In my last blog I talked about the intensity of seeing my polyacrylamide gel electrophoresis results since I have to wait overnight before I can scan the phosphor screen which has absorbed the spots where radioactive material was on the gel.  I was able to visualize the results of my gels from the first set of mutant experiments that I ran and the results were somewhat mixed.  I tested the fiber and square motifs along with two different forms of the fiber motif.  We expected that the fiber dimers would conglomerate together forming long molecules or “fibers” while the square dimer system could form different species in multiples of two.  The square motif looks like a corner to a cube.  Two of the sides to the square motif have kissing loops that are complementary to kissing loops on other square motifs.  Hence we have square A that has two kissing loops complementary to two kissing loops on the ends of the square B motif.  When the two pairs of complementary kissing loops connect they act as velcro sticking the two motifs together to form a table-like structure that could serve as the base of a cube for further RNA architectonics construction.  The square A-B system can form dimers like the table-like structure described or higher ordered species such as tetramers, however each species will be even-numbered because square A, containing A kissing loops, are only complementary to square B’s containing B kissing loops; they cannot form self-dimers, thus no odd numbered species.  Some of my gel results reflected the ideas I have just expressed, however some of them did not because the fiber A-B system was also forming distinct species in some cases meaning that the fiber motif is not as floppy as we imagined but possibly more rigid like the square motif.  Or else there is something suspicious going on with my experimental technique.