This study examined the characteristics of virtual and hands-on inquiry environments for the development of blended learning in a popular domain of bio-nanotechnology: the separation of different-sized DNA fragments using gel-electrophoresis, also known as DNA-fingerprinting. Since the latest scientific developments in nano- and micro-scale tools are based on molecular movement in electric fields, gel electrophoresis is an excellent model for learning-related concepts and processes. This study employed two environments (a 2D virtual laboratory (VRL) and a hands-on laboratory (HOL)) and documented the benefit of using VRLs to ground students' knowledge construction, before more complex, hands-on investigation. A comparative analysis explored how the perceptual features of the two learning environments supported students in designing experiments, evaluating data from experimental trials and reasoning for the mechanisms by which these data came about. The findings provide evidence for the design of blended inquiry-learning environments that integrate virtual and hands-on laboratories.