A set of tests similar to that used to investigate recombination-induced protein folding disruption was devised to test whether recombination-induced RNA folding disruption has had a detectable influence on recombination breakpoint distributions that are detectable in natural HIV- 1M recombinants. Whereas the first of these tests measured the number of aberrant base-pairs in the recombinant secondary structures, tests 2 to 4 examined whether individual base-pairs within the minor and major parent secondary DCMU structures were maintained in the secondary structures of M-/S- recombinants. The results of test 1 indicate that M-recombinants tend to have significantly fewer aberrant base-pairs than S-recombinants. The results of test 2 suggest that the number of disrupted base-pairings in the M-recombinants was significantly lower than those in the S-recombinants. These two tests KT109 collectively imply that, relative to parental sequences, the M-recombinants have significantly better preserved base-pairing configurations than do the S-recombinants. Tests 3 and 4 relaxed the criterion in test 2 that considered only base-pairs that were present in both the minor and major parental sequence secondary structures. Specifically, test 3 counted the number of disrupted base-pairings between the minor parental and M-/S-recombinant sequence secondary structures, whereas test 4 counted the number of disrupted base-pairings between the major parental and the M-/S-recombinant sequence secondary structures. For test 3 there was no significant evidence that fewer base-pairs present in the minor parental sequence secondary structures were disrupted in the M-recombinants than in the Srecombinants. Test 4, however, yielded marginal evidence that fewer major parental sequence base-pairings were disrupted in the M-recombinants than were disrupted in the S-recombinants.In these two tests it is entirely understandable that, relative to minor parental base-pairing disruptions, there were far fewer major parental base-pairing disruptions in both the Srecombinants since by definition the M/S-recombinants are genetically far more similar to their major parents than their minor parents.