Previously, we have described inhibition of HIV-1
infection by
T30177, 5'-(GTGGTGGGTGGGTGGGT)-3', an
oligonucleotide that is a potent inhibitor of
HIV-1 integrase in vitro (Mazumder et al. (1996) Biochemistry 35, 13762). Here a family of
oligonucleotides, analogs of
T30177, has been studied. On the basis of thermal denaturation, we show that a folded structure of
T30177 is much more stable than that of the
thrombin binding aptamer, which only differs with
T30177 in the loop sequence. Sequence changes reveal that loop interactions are solely responsible for this observed stability difference. In the presence of K+ ion, the fold of
T30695, a designed 16mer derivative, is indeed more stable than
T30177. Loop folding within
T30695 is very ion selective. Quantitative analysis of thermal denaturation suggests that the loops of
T30695, 5'-(GGGTGGGTGGGTGGGT)-3', and
T30177 confer the ability to coordinate three equivalents of K+ ion (one bound to the core octet and two bound to the loops); however, the
thrombin binding aptamer is shown to bind only one K+ equivalent. Folding kinetics and CD titration demonstrate that K+-induced folding of
T30695 and
T30177 is a two-step process, consistent with a sequential model in which a first equivalent of K+ binds to the octet core, followed by
slow K+-induced rearrangement of the loop domains. Comparing structural stability with the capacity of the folded oligomers to inhibit the
HIV-1 integrase enzyme in vitro or HIV-1
infection in cell culture, we have found that the folding and activity data are highly correlated, suggesting that formation of an orderly, ion-coordinated loop structure similar to that in
T30177 or
T30695 may be a prerequisite for both
integrase inhibition and anti-HIV-1 activity.