CHARACTERIZATION OF THE DYNAMIC BEHAVIOR OF R(ACC) AND R(AAC) WITH NMR RELAXATION DATA AND BOTH METROPOLIS MONTE-CARLO AND MOLECULAR-DYNAMICS SIMULATIONS

The solution-state behavior of two triribonucleotides, adenylyl (3'-5' ) adenylyl (3'-5') cytidine [r(AAC)] and adenylyl(3'-5') cytidyly l(3' -5') cytidine [r(ACC)], was studied with spectroscopic and molecular m odeling methods. Melting temperatures of 299 and 294 K for r(AAC) and r(ACC), respectively, were obtained from ultraviolet absorption (UV) a nd circular dichroism (CD) temperature profiles of the order-disorder transition. The behavior of the Raman marker modes is consistent with greater stability of r(AAC) compared to that of r(ACC). Nuclear magnet ic resonance (nmr) relaxation data (homonuclear cross-relaxation rates , proton selective and nonselective longitudinal relaxation times, and carbon longitudinal relaxation times) were measured at 283, 296, and 318 K for both trimers. In parallel, the major types of conformations were explored with Metropolis Monte Carlo (MMC) and molecular dynamics (MD) simulations to obtain representations of both slow and fast even ts. Fitting of experimental data showed that although the MMC conforma tions do not represent an exhaustive list of conformers in solution, t he canonical helical form (A-RNA type) should coexist at low temperatu re with significant populations of other less classical conformers suc h as half-stacked (HS), bulged (BU), and reverse-stacked (RS). Fitting of the experimental relaxation data ensemble al 283 K [ed to very dif ferent representations for the two trimers. r(AAC) was shown to have a fairly compact, rigid structure (angular order parameter, S-ang(2) si milar to 0.9, correlation time for internal motion, tau(e) similar to 0.1 ns), which undergoes fairly rapid overall tumbling characterized b y the correlation time tau(c) similar to 0.6 ns, whereas r(ACC) exhibi ts much more flexibility (S-ang(2) similar to 0.7, tau(e) similar to 0 .1 ns) and slower molecular reorientation (tau(c) similar to 1.0 ns). The values of S-ang(2) tended to confirm that large amplitude fluctuat ions did not occur on the relaxation timescale (ns). In the course of this paper a widely accepted concept was shown to be questionable. As regards the nmr relaxation data, simulations show that for fairly smal l nucleic acids (tau(c) < 2.0 ns) the second term of the model-free sp ectral densities is not negligible for representative motional models (S-ang(2) values < 0.9 and tau(e) values in the 0.05-0.2 ns range). Th e difference in the dynamic behavior of r(AAC) and r(ACC) can be expla ined by the greater propensity of the A-A sequence to stack as compare d to that of A-C. (C) 1996 John Wiley & Sons, Inc.