Conformational analyses of DNA show that the origin of the specific type of double helix depends mainly on the stacking interactions with its neighboring bases. In addition to sequence specific preferences for mean positions of stacking there are also substantial sequence specific dependences in the conformational fluctuations. Both effects manifest themselves in the bending behavior. To investigate these effects Monte Carlo samples of DNA double helical conformations have been generated. Consideration of the fluctuations was shown to be especially important for sequences with only small intrinsic static bends. Good agreement was shown between calculations of groove widths for such ensembles of helical forms and the reported hydroxyl radical cut data. Such calculations depend in detail on the way in which the electric interactions in the DNA polyelectrolyte chain are treated. A new approach for treating the dielectric function was developed and favorable results were found that indicate the type of helix taken by different sequences. Ways to treat RNA folding in three dimensions were considered. Transfer RNA was used as a test molecule to investigate large numbers of possible arrangements. In the largest generation of such conformations, over 2 million, several types of variant conformations were observed. There was some flexibility in the anticodon loop and several cases of slip pairing with a single base bulge"""""""". This later case requires two identical bases at the helical boundary on one strand. For example, for sequential bases a,b,c,d,e, and f on one strand and D,C,B,E and F on the other, where a can pair with A, b with B, etc.
