The overall plan is to develop a chemical method for the synthesis of defined sequence oligoribonucleotides in 10-20 mg quantities and to sue these molecules to evaluate the thermodynamic stabilities of various structures that occur in RNA. The synthetic strategy will require a study of the appropriate chemical protection of ribonucleosides and the preparation of barium salts of the four protected ribonucleoside-3' aryl phosphodiesters. The condensation of pairs of these monomers will generate a dinucleotide """"""""library"""""""" containing all 16 possible arrangements. The monomeric and dimeric synthetic units will be used in the construction of oligoribonucleotides in solution and in the development of a solid-phase synthetic system that will incorporate a mechanism for the recovery and recycling of the units. Special sets of oligonucleotides will be prepared for the evaluation of energy parameters (changes in enthalpy and entropy) arising out the formation of secondary structures such as helices, hair-pin loops, bulges, mismatches and interior loops. Nearest neighbor contributions to these parameters will be determined by comparing the energies of parent molecules with those of derivative species formed from them either by specific nucleotide insertions or by rearrangements of portions of their sequences. These energy values are expected to constitute a significant quantitative basis for the prediction of RNA secondary structure from the knowledge of nucleotide sequence.
