Vibrational circular dichroism (VCD) spectra were measured in the C = O stretching region for poly(U)*poly(A).poly(U), poly(dT)*poly(dA).poly(dT), and poly(U)*poly(dA). poly(dT). These VCD spectra of the triple-helical structure were dramatically different from those of the corresponding duplexes. The VCD indicates that a very similar base-pair structure is present in these triplexes. The same sign pattern was found for poly(C+)*poly(I).poly(C), which implies a generality of structure than can result from the steric constraint of the triple helix conformation. By contrast, the corresponding duplexes are quite different in terms of their VCD. The transitions between triplex, duplex, and single-stranded forms were studied as a function of temperature and interpreted using factor analysis. The relative stabilities of the triplexes lie in the order RNA > DNA > hybrid. Nondegenerate dipole-coupling calculations for a U*A.U oligomer were carried out for the C = O stretching modes to model the spectral changes observed. The experimental absorbance spectra indicate that the bases have nonequivalent H-bonds which can be achieved if a reverse Hoogsteen base-pairing scheme is assumed. The computational VCD results with such a scheme were in better qualitative agreement with experiment than those using the expected Hoogsteen base-pairing scheme.