue.