Basic studies of the solvation and ion stabilization of three stranded and four stranded nucleic acid structures continued. New applications of these studies included: 1. Novel atom-atom potential functions were developed for interactions of phosphates with sodium and potassium ions. These potentials will be used to simulate three and four stranded DNA and RNA helices under various conditions. 2. The recombination triplex in the complex with RecA protein calculated by us earlier (denoted R-form DNA) was studied by a novel method based on the radioactive decay of 125I, incorporated into cytosine. The low energy electrons emitted caused DNA cleavage, leading to estimates of the distances between the DNA strands and the Iodine atom. Cleavage results agree with our model predicting the recognition between the DNA duplex and the position of the third strand in the major groove. 3. The same method was applied for studying the mutual positions of the two DNA strands and the newly synthesized RNA strand in the complex with RNA polymerase. The results indicate formation of a stable about 10 bp long duplex between the transcribed DNA strand and RNA. The average distance from the more flexible non-transcribed strand to RNA is estimated at 15- 20+. This information will be used in planning new experiments to elucidate the role of the non-transcribed strand in increasing the fidelity of transcription. 4. A new project has been initiated to study the R-form triplex in solution. This is based on the synthesis of oligonucleotides with non- nucleotide linkers which stabilize the formation of intramolecular triplexes at relatively low concentrations, avoiding aggregation. This method allows us to discriminate unambiguously between parallel and anti-parallel triplexes. Preliminary calorimetric studies showed that the R-like parallel triplex is stable at sub-room temperatures. This leads to the possibility of determining the structure of the parallel triplex by NMR.
