However, focusing our analyses on recombination events in CRFs and on only the most plausible biologically well characterised secondary structure elements failed to yield any stronger evidence of selection disfavouring the survival of recombinants with disrupted genomic secondary structures. We have confirmed here that recombination events detectable in the coding regions of a number of HIV-1 proteins tend to be less disruptive of both intra-protein Ophiobolin A amino-acid �C amino-acid interactions and intra-genomic nucleotide �C nucleotide secondary structural interactions than would be expected if recombination were random and all recombinants were equally viable. Although this result is entirely consistent with the hypothesis that natural selection has strongly Calindol hydrochloride impacted the distribution of recombination events that are detectable within HIV genomes that have been sampled from the global epidemic, it does not indicate the timescale of this selection. Specifically, while it is likely that selection over the short-term acts against newly generated recombinant genomes that have either misfolded RNA structures or express misfolded chimaeric proteins, it is similarly plausible that selection acting over the longer-term has configured the underlying structure of HIV-1M genomes so as to minimise the deleterious effects of recombination. Specifically, Simon-Loriere et. al. have proposed that the distribution of secondary structural elements within the HIV-1M genome may maximise the chances that recombinant genomes will express properly folded chimaeric proteins by ����directing���� recombination breakpoints to protein domain boundaries. It remains unclear, however, how any analogous mechanism might maximise the probability of recombinant genomes having properly folded RNA secondary structures; especially since it is specifically the recombination breakpoints that occur within RNA structures that are expected to be the most disruptive of these structures. It is nevertheless possible that sequence determinants of recombination frequency besides secondary structure �C such as sequence conservation, or runs of guanosine nucleotides �C could also play a role in directing recombination to sites where it will have minimal impact on particular biologically functional RNA structures.