CONFORMATIONS OF TRANSFER-RNA - BASE-PAIRING AND STACKING

The Phe t-RNA structure can be fit with one point per nucleotide to la ttice models, and a fit for the 76 points to a face-centered cubic lat tice is achieved with an RMS of 1.76 A There are 32 chain folds possib le upon these points. Because it is impossible to calculate directly a ll combinations of potential base pairs for these cases, an alternativ e is to determine low energy secondary structures and subsequently the tertiary pairs. For each lattice fold, the low energy secondary struc tures are generated from a list of proximal bases. From the lists of r emaining possible tertiary pairs, all combinations are generated, and these include 2,365,440 allowed conformers. Among the possible types o f non-native conformational variations observed is slip pairing, accom panied by a bulge, at the end of a stem. Small changes in secondary st ructure can result in different tertiary pairs. Other calculations, no t constrained to the t-RNA shape, are presented that involve the packi ng of rigid stems on a flexible internal loop. For a simple cubic latt ice there are 36,484,128 lattice folds for the sixteen bases enclosing the internal loop. By attaching rigid stems and accounting for their excluded volume these are reduced to only 258,979 possible configurati ons. The most common stacking arrangements involve the usual two pairs of stacked stems indicated in the crystal structure. The present enum erations suggest that a completely thorough exploration of three dimen sional RNA structures is feasible only with prior specification of res trictions on conformational freedom, such as those given by secondary structures.