I am unable to get good contrast on negative staining of RNA-protein complex. There is too much background. However the perimeter of the complex can be marked, yet the contrast is weak as compared to protein TEM images.
It does look like artifacts to me. What do you have in the buffer? How exactly did you prepare the grids (did you glow-discharge? dry inbetween steps; which staining agent?)? What size of particle do you expect? Do you have experience with negative staining? If not, a good starting point could be to optimize the conditions for a sample that always works or that you can recognize easily (like worm hemoglobin), before complicating the process with a newly synthesized one.