RNA is one of the most important molecule essential for proper functioning of the cell. However, there are a growing number of RNAs for which biological function and structure are not known. Isoenergetic microarrays have been designed and apply as a new method to study the structure and interactions of RNAs. Isoenergetic microarrays are built with short modified RNA probes. The 2'-O-methylated and LNA-modified oligomer probes have been designed in such a way, that the interaction of each probe with its complementary single stranded fragment of target RNA has comparable thermodynamic stability (is isoenergetic). This method was tested and optimized on several native RNAs.